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BMC Genomics

Jiao Cheng, Min Hui, Zhongli Sha
BACKGROUND: Hydrothermal vents and cold seeps are typical deep-sea chemosynthetically-driven ecosystems that allow high abundance of specialized macro-benthos. To gather knowledge about the genetic basis of adaptation to these extreme environments, species shared between different habitats, especially for the dominant species, are of particular interest. The galatheid squat lobster, Shinkaia crosnieri Baba and Williams, 1998, is one of the few dominant species inhabiting both deep-sea hydrothermal vents and cold seeps...
May 18, 2019: BMC Genomics
Le Xue, Zilong He, Xiaochun Bi, Wei Xu, Ting Wei, Shuangxiu Wu, Songnian Hu
BACKGROUND: Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from terpene precursors, IPP and DMAPP, through the cytoplasmic mevalonate (MVA) pathway. Another plastic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was proved also contributing to ginsenoside generation in the roots of P. ginseng by using specific chemical inhibitors recently...
May 17, 2019: BMC Genomics
Michelle M Bertke, Kyle M Dubiak, Laura Cronin, Erliang Zeng, Paul W Huber
BACKGROUND: Adenovirus protein, Gam1, triggers the proteolytic destruction of the E1 SUMO-activating enzyme. Microinjection of an empirically determined amount of Gam1 mRNA into one-cell Xenopus embryos can reduce SUMOylation activity to undetectable, but nonlethal, levels, enabling an examination of the role of this post-translational modification during early vertebrate development. RESULTS: We find that SUMOylation-deficient embryos consistently exhibit defects in neural tube and heart development...
May 17, 2019: BMC Genomics
Yanjie Zhang, Qian Chen, James Y Xie, Yip Hung Yeung, Baohua Xiao, Baoling Liao, Jianliang Xu, Jian-Wen Qiu
BACKGROUND: Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species' stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea...
May 17, 2019: BMC Genomics
Pengfei Hu, Yuanchen Shao, Jiaping Xu, Tianjiao Wang, Yiqing Li, Huamiao Liu, Min Rong, Weilin Su, Binxi Chen, Songhuan Cui, Xuezhe Cui, Fuhe Yang, Hidetoshi Tamate, Xiumei Xing
BACKGROUND: Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. METHODS: In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. RESULTS: A total of 197,543 SNPs were identified with an average sequencing depth of 16 x...
May 17, 2019: BMC Genomics
Mahsa Mousavi-Derazmahalleh, Steven Chang, Geoff Thomas, Mark Derbyshire, Phillip E Bayer, David Edwards, Matthew N Nelson, William Erskine, Francisco J Lopez-Ruiz, Jon Clements, James K Hane
BACKGROUND: Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea - both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts...
May 17, 2019: BMC Genomics
Yihua Zhan, Qingfei Wu, Yue Chen, Mengling Tang, Chendong Sun, Junwei Sun, Chenliang Yu
BACKGROUND: Salinization seriously threatens land use efficiency and crop yields across the world. Understanding the mechanisms plants use to protect against salt stress will help breeders develop salt-tolerant vegetable crops. Okra (Abelmoschus esculentus L.) is an important vegetable crop of the mallow family, which is now cultivated in warm regions worldwide. To understand the effects of salt stress on the protein level of okra, a comparative proteomic analysis of okra seedlings grown in the presence of 0 or 300 mmol L- 1 NaCl treatment was performed using an integrated approach of Tandem Mass Tag labeling and LC-MS/MS integrated approach...
May 16, 2019: BMC Genomics
Nandhini Saranathan, Banhi Biswas, Anupam Patra, Perumal Vivekanandan
BACKGROUND: Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in human and microbial genomes, but their role in recombination has not been studied in DNA viruses. RESULTS: The availability of near full-length sequences from 40 HSV-1 recombinant strains with exact position of the recombination breakpoints provided us with a unique opportunity to investigate the role of G4-motifs in recombination among herpes viruses...
May 16, 2019: BMC Genomics
Mor Rubinstein, Ravit Eshed, Ada Rozen, Tali Zviran, David N Kuhn, Vered Irihimovitch, Amir Sherman, Ron Ophir
BACKGROUND: Discovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a costly process, due to loss of loci that are proven to be non-informative when genotyping the germplasm. RESULTS: Our study on a collection of 100 accessions comprised the three race types, Guatemalan, Mexican, and West Indian. To increase the chances of discovering polymorphic loci, three pools of genomic DNA, one from each race, were sequenced and the reads were aligned to a reference transcriptome...
May 15, 2019: BMC Genomics
Zhi Zou, Jianghua Yang
BACKGROUND: Aquaporins (AQPs) are a class of integral membrane proteins that facilitate the passive transport of water and other small solutes across biological membranes. Despite their importance, little information is available in cassava (Manihot esculenta), a perennial shrub of the Euphorbiaceae family that serves the sixth major staple crop in the world. RESULTS: This study presents a genome-wide analysis of the AQP gene family in cassava. The family of 42 members in this species could be divided into five subfamilies based on phylogenetic analysis, i...
May 15, 2019: BMC Genomics
Abhijeet Shah, Joseph I Hoffman, Holger Schielzeth
BACKGROUND: The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo transcriptome assembly as reference resource for gene expression studies. We used high-throughput Illumina sequencing to generate 5,070,036 paired-end reads after quality filtering...
May 14, 2019: BMC Genomics
Qiuyun Wu, Junwei Wang, Shuxiang Mao, Haoran Xu, Qi Wu, Mantian Liang, Yiming Yuan, Mingyue Liu, Ke Huang
BACKGROUND: Sulforaphane is a natural isothiocyanate available from cruciferous vegetables with multiple characteristics including antioxidant, antitumor and anti-inflammatory effect. Single-molecule real-time (SMRT) sequencing has been used for long-read de novo assembly of plant genome. Here, we investigated the molecular mechanism related to glucosinolates biosynthesis in Chinese kale using combined NGS and SMRT sequencing. RESULTS: SMRT sequencing produced 185,134 unigenes, higher than 129,325 in next-generation sequencing (NGS)...
May 14, 2019: BMC Genomics
Swati Sinha, Choy-Eng Nge, Chung Yan Leong, Veronica Ng, Sharon Crasta, Mohammad Alfatah, Falicia Goh, Kia-Ngee Low, Huibin Zhang, Prakash Arumugam, Alexander Lezhava, Swaine L Chen, Yoganathan Kanagasundaram, Siew Bee Ng, Frank Eisenhaber, Birgit Eisenhaber
BACKGROUND: Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis. RESULTS: Therefore, we sequenced the genome of one of our Phoma strains (F3723) previously identified as having antifungal activity in a high-throughput screen. We found a biosynthetic gene cluster that was predicted to synthesize a cyclic lipodepsipeptide that differs in the amino acid composition compared to Phomafungin...
May 14, 2019: BMC Genomics
Joanna Majka, Katarzyna Bzdęga, Agnieszka Janiak, Hanna Ćwiek-Kupczyńska, Paweł Krajewski, Tomasz Książczyk, Zbigniew Zwierzykowski
BACKGROUND: Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids can merge in their genomes agronomically important characteristics. However, in polyploid plants, especially in allopolyploids, the hybridization of divergent genomes could contribute to various abnormalities, such as variability in chromosome number, structural rearrangements, and/or disorders in inheritance patterns...
May 14, 2019: BMC Genomics
Congjun Jia, Hongbo Wang, Chen Li, Xiaoyun Wu, Linsen Zan, Xuezhi Ding, Xian Guo, Pengjia Bao, Jie Pei, Min Chu, Chunnian Liang, Ping Yan
BACKGROUND: Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we used the Illunima BovineHD BeadChip to conduct genome-wide detection of CNVs in 215 polled yaks. RESULTS: A total of 1066 CNV regions (CNVRs) were detected with a total length of 181.6 Mb, comprising ~ 7.2% of the bovine autosomal genome. The size of these CNVRs ranged from 5...
May 14, 2019: BMC Genomics
Georgina Mansell, Tyler J Gorrie-Stone, Yanchun Bao, Meena Kumari, Leonard S Schalkwyk, Jonathan Mill, Eilis Hannon
BACKGROUND: There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study design and interpretation have been discussed in detail, however there are analytical concerns that are outstanding and require further exploration. In this study we seek to address three analytical issues. First, we quantify the multiple testing burden and propose a standard statistical significance threshold for identifying DNA methylation sites that are associated with an outcome...
May 14, 2019: BMC Genomics
Guosong Wang, Long Jin, Yan Li, Qianzi Tang, Silu Hu, Hengyong Xu, Clare A Gill, Mingzhou Li, Jiwen Wang
BACKGROUND: Dysregulation of adipogenesis causes metabolic diseases, like obesity and fatty liver. Migratory birds such as geese have a high tolerance of massive energy intake and exhibit little pathological development. Domesticated goose breeds, derivatives of the wild greyleg goose (Anser anser) or swan goose (Anser cygnoides), have high tolerance of energy intake resembling their ancestor species. Thus, goose is potentially a model species to study mechanisms associated with adipogenesis...
May 14, 2019: BMC Genomics
Tong-Jin Liu, You-Jun Zhang, Niels Agerbirk, Hai-Ping Wang, Xiao-Chun Wei, Jiang-Ping Song, Hong-Ju He, Xue-Zhi Zhao, Xiao-Hui Zhang, Xi-Xiang Li
BACKGROUND: Barbarea vulgaris is a wild cruciferous plant and include two distinct types: the G- and P-types named after their glabrous and pubescent leaves, respectively. The types differ significantly in resistance to a range of insects and diseases as well as glucosinolates and other chemical defenses. A high-density linkage map was needed for further progress to be made in the molecular research of this plant. RESULTS: We performed restriction site-associated DNA sequencing (RAD-Seq) on an F2 population generated from G- and P-type B...
May 14, 2019: BMC Genomics
Rocío M Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramirez, Roberto Vera Alvarez, David Landsman, Leonardo Mariño-Ramírez
BACKGROUND: Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate into high farming costs and are hazardous to the environment when used excessively. Beneficial free-living soil bacteria that colonize the rhizosphere are known as plant growth-promoting rhizobacteria (PGPR). PGPR affect plant growth in direct or indirect ways and hold great promise for sustainable agriculture...
May 14, 2019: BMC Genomics
Alltalents T Murahwa, Fredrick Nindo, Harris Onywera, Tracy L Meiring, Darren P Martin, Anna-Lise Williamson
BACKGROUND: Human papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. All papillomaviruses have double stranded DNA genomes that are thought to evolve slowly because they co-opt high-fidelity host cellular DNA polymerases for their replication. Despite extensive efforts to catalogue all the HPV species that infect humans, it is likely that many still remain undiscovered. Here we use the sequences of ten novel Gammapapillomaviruses (Gamma-PVs) characterized in previous studies and related HPVs to analyse the evolutionary dynamics of these viruses at the whole genome and individual gene scales...
May 14, 2019: BMC Genomics
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