13,042 results match your criteria BMC Genomics [Journal]


Decoding the differentiation of mesenchymal stem cells into mesangial cells at the transcriptomic level.

BMC Genomics 2020 Jul 7;21(1):467. Epub 2020 Jul 7.

Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia.

Background: Mesangial cells play an important role in the glomerulus to provide mechanical support and maintaine efficient ultrafiltration of renal plasma. Loss of mesangial cells due to pathologic conditions may lead to impaired renal function. Mesenchymal stem cells (MSC) can differentiate into many cell types, including mesangial cells. Read More

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http://dx.doi.org/10.1186/s12864-020-06868-5DOI Listing

Phylogenetic analysis of the ATP-binding cassette proteins suggests a new ABC protein subfamily J in Aedes aegypti (Diptera: Culicidae).

BMC Genomics 2020 Jul 6;21(1):463. Epub 2020 Jul 6.

Laboratório de Bioquímica e Biologia Molecular de Vetores, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-909, Brazil.

Background: We performed an in-depth analysis of the ABC gene family in Aedes aegypti (Diptera: Culicidae), which is an important vector species of arthropod-borne viral infections such as chikungunya, dengue, and Zika. Despite its importance, previous studies of the Arthropod ABC family have not focused on this species. Reports of insecticide resistance among pests and vectors indicate that some of these ATP-dependent efflux pumps are involved in compound traffic and multidrug resistance phenotypes. Read More

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http://dx.doi.org/10.1186/s12864-020-06873-8DOI Listing

Genome-wide association analysis of canine T zone lymphoma identifies link to hypothyroidism and a shared association with mast-cell tumors.

BMC Genomics 2020 Jul 6;21(1):464. Epub 2020 Jul 6.

Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.

Background: T zone lymphoma (TZL), a histologic variant of peripheral T cell lymphoma, represents about 12% of all canine lymphomas. Golden Retrievers appear predisposed, representing over 40% of TZL cases. Prior research found that asymptomatic aged Golden Retrievers frequently have populations of T zone-like cells (phenotypically identical to TZL) of undetermined significance (TZUS), potentially representing a pre-clinical state. Read More

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http://dx.doi.org/10.1186/s12864-020-06872-9DOI Listing

Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max.

BMC Genomics 2020 Jul 6;21(1):465. Epub 2020 Jul 6.

Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China.

Background: Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of the PP2C family in soybean are yet to be reported. Read More

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http://dx.doi.org/10.1186/s12864-020-06877-4DOI Listing

RNA-Seq of three free-living flatworm species suggests rapid evolution of reproduction-related genes.

BMC Genomics 2020 Jul 6;21(1):462. Epub 2020 Jul 6.

Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.

Background: The genus Macrostomum consists of small free-living flatworms and contains Macrostomum lignano, which has been used in investigations of ageing, stem cell biology, bioadhesion, karyology, and sexual selection in hermaphrodites. Two types of mating behaviour occur within this genus. Some species, including M. Read More

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http://dx.doi.org/10.1186/s12864-020-06862-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336406PMC

Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.

BMC Genomics 2020 Jul 3;21(1):459. Epub 2020 Jul 3.

Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.

Background: In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant development and immunity. These plasma membrane receptors belong to large gene/protein families that are not easily classified computationally. This detailed analysis of these plasma membrane proteins brings a new source of information to the legume genetic, physiology and breeding research communities. Read More

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http://dx.doi.org/10.1186/s12864-020-06844-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333395PMC

High resolution mapping of restoration of fertility (Rf) by combining large population and high density genetic map in pigeonpea [Cajanus cajan (L.) Millsp].

BMC Genomics 2020 Jul 3;21(1):460. Epub 2020 Jul 3.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.

Background: Restoration of fertility (Rf) is an important trait for pigeonpea hybrid breeding. Few coarse quantitative trait locus (QTL) studies conducted in the past identified QTLs with large confidence intervals on the genetic map and could not provide any information on possible genes responsible for Rf in pigeonpea. Therefore, a larger population comprising of 369 Fs derived from ICPA 2039 × ICPL 87119 was genotyped with high density Axiom Cajanus SNP Array with 56 K single nucleotide polymorphism (SNPs) for high resolution mapping of Rf. Read More

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http://dx.doi.org/10.1186/s12864-020-06859-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333333PMC

TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis).

BMC Genomics 2020 Jul 3;21(1):461. Epub 2020 Jul 3.

School of sciences, Anhui Agricultural University, Hefei, China.

Background: Tea plant (Camellia sinensis) is one of the world's most important beverage crops due to its numerous secondary metabolites conferring tea quality and health effects. However, only a small fraction of tea genes (especially for those metabolite-related genes) have been functionally characterized to date. A cohesive bioinformatics platform is thus urgently needed to aid in the functional determination of the remaining genes. Read More

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http://dx.doi.org/10.1186/s12864-020-06839-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333269PMC

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus.

BMC Genomics 2020 Jul 2;21(1):457. Epub 2020 Jul 2.

State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.

Background: Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animals.

Results: Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. Read More

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http://dx.doi.org/10.1186/s12864-020-06866-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7330940PMC

Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms.

BMC Genomics 2020 Jul 2;21(1):456. Epub 2020 Jul 2.

Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.

Background: The increasing demand of single-cell RNA-sequencing (scRNA-seq) experiments, such as the number of experiments and cells queried per experiment, necessitates higher sequencing depth coupled to high data quality. New high-throughput sequencers, such as the Illumina NovaSeq 6000, enables this demand to be filled in a cost-effective manner. However, current scRNA-seq library designs present compatibility challenges with newer sequencing technologies, such as index-hopping, and their ability to generate high quality data has yet to be systematically evaluated. Read More

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http://dx.doi.org/10.1186/s12864-020-06843-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7331155PMC

Shedding light on cashmere goat hair follicle biology: from morphology analyses to transcriptomic landascape.

BMC Genomics 2020 Jul 2;21(1):458. Epub 2020 Jul 2.

School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy.

Background: Cashmere goat is known for its precious undercoat. Being photoperiod-dictated, cashmere growth has been studied focusing mainly on hair follicle cycle phases (anagen, catagen and telogen). An accurate molecular knowledge of the goat hair follicle cycle, disentangling gene expression changes during phases and recognizing timing boundaries, could be useful to improve cashmere goat management and ultimately cashmere production. Read More

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http://dx.doi.org/10.1186/s12864-020-06870-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7330943PMC

Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing.

BMC Genomics 2020 Jul 2;21(1):455. Epub 2020 Jul 2.

Institute of Biotechnology, University of Helsinki, Helsinki, Finland.

Background: High pressure processing (HPP; i.e. 100-600 MPa pressure depending on product) is a non-thermal preservation technique adopted by the food industry to decrease significantly foodborne pathogens, including Listeria monocytogenes, from food. Read More

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http://dx.doi.org/10.1186/s12864-020-06819-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7331262PMC

Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects of Fe, O, and Si irradiation on the induction of murine hepatocellular carcinoma.

BMC Genomics 2020 Jul 1;21(1):453. Epub 2020 Jul 1.

Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77550, USA.

Background: One of the health risks posed to astronauts during deep space flights is exposure to high charge, high-energy (HZE) ions (Z > 13), which can lead to the induction of hepatocellular carcinoma (HCC). However, little is known on the molecular mechanisms of HZE irradiation-induced HCC.

Results: We performed comparative RNA-Seq transcriptomic analyses to assess the carcinogenic effects of 600 MeV/n Fe (0. Read More

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http://dx.doi.org/10.1186/s12864-020-06869-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329445PMC

Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer.

BMC Genomics 2020 Jul 1;21(1):452. Epub 2020 Jul 1.

MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.

Background: Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT). Read More

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http://dx.doi.org/10.1186/s12864-020-06865-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329468PMC

Influence of genetic diversity of seventeen Beauveria bassiana isolates from different hosts on virulence by comparative genomics.

BMC Genomics 2020 Jun 30;21(1):451. Epub 2020 Jun 30.

Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture, Changchun, 130033, Jilin Province, P. R. China.

Background: Beauveria bassiana (B. bassiana) is a famous entomopathogenic fungus that could parasitize on hundreds of insect species, which are being used as an environmentally friendly mycoinsecticide. Nevertheless, the possible effect of genetic diversity of these B. Read More

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http://dx.doi.org/10.1186/s12864-020-06791-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329388PMC

Comparative transcriptome analysis of the rice leaf folder (Cnaphalocrocis medinalis) to heat acclimation.

BMC Genomics 2020 Jun 30;21(1):450. Epub 2020 Jun 30.

Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China.

Background: The rice leaf folder Cnaphalocrocis medinalis Güenée is a serious insect pest of rice in Asia. This pest occurs in summer, and it is sensitive to high temperature. However, the larvae exhibit heat acclimation/adaptation. Read More

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http://dx.doi.org/10.1186/s12864-020-06867-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325166PMC

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data.

BMC Genomics 2020 Jun 29;21(1):447. Epub 2020 Jun 29.

School of Life and Environmental Sciences, Deakin University, Geelong, Australia.

Background: Inference of biological pathway activity via gene set enrichment analysis is frequently used in the interpretation of clinical and other omics data. With the proliferation of new omics profiling approaches and ever-growing size of data sets generated, there is a lack of tools available to perform and visualise gene set enrichments in analyses involving multiple contrasts.

Results: To address this, we developed mitch, an R package for multi-contrast gene set enrichment analysis. Read More

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http://dx.doi.org/10.1186/s12864-020-06856-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325150PMC

An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.

BMC Genomics 2020 Jun 29;21(1):448. Epub 2020 Jun 29.

Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123, Uppsala, Sweden.

Background: Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Read More

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http://dx.doi.org/10.1186/s12864-020-06858-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325058PMC

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani.

BMC Genomics 2020 Jun 29;21(1):449. Epub 2020 Jun 29.

Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 58 Abrahama Street, 80-307, Gdansk, Poland.

Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. Read More

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http://dx.doi.org/10.1186/s12864-020-06863-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325237PMC

Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L).

BMC Genomics 2020 Jun 29;21(1):444. Epub 2020 Jun 29.

College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, P. R. China.

Background: The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

Results: We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Read More

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http://dx.doi.org/10.1186/s12864-020-06828-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325284PMC

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis.

BMC Genomics 2020 Jun 29;21(1):443. Epub 2020 Jun 29.

College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China.

Background: The gonad is the major factor affecting animal reproduction. The regulatory mechanism of the expression of protein-coding genes involved in reproduction still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. Read More

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http://dx.doi.org/10.1186/s12864-020-06826-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7322844PMC

Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum.

BMC Genomics 2020 Jun 29;21(1):445. Epub 2020 Jun 29.

State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China.

Background: Multiple C2 domains and transmembrane region proteins (MCTPs) may act as transport mediators of other regulators. Although increased number of MCTPs in higher plants implies their diverse and specific functions in plant growth and development, only a few plant MCTPs have been studied and no study on the MCTPs in cotton has been reported.

Results: In this study, we identified 31 MCTPs in G. Read More

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http://dx.doi.org/10.1186/s12864-020-06842-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325108PMC

Structural variation of the malaria-associated human glycophorin A-B-E region.

BMC Genomics 2020 Jun 29;21(1):446. Epub 2020 Jun 29.

Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.

Background: Approximately 5% of the human genome shows common structural variation, which is enriched for genes involved in the immune response and cell-cell interactions. A well-established region of extensive structural variation is the glycophorin gene cluster, comprising three tandemly-repeated regions about 120 kb in length and carrying the highly homologous genes GYPA, GYPB and GYPE. Glycophorin A (encoded by GYPA) and glycophorin B (encoded by GYPB) are glycoproteins present at high levels on the surface of erythrocytes, and they have been suggested to act as decoy receptors for viral pathogens. Read More

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http://dx.doi.org/10.1186/s12864-020-06849-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325229PMC

Transcriptome analysis of genes related to gonad differentiation and development in Muscovy ducks.

BMC Genomics 2020 Jun 26;21(1):438. Epub 2020 Jun 26.

College of Animal Sciences, Fujian Agricultural and Forestry University, Fuzhou, 350002, China.

Background: Sex-related genes play a crucial role in gonadal differentiation into testes or ovaries. However, the genetic control of gonadal differentiation in Muscovy ducks remains unknown. Therefore, the objective of our study was to screen new candidate genes associated with ovarian and testicular development. Read More

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http://dx.doi.org/10.1186/s12864-020-06852-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318502PMC

Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage.

BMC Genomics 2020 Jun 26;21(1):437. Epub 2020 Jun 26.

College of Food and Bioengineering, Henan University of Science and Technology, No. 263, Kaiyuan Avenue, Luolong District, Luoyang city, 471023, Henan, China.

Background: It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus. Read More

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http://dx.doi.org/10.1186/s12864-020-06850-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318492PMC

Genomic nucleotide-based distance analysis for delimiting old world monkey derived herpes simplex virus species.

BMC Genomics 2020 Jun 26;21(1):436. Epub 2020 Jun 26.

Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 550 Bardeen Laboratories, 1300 University Ave, Madison, WI, 53706, USA.

Background: Herpes simplex viruses form a genus within the alphaherpesvirus subfamily, with three identified viral species isolated from Old World monkeys (OWM); Macacine alphaherpesvirus 1 (McHV-1; herpes B), Cercopithecine alphaherpesvirus 2 (SA8), and Papiine alphaherpesvirus 2 (PaHV-2; herpes papio). Herpes B is endemic to macaques, while PaHV-2 and SA8 appear endemic to baboons. All three viruses are genetically and antigenically similar, with SA8 and PaHV-2 thought to be avirulent in humans, while herpes B is a biosafety level 4 pathogen. Read More

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http://dx.doi.org/10.1186/s12864-020-06847-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318535PMC

Maternal dietary resistant starch does not improve piglet's gut and liver metabolism when challenged with a high fat diet.

BMC Genomics 2020 Jun 26;21(1):439. Epub 2020 Jun 26.

Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux AgroBioTech, University of Liège, Passage des Déportes 2, 5030, Gembloux, Belgium.

Background: In the past several years, the use of resistant starch (RS) as prebiotic has extensively been studied in pigs, and this mostly in the critical period around weaning. RS is believed to exert beneficial effects on the gastrointestinal tract mainly due to higher levels of short chain fatty acids (SCFAs) and an improved microbiota profile. In this study, sows were fed digestible starch (DS) or RS during late gestation and lactation and the possible maternal effect of RS on the overall health of the progeny was assessed. Read More

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http://dx.doi.org/10.1186/s12864-020-06854-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318506PMC

Diverse and unique viruses discovered in the surface water of the East China Sea.

BMC Genomics 2020 Jun 26;21(1):441. Epub 2020 Jun 26.

College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.

Background: Viruses are the most abundant biological entities on earth and play import roles in marine biogeochemical cycles. Here, viral communities in the surface water of the East China Sea (ECS) were collected from three representative regions of Yangshan Harbor (YSH), Gouqi Island (GQI), and the Yangtze River Estuary (YRE) and explored primarily through epifluorescence microscopy (EM), transmission electron microscopy (TEM), and metagenomics analysis.

Results: The virus-like particles (VLPs) in the surface water of the ECS were measured to be 10 to 10 VLPs/ml. Read More

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http://dx.doi.org/10.1186/s12864-020-06861-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318539PMC

Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes.

BMC Genomics 2020 Jun 26;21(1):442. Epub 2020 Jun 26.

Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.

Background: Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily based on short and less informative rDNA sequences. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme, and to further understand the evolution of order Chaetophorales. Read More

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http://dx.doi.org/10.1186/s12864-020-06845-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320567PMC

Diversity of MSDIN family members in amanitin-producing mushrooms and the phylogeny of the MSDIN and prolyl oligopeptidase genes.

BMC Genomics 2020 Jun 26;21(1):440. Epub 2020 Jun 26.

College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China.

Background: Amanitin-producing mushrooms, mainly distributed in the genera Amanita, Galerina and Lepiota, possess MSDIN gene family for the biosynthesis of many cyclopeptides catalysed by prolyl oligopeptidase (POP). Recently, transcriptome sequencing has proven to be an efficient way to mine MSDIN and POP genes in these lethal mushrooms. Thus far, only A. Read More

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http://dx.doi.org/10.1186/s12864-020-06857-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318481PMC

Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs.

BMC Genomics 2020 Jun 25;21(1):428. Epub 2020 Jun 25.

Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.

Background: The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum.

Results: Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Read More

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http://dx.doi.org/10.1186/s12864-020-06824-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315539PMC

Protein acetylation in mitochondria plays critical functions in the pathogenesis of fatty liver disease.

BMC Genomics 2020 Jun 26;21(1):435. Epub 2020 Jun 26.

Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China.

Background: Fatty liver is a high incidence of perinatal disease in dairy cows caused by negative energy balance, which seriously threatens the postpartum health and milk production. It has been reported that lysine acetylation plays an important role in substance and energy metabolism. Predictably, most metabolic processes in the liver, as a vital metabolic organ, are subjected to acetylation. Read More

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http://dx.doi.org/10.1186/s12864-020-06837-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318365PMC

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure.

BMC Genomics 2020 Jun 26;21(1):433. Epub 2020 Jun 26.

Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA.

Background: Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Read More

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http://dx.doi.org/10.1186/s12864-020-06831-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318467PMC

Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium.

BMC Genomics 2020 Jun 26;21(1):434. Epub 2020 Jun 26.

Department of Agronomy and Horticulture, Plant Science Hall, UNL, Lincoln, NE, USA.

Background: Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat genotypes. Read More

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http://dx.doi.org/10.1186/s12864-020-06835-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318758PMC

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton.

BMC Genomics 2020 Jun 26;21(1):431. Epub 2020 Jun 26.

National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.

Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Read More

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http://dx.doi.org/10.1186/s12864-020-06800-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318736PMC

Mining ancient microbiomes using selective enrichment of damaged DNA molecules.

BMC Genomics 2020 Jun 26;21(1):432. Epub 2020 Jun 26.

Department of Molecular Biology, Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.

Background: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Read More

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http://dx.doi.org/10.1186/s12864-020-06820-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318760PMC

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus.

BMC Genomics 2020 Jun 25;21(1):429. Epub 2020 Jun 25.

Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.

Background: Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant. Read More

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http://dx.doi.org/10.1186/s12864-020-06853-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315500PMC

Chi-miR-30b-5p inhibits dermal papilla cells proliferation by targeting CaMKIIδ gene in cashmere goat.

BMC Genomics 2020 Jun 26;21(1):430. Epub 2020 Jun 26.

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: During goat embryonic morphogenesis and postnatal initiation of hair follicle (HF) regeneration, dermal papilla (DP) cells play a vital role in hair formation. Growing evidence shows that microRNAs (miRNAs) participate in HF development and DP cell proliferation. However, the molecular mechanisms have not been thoroughly investigated. Read More

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http://dx.doi.org/10.1186/s12864-020-06799-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318507PMC

Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus.

BMC Genomics 2020 Jun 26;21(1):422. Epub 2020 Jun 26.

Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.

Background: The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is one of the most important edible seaweeds, and it is cultivated for market primarily in Okinawa, Japan. Four strains, denominated S, K, O, and C, with distinctively different morphologies, have been cultivated commercially since the early 2000s. We previously reported a draft genome of the S-strain. Read More

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http://dx.doi.org/10.1186/s12864-020-06792-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318753PMC

Transcriptome profiling of venom gland from wasp species: de novo assembly, functional annotation, and discovery of molecular markers.

BMC Genomics 2020 Jun 24;21(1):427. Epub 2020 Jun 24.

CDC of Western Theater Command, PLA, Chengdu, 610021, China.

Background: Vespa velutina, one of the most aggressive and fearful wasps in China, can cause grievous allergies and toxic reactions, leading to organ failure and even death. However, there is little evidence on molecular data regarding wasps. Therefore, we aimed to provide an insight into the transcripts expressed in the venom gland of wasps. Read More

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http://dx.doi.org/10.1186/s12864-020-06851-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315503PMC

Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites.

BMC Genomics 2020 Jun 24;21(1):424. Epub 2020 Jun 24.

Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.

Background: Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. However, there is currently little understanding of endophytic fungi at the omics levels about their potential in secondary metabolites. Calcarisporium arbuscula, an endophytic fungus from the fruit bodies of Russulaceae, produces a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic activities. Read More

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http://dx.doi.org/10.1186/s12864-020-06813-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315530PMC

Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis.

BMC Genomics 2020 Jun 24;21(1):426. Epub 2020 Jun 24.

Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Background: Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation.

Results: Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Read More

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http://dx.doi.org/10.1186/s12864-020-06846-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315562PMC

Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis.

BMC Genomics 2020 Jun 24;21(1):425. Epub 2020 Jun 24.

Division of Plant Biology, Bose Institute, P1/12 CIT Scheme VII M, Kolkata, 700054, India.

Background: Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. Read More

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http://dx.doi.org/10.1186/s12864-020-06841-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315535PMC

De novo transcriptome sequencing and analysis of salt-, alkali-, and drought-responsive genes in Sophora alopecuroides.

BMC Genomics 2020 Jun 23;21(1):423. Epub 2020 Jun 23.

College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun City, Jilin Province, China.

Background: Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-tolerant sand-fixing pioneer species distributed mostly in Western Asia and northwestern China. Read More

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http://dx.doi.org/10.1186/s12864-020-06823-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310485PMC

High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing.

BMC Genomics 2020 Jun 22;21(1):419. Epub 2020 Jun 22.

College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China.

Background: Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the maternal parent 'Cabernet sauvignon' and paternal parent 'Zuoyouhong'. Read More

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http://dx.doi.org/10.1186/s12864-020-06836-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310074PMC

The effect of variant interference on de novo assembly for viral deep sequencing.

BMC Genomics 2020 Jun 22;21(1):421. Epub 2020 Jun 22.

Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.

Background: Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored.

Results: Our results from > 15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. Read More

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http://dx.doi.org/10.1186/s12864-020-06801-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306937PMC

RNA-sequencing reveals positional memory of multipotent mesenchymal stromal cells from oral and maxillofacial tissue transcriptomes.

BMC Genomics 2020 Jun 22;21(1):417. Epub 2020 Jun 22.

Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan.

Background: Multipotent mesenchymal stromal cells (MSCs) can be isolated from numerous tissues and are attractive candidates for therapeutic clinical applications due to their immunomodulatory and pro-regenerative capacity. Although the minimum criteria for defining MSCs have been defined, their characteristics are known to vary depending on their tissue of origin.

Results: We isolated and characterized human MSCs from three different bones (ilium (I-MSCs), maxilla (Mx-MSCs) and mandible (Md-MSCs)) and proceeded with next generation RNA-sequencing. Read More

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http://dx.doi.org/10.1186/s12864-020-06825-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310078PMC
June 2020
3.986 Impact Factor

Gene expression predictions and networks in natural populations supports the omnigenic theory.

BMC Genomics 2020 Jun 22;21(1):416. Epub 2020 Jun 22.

BioForA, INRAE, ONF, Orléans, France.

Background: Recent literature on the differential role of genes within networks distinguishes core from peripheral genes. If previous works have shown contrasting features between them, whether such categorization matters for phenotype prediction remains to be studied.

Results: We measured 17 phenotypic traits for 241 cloned genotypes from a Populus nigra collection, covering growth, phenology, chemical and physical properties. Read More

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http://dx.doi.org/10.1186/s12864-020-06809-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310122PMC

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications.

BMC Genomics 2020 Jun 22;21(1):415. Epub 2020 Jun 22.

Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea.

Background: Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge. Read More

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http://dx.doi.org/10.1186/s12864-020-06812-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310033PMC

Replication origin location might contribute to genetic variability in Trypanosoma cruzi.

BMC Genomics 2020 Jun 22;21(1):414. Epub 2020 Jun 22.

Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil.

Background: DNA replication in trypanosomatids operates in a uniquely challenging environment, since most of their genomes are constitutively transcribed. Trypanosoma cruzi, the etiological agent of Chagas disease, presents high variability in both chromosomes size and copy number among strains, though the underlying mechanisms are unknown.

Results: Here we have mapped sites of DNA replication initiation across the T. Read More

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http://dx.doi.org/10.1186/s12864-020-06803-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310030PMC