Publications by authors named "Tariq Ezaz"

88 Publications

Balanced Chromosomal Rearrangements Associated with Hypoprolificacy in Australian Boars ().

Cells 2021 Aug 6;10(8). Epub 2021 Aug 6.

Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617, Australia.

Balanced chromosomal rearrangements, mainly reciprocal translocations, are considered to be the causative agent of several clinical conditions in farmed pigs, resulting in hypoprolificacy and economic losses. Literature suggests that reciprocal translocations are heritable and can occur de novo. The prevalence rate of these balanced structural rearrangements of chromosomes differs from country to country and varies between 0.5% and 3.3%. The Australian pig population is descendent of a small founder population and has since been a closed genetic group since the 1980s. Hence, any incident of reciprocal translocation along with the pedigree of boars that contribute sperm for artificial insemination has the potential to have an economic consequence. To date, there has been no published account for screening of reciprocal translocation associated with hypoprolificacy in the Australian pig population. In this study, we performed standard and molecular cytogenetic analyses to identify evidence of chromosome rearrangements and their association with hypoprolificacy in a representative 94 boar samples from a commercial nucleus herd. We identified three novel rearrangements between chromosomes 5 and 14, between chromosomes 9 and 10, and between chromosomes 10 and 12. In addition, we also detected a reciprocal translocation between chromosomes 3 and 16 that has previously been detected in pig herds in France. The prevalence rate was 6.38% within the samples used in this study. All four rearrangements were found to have an association with hypoprolificacy. Further study and routine monitoring will be necessary to identify any further rearrangements that will allow breeders to prevent the propagation of reciprocal translocations from generation to generation within the Australian pig population.
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http://dx.doi.org/10.3390/cells10082000DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8394656PMC
August 2021

Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos.

Philos Trans R Soc Lond B Biol Sci 2021 09 26;376(1833):20200102. Epub 2021 Jul 26.

Department of Ecology, Charles University, Prague, CZ 12844, Czech Republic.

Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here, we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32-72 Ma, one species in particular, Burton's legless lizard (), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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http://dx.doi.org/10.1098/rstb.2020.0102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310713PMC
September 2021

Revisiting the Karyotypes of Alligators and Caimans (Crocodylia, Alligatoridae) after a Half-Century Delay: Bridging the Gap in the Chromosomal Evolution of Reptiles.

Cells 2021 Jun 5;10(6). Epub 2021 Jun 5.

Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil.

Although crocodilians have attracted enormous attention in other research fields, from the cytogenetic point of view, this group remains understudied. Here, we analyzed the karyotypes of eight species formally described from the Alligatoridae family using differential staining, fluorescence in situ hybridization with rDNA and repetitive motifs as a probe, whole chromosome painting (WCP), and comparative genome hybridization. All Caimaninae species have a diploid chromosome number (2n) 42 and karyotypes dominated by acrocentric chromosomes, in contrast to both species of Alligatorinae, which have 2n = 32 and karyotypes that are predominantly metacentric, suggesting fusion/fission rearrangements. Our WCP results supported this scenario by revealing the homeology of the largest metacentric pair present in both spp. with two smaller pairs of acrocentrics in Caimaninae species. The clusters of 18S rDNA were found on one chromosome pair in all species, except for spp., which possessed three chromosome pairs bearing these sites. Similarly, comparative genomic hybridization demonstrated an advanced stage of sequence divergence among the caiman genomes, with standing out as the most divergent. Thus, although Alligatoridae exhibited rather low species diversity and some level of karyotype stasis, their genomic content indicates that they are not as conserved as previously thought. These new data deepen the discussion of cytotaxonomy in this family.
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http://dx.doi.org/10.3390/cells10061397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8228166PMC
June 2021

Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination.

Ecol Evol 2021 May 25;11(10):5575-5583. Epub 2021 Mar 25.

Discipline of Biological Sciences University of Tasmania Sandy Bay Tas. Australia.

Polymorphisms can lead to genetic isolation if there is differential mating success among conspecifics divergent for a trait. Polymorphism for sex-determining system may fall into this category, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane's rule). Here we investigated whether populations exhibiting polymorphism for sex determination are genetically isolated, using the viviparous snow skink . While a comparatively high elevation population has genotypic sex determination, in a lower elevation population there is an additional temperature component to sex determination. Based on 11,107 SNP markers, these populations appear genetically isolated. "Isolation with Migration" analysis also suggests these populations diverged in the absence of gene flow, across a period encompassing multiple Pleistocene glaciations and likely greater geographic proximity of populations. However, further experiments are required to establish whether genetic isolation may be a cause or consequence of differences in sex determination. Given the influence of temperature on sex in one lineage, we also discuss the implications for the persistence of this polymorphism under climate change.
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http://dx.doi.org/10.1002/ece3.7458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131762PMC
May 2021

A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, .

Proc Natl Acad Sci U S A 2021 03;118(11)

Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia 2617

The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog () from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ∼1.06 gigabases (Gb), the genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Genome skimming of two closely related frog species ( and ) confirms a reduction in TEs as a major driver of genome reduction in and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.
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http://dx.doi.org/10.1073/pnas.2011649118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7980411PMC
March 2021

Evolution of a Multiple Sex-Chromosome System by Three-Sequential Translocations among Potential Sex-Chromosomes in the Taiwanese Frog .

Cells 2021 03 16;10(3). Epub 2021 Mar 16.

Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.

Translocation between sex-chromosomes and autosomes generates multiple sex-chromosome systems. It happens unexpectedly, and therefore, the evolutionary meaning is not clear. The current study shows a multiple sex chromosome system comprising three different chromosome pairs in a Taiwanese brown frog (). The male-specific three translocations created a system of six sex-chromosomes, ♂XYXYXY-♀XXXXXX. It is unique in that the translocations occurred among three out of the six members of potential sex-determining chromosomes, which are known to be involved in sex-chromosome turnover in frogs, and the two out of three include orthologs of the sex-determining genes in mammals, birds and fishes. This rare case suggests sex-specific, nonrandom translocations and thus provides a new viewpoint for the evolutionary meaning of the multiple sex chromosome system.
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http://dx.doi.org/10.3390/cells10030661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8002213PMC
March 2021

Cytogenetic Analysis of Panaqolus tankei Cramer & Sousa, 2016 (Siluriformes, Loricariidae), an Ornamental Fish Endemic to Xingu River, Brazil.

Cytogenet Genome Res 2021 19;161(3-4):187-194. Epub 2021 Mar 19.

Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil.

Despite conservation of the diploid number, a huge diversity in karyotype formulae is found in the Ancistrini tribe (Loricariidae, Hypostominae). However, the lack of cytogenetic data for many groups impairs a comprehensive understanding of the chromosomal relationships and the impact of chromosomal changes on their evolutionary history. Here, we present for the first time the karyotype of Panaqolus tankei Cramer & Sousa, 2016. We focused on the chromosomal characterization, using conventional and molecular cytogenetic techniques to unravel the evolutionary trends of this tribe. P. tankei, as most species of its sister group Pterygoplichthini, also possessess a conserved diploid number of 52 chromosomes. We observed heterochromatin regions in the centromeres of many chromosomes; pairs 5 and 6 presented interstitial heterochromatin regions, whereas pairs 23 and 24 showed extensive heterochromatin regions in their q arms. In situ localization of 18S rDNA showed hybridization signals correlating with the nucleolus organizer regions, which are located in the q arms of pair 5. However, the 5S rDNA was detected in the centromeric and terminal regions of the q arms of pair 8. (TTAGGG)n hybridized only in the terminal regions of all chromosomes. Microsatellite in situ localization showed divergent patterns, (GA)15 repeated sequences were restricted to the terminal regions of some chromosomes, whereas (AC)15 and (GT)15 showed a scattered hybridization pattern throughout the genome. Intraspecific comparative genomic hybridization was performed on the chromosomes of P. tankei to verify the existence of sex-specific regions. The results revealed only a limited number of overlapping hybridization signals, coinciding with the heterochromatin in centromeric regions without any sex-specific signals in both males and females. Our study provides a karyotype description of P. tankei, highlighting extensive differences in the karyotype formula, the heterochromatin regions, and sites of 5S and 18S rDNA, as compared with data available for the genus.
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http://dx.doi.org/10.1159/000514061DOI Listing
August 2021

Uniparental Genome Elimination in Australian Carp Gudgeons.

Genome Biol Evol 2021 Jun;13(6)

Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, ACT, Australia.

Metazoans usually reproduce sexually, blending the unique identity of parental genomes for the next generation through functional crossing-over and recombination in meiosis. However, some metazoan lineages have evolved reproductive systems where offspring are either full (clonal) or partial (hemiclonal) genetic replicas. In the latter group, the process of uniparental genome elimination selectively eliminates either the maternal or paternal genome from germ cells, and only one parental genome is selected for transmission. Although fairly common in plants, hybridogenesis (i.e., clonal haploidization via chromosome elimination) remains a poorly understood process in animals. Here, we explore the proximal cytogenomic mechanisms of somatic and germ cell chromosomes in sexual and hybrid genotypes of Australian carp gudgeons (Hypseleotris) by tracing the fate of each set during mitosis (in somatic tissues) and meiosis (in gonads). Our comparative study of diploid hybrid and sexual individuals revealed visually functional gonads in male and female hybrid genotypes and generally high karyotype variability, although the number of chromosome arms remains constant. Our results delivered direct evidence for classic hybridogenesis as a reproductive mode in carp gudgeons. Two parental sets with integral structure in the hybrid soma (the F1 constitution) contrasted with uniparental chromosomal inheritance detected in gonads. The inheritance mode happens through premeiotic genome duplication of the parental genome to be transmitted, whereas the second parental genome is likely gradually eliminated already in juvenile individuals. The role of metacentric chromosomes in hybrid evolution is also discussed.
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http://dx.doi.org/10.1093/gbe/evab030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245195PMC
June 2021

Differences in Homomorphic Sex Chromosomes Are Associated with Population Divergence in Sex Determination in (Scincidae: Lygosominae).

Cells 2021 02 1;10(2). Epub 2021 Feb 1.

Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia.

Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains elusive. Here we explore the links between mechanisms of transitions in sex determination and sex chromosome evolution at both recent and deeper temporal scales (<1 Myr; ~79 Myr). We studied a rare example of a species with intraspecific variation in sex determination, , and a relative, , using c-banding and mapping of repeat motifs and a custom Y chromosome probe set to identify the sex chromosomes. We identified both unique and conserved regions of the Y chromosome among populations differing in sex determination. There was no evidence for homology of sex chromosomes between and , suggesting independent evolutionary origins. We discuss sex chromosome homology between members of the subfamily Lygosominae and propose links between sex chromosome evolution, sex determination transitions, and karyotype evolution.
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http://dx.doi.org/10.3390/cells10020291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7912723PMC
February 2021

A Novel Paradigm for Sex Chromosome Turnover: Y and W Changes, X and Z Remain.

Authors:
Tariq Ezaz

Bioessays 2020 09 27;42(9):e2000152. Epub 2020 Jul 27.

Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, ACT2617, Australia.

On the Black Swans of conventional sex determination theory: There aren't many, but when an exception to the standard model of sex determination (evolutionary turnover of genes playing the role of "master sex determiner") arises, it certainly screams out for an explanation. In this issue, a novel one is put forward. It now awaits testing, particularly at the population level.
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http://dx.doi.org/10.1002/bies.202000152DOI Listing
September 2020

Karyotype Characterisation of Two Australian Dragon Lizards (Squamata: Agamidae: Amphibolurinae) Reveals Subtle Chromosomal Rearrangements Between Related Species with Similar Karyotypes.

Cytogenet Genome Res 2020 18;160(10):610-624. Epub 2020 Nov 18.

Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia.

Agamid lizards (Squamata: Agamidae) are karyotypically heterogeneous. Among the 101 species currently described from Australia, all are from the subfamily Amphibolurinae. This group is, with some exceptions, karyotypically conserved, and all species involving heterogametic sex show female heterogamety. Here, we describe the chromosomes of 2 additional Australian agamid lizards, Tympanocryptis lineata and Rankinia diemensis. These species are phylogenetically and cytogenetically sisters to the well-characterised Pogona vitticeps, but their sex chromosomes and other chromosomal characteristics are unknown. In this study, we applied advanced molecular cytogenetic techniques, such as fluorescence in situ hybridisation (FISH) and cross-species gene mapping, to characterise chromosomes and to identify sex chromosomes in these species. Our data suggest that both species have a conserved karyotype with P. vitticeps but with subtle rearrangements in the chromosomal landscapes. We could identify that T. lineata possesses a female heterogametic system (ZZ/ZW) with a pair of sex microchromosomes, while R. diemensis may have heterogametic sex chromosomes, but this requires further investigations. Our study shows the pattern of chromosomal rearrangements between closely related species, explaining the speciation within Australian agamid lizards of similar karyotypes.
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http://dx.doi.org/10.1159/000511344DOI Listing
January 2021

Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana () Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes.

Front Genet 2020 20;11:556267. Epub 2020 Oct 20.

Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.

The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken () chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseq) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.
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http://dx.doi.org/10.3389/fgene.2020.556267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7606854PMC
October 2020

Revisiting the Karyotype Evolution of Neotropical Boid Snakes: A Puzzle Mediated by Chromosomal Fissions.

Cells 2020 10 10;9(10). Epub 2020 Oct 10.

Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil.

The Boidae family is an ancient group of snakes widely distributed across the Neotropical region, where several biogeographic events contributed towards shaping their evolution and diversification. Most species of this family have a diploid number composed of 2n = 36; however, among Booidea families, the Boidae stands out by presenting the greatest chromosomal diversity, with 2n ranging between 36 and 44 chromosomes and an undifferentiated XY sex chromosome system. Here, we applied a comparative chromosome analysis using cross-species chromosome paintings in five species representing four Boidae genera, to decipher the evolutionary dynamics of some chromosomes in these Neotropical snakes. Our study included all diploid numbers (2n = 36, 40, and 44) known for this family and our comparative chromosomal mappings point to a strong evolutionary relationship among the genera , , , and . The results also allowed us to propose the cytogenomic diversification that had occurred in this family: a process mediated by centric fissions, including fission events of the putative and undifferentiated XY sex chromosome system in the 2n = 44 karyotype, which is critical in solving the puzzle of the karyotype evolution of boid snakes.
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http://dx.doi.org/10.3390/cells9102268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7601083PMC
October 2020

Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes.

Genomics 2021 Jan 28;113(1 Pt 2):624-636. Epub 2020 Sep 28.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand, (CASTNAR, NRU-KU, Thailand); Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan. Electronic address:

Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome.
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http://dx.doi.org/10.1016/j.ygeno.2020.09.058DOI Listing
January 2021

The Amazonian Red Side-Necked Turtle (Spix, 1824) (Testudines, Chelidae) Has a GSD Sex-Determining Mechanism with an Ancient XY Sex Microchromosome System.

Cells 2020 09 12;9(9). Epub 2020 Sep 12.

Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, ACT 12 2616, Australia.

The Amazonian red side-necked turtle is an endemic Amazonian Chelidae species that occurs in small streams throughout Colombia and Brazil river basins. Little is known about various biological aspects of this species, including its sex determination strategies. Among chelids, the greatest karyotype diversity is found in the Neotropical species, with several 2 configurations, including cases of triploidy. Here, we investigate the karyotype of by applying combined conventional and molecular cytogenetic procedures. This allowed us to discover a genetic sex-determining mechanism that shares an ancestral micro XY sex chromosome system. This ancient micro XY system recruited distinct repeat motifs before it diverged from several South America and Australasian species. We propose that such a system dates back to the earliest lineages of the chelid species before the split of South America and Australasian lineages.
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http://dx.doi.org/10.3390/cells9092088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563702PMC
September 2020

Landscape of snake' sex chromosomes evolution spanning 85 MYR reveals ancestry of sequences despite distinct evolutionary trajectories.

Sci Rep 2020 07 27;10(1):12499. Epub 2020 Jul 27.

Coordenação de Biodiversidade, Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.

Most of snakes exhibit a ZZ/ZW sex chromosome system, with different stages of degeneration. However, undifferentiated sex chromosomes and unique Y sex-linked markers, suggest that an XY system has also evolved in ancestral lineages. Comparative cytogenetic mappings revealed that several genes share ancestry among X, Y and Z chromosomes, implying that XY and ZW may have undergone transitions during serpent's evolution. In this study, we performed a comparative cytogenetic analysis to identify homologies of sex chromosomes across ancestral (Henophidia) and more recent (Caenophidia) snakes. Our analysis suggests that, despite ~ 85 myr of independent evolution, henophidians and caenophidians retained conserved synteny over much of their genomes. However, our findings allowed us to discover that ancestral and recent lineages of snakes do not share the same sex chromosome and followed distinct pathways for sex chromosomes evolution.
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http://dx.doi.org/10.1038/s41598-020-69349-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7385105PMC
July 2020

Evidence of Interspecific Chromosomal Diversification in Rainbowfishes (Melanotaeniidae, Teleostei).

Genes (Basel) 2020 07 18;11(7). Epub 2020 Jul 18.

Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia.

Rainbowfishes (Melanotaeniidae) are the largest monophyletic group of freshwater fishes occurring in Australia and New Guinea, with 112 species currently recognised. Despite their high taxonomic diversity, rainbowfishes remain poorly studied from a cytogenetic perspective. Using conventional (Giemsa staining, C banding, chromomycin A staining) and molecular (fluorescence in situ hybridisation with ribosomal DNA (rDNA) and telomeric probes) cytogenetic protocols, karyotypes and associated chromosomal characteristics of five species were examined. We covered all major lineages of this group, namely, Running River rainbowfish sp., red rainbowfish , threadfin rainbowfish , ornate rainbowfish , and Cairns rainbowfish . All species had conserved diploid chromosome numbers 2n = 48, but karyotypes differed among species; while sp., , and possessed karyotypes composed of exclusively subtelo/acrocentric chromosomes, the karyotype of displayed six pairs of submetacentric and 18 pairs of subtelo/acrocentric chromosomes, while possessed a karyotype composed of four pairs of submetacentric and 20 pairs of subtelo/acrocentric chromosomes. No heteromorphic sex chromosomes were detected using conventional cytogenetic techniques. Our data indicate a conserved 2n in Melanotaeniidae, but morphologically variable karyotypes, rDNA sites, and heterochromatin distributions. Differences were observed especially in taxonomically divergent species, suggesting interspecies chromosome rearrangements.
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http://dx.doi.org/10.3390/genes11070818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397213PMC
July 2020

Cross-Species BAC Mapping Highlights Conservation of Chromosome Synteny across Dragon Lizards (Squamata: Agamidae).

Genes (Basel) 2020 06 25;11(6). Epub 2020 Jun 25.

Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia.

Dragon lizards (Squamata: Agamidae) comprise about 520 species in six subfamilies distributed across Asia, Australasia and Africa. Only five species are known to have sex chromosomes. All of them possess ZZ/ZW sex chromosomes, which are microchromosomes in four species from the subfamily Amphibolurinae, but much larger in from the subfamily Agaminae. In most previous studies of these sex chromosomes, the focus has been on Australian species from the subfamily Amphibolurinae, but only the sex chromosomes of the Australian central bearded dragon () are well-characterized cytogenetically. To determine the level of synteny of the sex chromosomes of across agamid subfamilies, we performed cross-species two-colour FISH using two bacterial artificial chromosome (BAC) clones from the pseudo-autosomal regions of . We mapped these two BACs across representative species from all six subfamilies as well as two species of chameleons, the sister group to agamids. We found that one of these BAC sequences is conserved in macrochromosomes and the other in microchromosomes across the agamid lineages. However, within the Amphibolurinae, there is evidence of multiple chromosomal rearrangements with one of the BACs mapping to the second-largest chromosome pair and to the microchromosomes in multiple species including the sex chromosomes of . Intriguingly, no hybridization signal was observed in chameleons for either of these BACs, suggesting a likely agamid origin of these sequences. Our study shows lineage-specific evolution of sequences/syntenic blocks and successive rearrangements and reveals a complex history of sequences leading to their association with important biological processes such as the evolution of sex chromosomes and sex determination.
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http://dx.doi.org/10.3390/genes11060698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7348930PMC
June 2020

Molecular Cytogenetic Analysis in Freshwater Prawns of the Genus (Crustacea: Decapoda: Palaemonidae).

Int J Mol Sci 2020 Apr 9;21(7). Epub 2020 Apr 9.

Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP C.P. 676, Brazil.

Freshwater prawns of the genus are one of the important components of circumtropical marine, estuarine, and freshwater environments. They have been extensively exploited for human consumption for many years. More than 250 species reflect the evolutionary success of this highly diversified group, with a complex and challenging taxonomy due to morphological variations and vast geographical distribution. Although genetic approaches have been used to clarify phylogenetic and taxonomic aspects of species, cytogenetic information is still very scarce and mostly focused on chromosome number and morphology. Here, we present chromosome data for three species from the Neotropical region, and , and one species from the Oriental region, . Using conventional cytogenetic approaches and chromosome mapping of repetitive DNAs by fluorescence hybridization (FISH), we identified numerical diversification of the diploid set, within and between both zoogeographic regions. These included and sharing diploid chromosomes of 98, while has 94, and has 118 chromosomes. Argentophilic sites are also variable in number, but they occur in a much higher number than 18S rDNA, representing two to 10 sites within the study species. Microsatellites repeat motifs are also abundant in the chromosomes, with a co-localization and uniform distribution along the chromosome arms, but completely absent in the AT-rich centromeric regions. As a whole, our study suggests that the 2n divergence was followed by a considerable rDNA diversification. The abundance of the exceptional amount of microsatellite sequences in the chromosomes also suggests that they are essential components of the genome and, therefore, maintained as a shared feature by the species, the reason for which is yet unknown.
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http://dx.doi.org/10.3390/ijms21072599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178241PMC
April 2020

Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua.

PLoS One 2019 12;14(12):e0226365. Epub 2019 Dec 12.

Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.

Bi-allelic Single Nucleotide Polymorphism (SNP) markers are widely used in population genetic studies. In most studies, sequences either side of the SNPs remain unused, although these sequences contain information beyond that used in population genetic studies. In this study, we show how these sequence tags either side of a single nucleotide polymorphism can be used for comparative genome analysis. We used DArTseq (Diversity Array Technology) derived SNP data for a non-model Australian native freshwater fish, Macquaria ambigua, to identify genes linked to SNP associated sequence tags, and to discover homologies with evolutionarily conserved genes and genomic regions. We concatenated 6,776 SNP sequence tags to create a hypothetical genome (representing 0.1-0.3% of the actual genome), which we used to find sequence homologies with 12 model fish species using the Ensembl genome browser with stringent filtering parameters. We identified sequence homologies for 17 evolutionarily conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63) along with an ancestral evolutionarily conserved syntenic block (euteleostomi Block_210). Our analysis also revealed repetitive sequences covering approximately 12% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons were most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for repeatability. This new approach of using SNP associated sequence tags for comparative genome analysis may provide insight into the genome evolution of non-model species where whole genome sequences are unavailable.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226365PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6907852PMC
March 2020

Identifying sex-linked markers in Litoria aurea: a novel approach to understanding sex chromosome evolution in an amphibian.

Sci Rep 2019 11 12;9(1):16591. Epub 2019 Nov 12.

Institute for Applied Ecology, University of Canberra, Bruce 2617, Canberra, Australia.

Few taxa exhibit the variability of sex-determining modes as amphibians. However, due to the presence of homomorphic sex chromosomes in many species, this phenomenon has been difficult to study. The Australian frog, Litoria aurea, has been relatively well studied over the past 20 years due to widespread declines largely attributable to chytrid fungus. However, it has been subject to few molecular studies and its mode of sex determination remained unknown. We applied DArTseq™ to develop sex-linked single nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 44 phenotypically sexed L. aurea individuals from the Molonglo River in NSW, Australia. We conclusively identified a male heterogametic (XX-XY) sex determination mode in this species, identifying 11 perfectly sex-linked SNP and six strongly sex-linked PA markers. We identified a further 47 moderately sex-linked SNP loci, likely serving as evidence indicative of XY recombination. Furthermore, within these 47 loci, a group of nine males were found to have a feminised Y chromosome that significantly differed to all other males. We postulate ancestral sex-reversal as a means for the evolution of this now pseudoautosomal region on the Y chromosome. Our findings present new evidence for the 'fountain of youth' hypothesis for the retention of homomorphic sex chromosomes in amphibians and describe a novel approach for the study of sex chromosome evolution in amphibia.
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http://dx.doi.org/10.1038/s41598-019-52970-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851140PMC
November 2019

ZW Sex Chromosomes in Australian Dragon Lizards (Agamidae) Originated from a Combination of Duplication and Translocation in the Nucleolar Organising Region.

Genes (Basel) 2019 10 30;10(11). Epub 2019 Oct 30.

Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra ACT 2617, Australia.

Sex chromosomes in some reptiles share synteny with distantly related amniotes in regions orthologous to squamate chromosome 2. The latter finding suggests that chromosome 2 was formerly part of a larger ancestral (amniote) super-sex chromosome and raises questions about how sex chromosomes are formed and modified in reptiles. Australian dragon lizards (Agamidae) are emerging as an excellent model for studying these processes. In particular, they exhibit both genotypic (GSD) and temperature-dependent (TSD) sex determination, show evidence of transitions between the two modes and have evolved non-homologous ZW sex microchromosomes even within the same evolutionary lineage. They therefore represent an excellent group to probe further the idea of a shared ancestral super-sex chromosome and to investigate mechanisms for transition between different sex chromosome forms. Here, we compare sex chromosome homology among eight dragon lizard species from five genera to identify key cytological differences and the mechanisms that may be driving sex chromosome evolution in this group. We performed fluorescence in situ hybridisation to physically map bacterial artificial chromosome (BAC) clones from the bearded dragon, ZW sex chromosomes and a nucleolar organising region (NOR) probe in males and females of eight Agamid species exhibiting either GSD or TSD. We show that the sex chromosome derived BAC clone hybridises near the telomere of chromosome 2q in all eight species examined. This clone also hybridises to the sex microchromosomes of three species (, and ) and a pair of microchromosomes in three others (, and ). No other chromosomes are marked by the probe in two species from the closely related genus . A probe bearing nucleolar organising region (NOR) sequences maps close to the telomere of chromosome 2q in all eight species, and to the ZW pair in and , the W microchromosome in , and several microchromosomes in . Our findings provide evidence of sequence homology between chromosome 2 and the sex chromosomes of multiple agamids. These data support the hypothesis that there was an ancestral sex chromosome in amniotes that gave rise to squamate chromosome 2 and raises the prospect that some particular property of this chromosome has favoured its role as a sex chromosome in amniotes. It is likely that the amplification of repetitive sequences associated with this region has driven the high level of heterochromatinisation of the sex-specific chromosomes in three species of agamid. Our data suggest a possible mechanism for chromosome rearrangement, including inversion and duplication near the telomeric regions of the ancestral chromosome 2 and subsequent translocation to the ZW sex microchromosomes in three agamid species. It is plausible that these chromosome rearrangements involving sex chromosomes also drove speciation in this group.
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http://dx.doi.org/10.3390/genes10110861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895791PMC
October 2019

Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, ).

Genes (Basel) 2019 09 9;10(9). Epub 2019 Sep 9.

Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.

The South American arowanas (Osteoglossiformes, Osteoglossidae, ) are emblematic species widely distributed in the Amazon and surrounding basins. Arowana species are under strong anthropogenic pressure as they are extensively exploited for ornamental and food purposes. Until now, limited genetic and cytogenetic information has been available, with only a few studies reporting to their genetic diversity and population structure. In the present study, cytogenetic and DArTseq-derived single nucleotide polymorphism (SNP) data were used to investigate the genetic diversity of the two species, the silver arowana , and the black arowana . Both species differ in their 2n (with 2n = 54 and 56 for and , respectively) and in the composition and distribution of their repetitive DNA content, consistent with their taxonomic status as different species. Our genetic dataset was coupled with contemporary and paleogeographic niche modeling, to develop concurrent demographic models that were tested against each other with a deep learning approach in . Our genetic results reveal that colonized the Tocantins-Araguaia basin from the Amazon basin about one million years ago. In addition, we highlighted a higher genetic diversity of in the Amazon populations in comparison to those from the Tocantins-Araguaia basin.
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http://dx.doi.org/10.3390/genes10090693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771150PMC
September 2019

Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics.

Int J Mol Sci 2019 Sep 2;20(17). Epub 2019 Sep 2.

Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-090, Brazil.

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera ( and ) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2 = 56 and 54 in and , respectively, and 2 = 50 in while and presented 2 = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that and divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian and Australian diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale.
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http://dx.doi.org/10.3390/ijms20174296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747201PMC
September 2019

Karyotypes and Sex Chromosomes in Two Australian Native Freshwater Fishes, Golden Perch () and Murray Cod () (Percichthyidae).

Int J Mol Sci 2019 Aug 30;20(17). Epub 2019 Aug 30.

Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia.

Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch () and Murray cod () are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational and commercial value. The arid landscape over much of these fishes' range, coupled with the boom and bust hydrology of their habitat, means that these species have potential to provide useful evolutionary insights, such as karyotypes and sex chromosome evolution in vertebrates. Here we applied standard and molecular cytogenetic techniques to characterise karyotypes for golden perch and Murray cod. Both species have a diploid chromosome number 2 = 48 and a male heterogametic sex chromosome system (XX/XY). While the karyotype of golden perch is composed exclusively of acrocentric chromosomes, the karyotype of Murray cod consists of two submetacentric and 46 subtelocentric/acrocentric chromosomes. We have identified variable accumulation of repetitive sequences (AAT) and (CGG) along with diverse methylation patterns, especially on the sex chromosomes in both species. Our study provides a baseline for future cytogenetic analyses of other Australian freshwater fishes, especially species from the family Percichthyidae, to better understand their genome and sex chromosome evolution.
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http://dx.doi.org/10.3390/ijms20174244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747191PMC
August 2019

Chromosomics: Bridging the Gap between Genomes and Chromosomes.

Genes (Basel) 2019 08 20;10(8). Epub 2019 Aug 20.

Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.

The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.
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http://dx.doi.org/10.3390/genes10080627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723020PMC
August 2019

Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead (Atheriniformes, Teleostei).

PeerJ 2019 30;7:e7347. Epub 2019 Jul 30.

Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.

Belonging to the order Atheriniformes, is one of the most widespread genera of freshwater fishes in Australia, spanning along the northern coast from central Western Australia to central New South Wales and across the Murray-Darling and Lake Eyre basins. In this study, both conventional cytogenetic techniques (Giemsa, C-banding, CMA/DAPI staining), and fluorescence hybridization (FISH) with telomeric DNA and rDNA probes were used to examine the karyotypes and other chromosomal characteristics of Darling hardyhead () from New South Wales, Australia. We identified a diploid chromosome number 2 = 48 ( = 58) in all studied individuals. FISH with rDNA probes showed a nonsyntenic pattern, with signals on one pair of subtelocentric chromosomes for 5S rDNA and one pair of submetacentric chromosomes for 28S rDNA. C-banding displayed the accumulation of constitutive heterochromatin in the centromeric regions of approximately 40 chromosomes. CMA/DAPI fluorescence staining revealed extremely GC-rich signals in the pericentromeric region of one submetacentric chromosomal pair with size polymorphism. We detected telomeric signals at the end of all chromosomes and no interstitial signals.
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http://dx.doi.org/10.7717/peerj.7347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677120PMC
July 2019

Sexual conflict in action: An antagonistic relationship between maternal and paternal sex allocation in the tammar wallaby, .

Ecol Evol 2019 Apr 5;9(8):4340-4348. Epub 2019 Apr 5.

Department of Ecology, Environment and Evolution, School of Life Sciences La Trobe University Melbourne Victoria Australia.

Sex ratio biases are often inconsistent, both among and within species and populations. While some of these inconsistencies may be due to experimental design, much of the variation remains inexplicable. Recent research suggests that an exclusive focus on mothers may account for some of the inconsistency, with an increasing number of studies showing variation in sperm sex ratios and seminal fluids. Using fluorescent in-situ hybridization, we show a significant population-level Y-chromosome bias in the spermatozoa of wild tammar wallabies, but with significant intraindividual variation between males. We also show a population-level birth sex ratio trend in the same direction toward male offspring, but a weaning sex ratio that is significantly female-biased, indicating that males are disproportionately lost during lactation. We hypothesize that sexual conflict between parents may cause mothers to adjust offspring sex ratios after birth, through abandonment of male pouch young and reactivation of diapaused embryos. Further research is required in a captive, controlled setting to understand what is driving and mechanistically controlling sperm sex ratio and offspring sex ratio biases and to understand the sexually antagonistic relationship between mothers and fathers over offspring sex. These results extend beyond sex allocation, as they question studies of population processes that assume equal input of sex chromosomes from fathers, and will also assist with future reproduction studies for management and conservation of marsupials.
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http://dx.doi.org/10.1002/ece3.4813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476839PMC
April 2019

Evolutionary Insights of the ZW Sex Chromosomesin Snakes: A New Chapter Added by the AmazonianPuffing Snakes of the Genus .

Genes (Basel) 2019 04 9;10(4). Epub 2019 Apr 9.

Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Laboratory of Animal Genetics, Av. André Araújo 2936, Petrópolis, Manaus CEP: 69067-375, AM, Brazil.

Amazonian puffing snakes ( Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and trends for sex chromosomes in two Amazonian Puffer Snakes ( and ). We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches. The karyotype of (presented here for the first time) exhibits a 2n = 36, similar to that previously described in . Both species have highly differentiated ZZ/ZW sex chromosomes, where the W chromosome is highly heterochromatic in but euchromatic in . Both W chromosomes are homologous between these species as revealed by cross-species comparative genomic hybridization, even with heterogeneous distributions of several repetitive sequences across their genomes, including on the Z and on the W chromosomes. Our study provides evidence that W chromosomes in these two species have shared ancestry.
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http://dx.doi.org/10.3390/genes10040288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6523457PMC
April 2019

Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes).

PLoS One 2019 25;14(3):e0214225. Epub 2019 Mar 25.

Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil.

Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214225PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433368PMC
December 2019
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