Publications by authors named "Daniel S Rokhsar"

94 Publications

Analysis of meiosis in reveals plasticity in homolog pairing and synapsis in the nematode lineage.

Elife 2021 08 24;10. Epub 2021 Aug 24.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.

Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode , a distant relative of the widely studied model organism shares many anatomical and other features that facilitate analysis of meiosis in . However, while has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for that reveals a crossover landscape very similar to that of , despite marked divergence in the regulation of synapsis and crossing-over between these lineages.
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http://dx.doi.org/10.7554/eLife.70990DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8455136PMC
August 2021

Beyond "living fossils": Can comparative genomics finally reveal novelty?

Mol Ecol Resour 2021 Aug 18. Epub 2021 Aug 18.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.

Cephalopods have recently moved into the research focus due to the growing number of sequenced genomes, molecular tools, and laboratory culture (Albertin & Simakov, 2020)⁠. Genome data now allows us to ask how the many known novelties of cephalopod morphology are reflected in their genomes and gene regulation. A crucial gap in this understanding has been the limited information for the Nautilus, the last survivor of a cephalopod lineage that diverged from the highly derived coleoid clade (octopus, squid, cuttlefish) around 400 million years ago. The publication of Nautilus genomes (in this issue of Molecular Ecology [Huang et al., 2021; Zhang et al., 2021])⁠ will help us understand which genetic changes happened when, and ultimately how they contributed to cephalopod evolution.
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http://dx.doi.org/10.1111/1755-0998.13488DOI Listing
August 2021

Diversification of mandarin citrus by hybrid speciation and apomixis.

Nat Commun 2021 07 26;12(1):4377. Epub 2021 Jul 26.

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.
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http://dx.doi.org/10.1038/s41467-021-24653-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8313541PMC
July 2021

Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida).

Commun Biol 2021 06 29;4(1):819. Epub 2021 Jun 29.

Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.

Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic environments around the world's oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bobtail and bottletail squids to estimate their evolutionary relationships and divergence time. Our phylogenetic analyses show that each of Sepiadariidae, Sepiolidae, and the three subfamilies of the Sepiolidae are monophyletic. We found that the ancestor of the Sepiolinae very likely possessed a bilobed light organ with bacteriogenic luminescence. Sepiolinae forms a sister group to Rossinae and Heteroteuthinae, and split into Indo-Pacific and Atlantic-Mediterranean lineages. The origin of these lineages coincides with the end of the Tethys Sea and the separation of these regions during the Eocene and the beginning of the Oligocene. We demonstrated that sepiolids radiated after the Late Cretaceous and that major biogeographic events might have shaped their distribution and speciation.
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http://dx.doi.org/10.1038/s42003-021-02348-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8241861PMC
June 2021

Plant Pan-Genomics Comes of Age.

Annu Rev Plant Biol 2021 06 13;72:411-435. Epub 2021 Apr 13.

DOE Joint Genome Institute, Berkeley, California 94720, USA; email:

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools.
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http://dx.doi.org/10.1146/annurev-arplant-080720-105454DOI Listing
June 2021

Current status and impending progress for cassava structural genomics.

Plant Mol Biol 2021 Feb 18. Epub 2021 Feb 18.

Donald Danforth Plant Science Center (DDPSC), St. Louis, MO, 63132, USA.

Key Message: We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.
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http://dx.doi.org/10.1007/s11103-020-01104-wDOI Listing
February 2021

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Nature 2021 02 27;590(7846):438-444. Epub 2021 Jan 27.

School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.

Long-term climate change and periodic environmental extremes threaten food and fuel security and global crop productivity. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.
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http://dx.doi.org/10.1038/s41586-020-03127-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7886653PMC
February 2021

Genome biology of the paleotetraploid perennial biomass crop Miscanthus.

Nat Commun 2020 10 28;11(1):5442. Epub 2020 Oct 28.

Department of Agronomy, Zhejiang University, Hangzhou, 310058, China.

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.
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http://dx.doi.org/10.1038/s41467-020-18923-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595124PMC
October 2020

A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus.

Plant J 2020 12 18;104(5):1215-1232. Epub 2020 Oct 18.

Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA.

Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high-quality, chromosome-scale genome assembly of P. trifoliata. The 264.9-Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein-coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species-specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C-repeat/DREB binding factor (CBF)-dependent and CBF-independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non-dwarfing type. The high-quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.
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http://dx.doi.org/10.1111/tpj.14993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756384PMC
December 2020

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution.

Commun Biol 2020 09 1;3(1):480. Epub 2020 Sep 1.

Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.

Closely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2n = 46) and Muntiacus muntjak vaginalis (2n = 6/7), and analyze their evolution and architecture. The genomes show extensive collinearity with each other and with other deer and cattle. We identified numerous fusion events unique to and shared by muntjacs relative to the cervid ancestor, confirming many cytogenetic observations with genome sequence. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites. A few genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype.
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http://dx.doi.org/10.1038/s42003-020-1096-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463020PMC
September 2020

Deeply conserved synteny resolves early events in vertebrate evolution.

Nat Ecol Evol 2020 06 20;4(6):820-830. Epub 2020 Apr 20.

Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.

Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid-late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.
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http://dx.doi.org/10.1038/s41559-020-1156-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269912PMC
June 2020

New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis.

Commun Biol 2019 11;2:465. Epub 2019 Dec 11.

1Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan.

Bobtail squid are emerging models for host-microbe interactions, behavior, and development, yet their species diversity and distribution remain poorly characterized. Here, we combine mitochondrial and transcriptome sequences with morphological analysis to describe three species of bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu archipelago, and compare them with related taxa. One Ryukyuan type was previously unknown, and is described here as sp. nov. Another Ryukyuan type is morphologically indistinguishable from Sasaki, 1913. Molecular analyses, however, place this taxon within the genus Steenstrup, 1887, and additional morphological investigation led to formal rediagnosis of and reassignment of this species as comb. nov. While no adults from the third Ryukyuan type were found, sequences from hatchlings suggest a close relationship with Reid, 2011, known from Australia and East Timor. The broadly sampled transcriptomes reported here provide a foundation for future phylogenetic and comparative studies.
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http://dx.doi.org/10.1038/s42003-019-0661-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6906322PMC
July 2020

Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Genome Biol 2019 08 9;20(1):161. Epub 2019 Aug 9.

Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.

Following publication of the original article [1], the authors reported that the Availability of data and materials section required updating. The updated text reads as follows.
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http://dx.doi.org/10.1186/s13059-019-1781-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689176PMC
August 2019

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Genome Biol 2019 06 21;20(1):126. Epub 2019 Jun 21.

Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.

Background: Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species.

Results: Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (d), and lower relative divergence (F) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high F and d among the groups, termed F-islands. Population genetic signatures indicate that F-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms.

Conclusions: Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.
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http://dx.doi.org/10.1186/s13059-019-1729-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6587263PMC
June 2019

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.

Dev Biol 2019 08 10;452(1):8-20. Epub 2019 Apr 10.

University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 9040495, Japan. Electronic address:

The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.
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http://dx.doi.org/10.1016/j.ydbio.2019.03.015DOI Listing
August 2019

Acoel genome reveals the regulatory landscape of whole-body regeneration.

Science 2019 03;363(6432)

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

Whole-body regeneration is accompanied by complex transcriptomic changes, yet the chromatin regulatory landscapes that mediate this dynamic response remain unexplored. To decipher the regulatory logic that orchestrates regeneration, we sequenced the genome of the acoel worm , a highly regenerative member of the sister lineage of other bilaterians. Epigenomic profiling revealed thousands of regeneration-responsive chromatin regions and identified dynamically bound transcription factor motifs, with the early growth response (EGR) binding site as the most variably accessible during regeneration. Combining inhibition with chromatin profiling suggests that Egr functions as a pioneer factor to directly regulate early wound-induced genes. The genetic connections inferred by this approach allowed the construction of a gene regulatory network for whole-body regeneration, enabling genomics-based comparisons of regeneration across species.
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http://dx.doi.org/10.1126/science.aau6173DOI Listing
March 2019

A large CRISPR-induced bystander mutation causes immune dysregulation.

Commun Biol 2019 18;2:70. Epub 2019 Feb 18.

Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA.

A persistent concern with CRISPR-Cas9 gene editing has been the potential to generate mutations at off-target genomic sites. While CRISPR-engineering mice to delete a ~360 bp intronic enhancer, here we discovered a founder line that had marked immune dysregulation caused by a 24 kb tandem duplication of the sequence adjacent to the on-target deletion. Our results suggest unintended repair of on-target genomic cuts can cause pathogenic "bystander" mutations that escape detection by routine targeted genotyping assays.
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http://dx.doi.org/10.1038/s42003-019-0321-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379443PMC
April 2020

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans.

Curr Biol 2019 01 10;29(2):312-318.e3. Epub 2019 Jan 10.

Molecular Genetics Unit, Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna 904-0495, Japan; Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720, USA.

Chaetognaths (arrow worms) are an enigmatic group of marine animals whose phylogenetic position remains elusive, in part because they display a mix of developmental and morphological characters associated with other groups [1, 2]. In particular, it remains unclear whether they are a sister group to protostomes [1, 2], one of the principal animal superclades, or whether they bear a closer relationship with some spiralian phyla [3, 4]. Addressing the phylogenetic position of chaetognaths and refining our understanding of relationships among spiralians are essential to fully comprehend character changes during bilaterian evolution [5]. To tackle these questions, we generated new transcriptomes for ten chaetognath species, compiling an extensive phylogenomic dataset that maximizes data occupancy and taxonomic representation. We employed inference methods that consider rate and compositional heterogeneity across taxa to avoid limitations of earlier analyses [6]. In this way, we greatly improved the resolution of the protostome tree of life. We find that chaetognaths cluster together with rotifers, gnathostomulids, and micrognathozoans within an expanded Gnathifera clade and that this clade is the sister group to other spiralians [7, 8]. Our analysis shows that several previously proposed groupings are likely due to systematic error, and we propose a revised organization of Lophotrochozoa with three main clades: Tetraneuralia (mollusks and entoprocts), Lophophorata (brachiopods, phoronids, and ectoprocts), and a third unnamed clade gathering annelids, nemerteans, and platyhelminthes. Consideration of classical morphological, developmental, and genomic characters in light of this topology indicates secondary loss as a fundamental trend in spiralian evolution.
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http://dx.doi.org/10.1016/j.cub.2018.11.042DOI Listing
January 2019

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.

Proc Natl Acad Sci U S A 2019 02 11;116(8):3030-3035. Epub 2019 Jan 11.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269;

Microbes have been critical drivers of evolutionary innovation in animals. To understand the processes that influence the origin of specialized symbiotic organs, we report the sequencing and analysis of the genome of , a model cephalopod with richly characterized host-microbe interactions. We identified large-scale genomic reorganization shared between and and posit that this reorganization has contributed to the evolution of cephalopod complexity. To reveal genomic signatures of host-symbiont interactions, we focused on two specialized organs of : the light organ, which harbors a monoculture of , and the accessory nidamental gland (ANG), a reproductive organ containing a bacterial consortium. Our findings suggest that the two symbiotic organs within originated by different evolutionary mechanisms. Transcripts expressed in these microbe-associated tissues displayed their own unique signatures in both coding sequences and the surrounding regulatory regions. Compared with other tissues, the light organ showed an abundance of genes associated with immunity and mediating light, whereas the ANG was enriched in orphan genes known only from Together, these analyses provide evidence for different patterns of genomic evolution of symbiotic organs within a single host.
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http://dx.doi.org/10.1073/pnas.1817322116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386654PMC
February 2019

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

Genes (Basel) 2018 Mar 28;9(4). Epub 2018 Mar 28.

Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.

Closely related to the model plant , the genus is known to contain both sexual and apomictic species or accessions. is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease locus, related to apomixis in , and proposed model of its evolution through the series of duplications. An assembled genome of will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species
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http://dx.doi.org/10.3390/genes9040185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924527PMC
March 2018

Genomics of the origin and evolution of Citrus.

Nature 2018 02 7;554(7692):311-316. Epub 2018 Feb 7.

Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain.

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.
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http://dx.doi.org/10.1038/nature25447DOI Listing
February 2018

Publisher correction: Young inversion with multiple linked QTLs under selection in a hybrid zone.

Nat Ecol Evol 2017 10;1(10):1585

Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA.

In Fig. 5 of the version of this Article originally published, the final number on the x axes of each panel was incorrectly written as 1.5; it should have read 7.5. This has now been corrected in all versions of the Article.
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http://dx.doi.org/10.1038/s41559-017-0310-8DOI Listing
October 2017

Young inversion with multiple linked QTLs under selection in a hybrid zone.

Nat Ecol Evol 2017 Apr 3;1(5):119. Epub 2017 Apr 3.

Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA.

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.
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http://dx.doi.org/10.1038/s41559-017-0119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607633PMC
April 2017

QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from .

Front Plant Sci 2017 21;8:1168. Epub 2017 Jul 21.

International Institute of Tropical AgricultureNairobi, Kenya.

Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), cassava mosaic disease (CMD), and cassava green mite (CGM) was performed using an F cross developed between the Tanzanian landrace, Kiroba, and a breeding line, AR37-80. The population was evaluated for two consecutive years in two sites in Tanzania. A genetic linkage map was derived from 106 F progeny and 1,974 SNP markers and spanned 18 chromosomes covering a distance of 1,698 cM. Fifteen significant QTL were identified; two are associated with CBSD root necrosis only, and were detected on chromosomes V and XII, while seven were associated with CBSD foliar symptoms only and were detected on chromosomes IV, VI, XVII, and XVIII. QTL on chromosomes 11 and 15 were associated with both CBSD foliar and root necrosis symptoms. Two QTL were found to be associated with CMD and were detected on chromosomes XII and XIV, while two were associated with CGM and were identified on chromosomes V and X. There are large introgression regions in Kiroba on chromosomes I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. The introgression region on chromosome I is of a different haplotype to the characteristic "Amani haplotype" found in the landrace Namikonga and others, and unlike some other genotypes, Kiroba does not have a large introgression block on chromosome IV. Kiroba is closely related to a sampled Tanzanian "tree cassava." This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in another variety, Namikonga.
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http://dx.doi.org/10.3389/fpls.2017.01168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5519584PMC
July 2017

Insights into the red algae and eukaryotic evolution from the genome of (Bangiophyceae, Rhodophyta).

Proc Natl Acad Sci U S A 2017 08 17;114(31):E6361-E6370. Epub 2017 Jul 17.

Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, NJ 08901.

(laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including , lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.
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http://dx.doi.org/10.1073/pnas.1703088114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547612PMC
August 2017

Genome evolution in the allotetraploid frog Xenopus laevis.

Nature 2016 10;538(7625):336-343

US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
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http://dx.doi.org/10.1038/nature19840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313049PMC
October 2016

Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.

Proc Natl Acad Sci U S A 2016 06 6;113(23):6508-13. Epub 2016 May 6.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544;

Transcriptional enhancers are short segments of DNA that switch genes on and off in response to a variety of intrinsic and extrinsic signals. Despite the discovery of the first enhancer more than 30 y ago, the relationship between primary DNA sequence and enhancer activity remains obscure. In particular, the importance of "syntax" (the order, orientation, and spacing of binding sites) is unclear. A high-throughput screen identified synthetic notochord enhancers that are activated by the combination of ZicL and ETS transcription factors in Ciona embryos. Manipulation of these enhancers elucidated a "regulatory code" of sequence and syntax features for notochord-specific expression. This code enabled in silico discovery of bona fide notochord enhancers, including those containing low-affinity binding sites that would be excluded by standard motif identification methods. One of the newly identified enhancers maps upstream of the known enhancer that regulates Brachyury (Ci-Bra), a key determinant of notochord specification. This newly identified Ci-Bra shadow enhancer contains binding sites with very low affinity, but optimal syntax, and therefore mediates surprisingly strong expression in the notochord. Weak binding sites are compensated by optimal syntax, whereas enhancers containing high-affinity binding affinities possess suboptimal syntax. We suggest this balance has obscured the importance of regulatory syntax, as noncanonical binding motifs are typically disregarded by enhancer detection methods. As a result, enhancers with low binding affinities but optimal syntax may be a vastly underappreciated feature of the regulatory genome.
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http://dx.doi.org/10.1073/pnas.1605085113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988596PMC
June 2016

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

Nat Biotechnol 2016 05 18;34(5):562-70. Epub 2016 Apr 18.

Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.
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http://dx.doi.org/10.1038/nbt.3535DOI Listing
May 2016

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

Genome Res 2016 Mar 4;26(3):342-50. Epub 2016 Feb 4.

Dovetail Genomics LLC, Santa Cruz, California 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, California 95066, USA;

Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach ("Chicago") based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline ("HiRise") that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.
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http://dx.doi.org/10.1101/gr.193474.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772016PMC
March 2016
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