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BMC Genomics | Page 2

Moyang Liu, Yongdi Wen, Wenjun Sun, Zhaotang Ma, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li, Hui Chen
BACKGROUND: In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein, abiotic and biological stress and other biological processes. While, no detailed identification and genome-wide analysis of bZIP family genes in Fagopyum talaricum (tartary buckwheat) has previously been published. The recently reported genome sequence of tartary buckwheat provides theoretical basis for us to study and discuss the characteristics and expression of bZIP genes in tartary buckwheat based on the whole genome...
June 11, 2019: BMC Genomics
Paul I Otyama, Andrew Wilkey, Roshan Kulkarni, Teshale Assefa, Ye Chu, Josh Clevenger, Dan J O'Connor, Graeme C Wright, Stanley W Dezern, Gregory E MacDonald, Noelle L Anglin, Ethalinda K S Cannon, Peggy Ozias-Akins, Steven B Cannon
BACKGROUND: Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources of variation and to leverage the power of genome-wide association studies (GWAS) to discover markers associated with traits of interest. We report an analysis of linkage disequilibrium (LD), population structure, and genetic diversity, and examine the ability of GWA to infer marker-trait associations in the U...
June 11, 2019: BMC Genomics
Yanzhou Wang, Zheng Zeng, Fu Li, Xiufeng Yang, Xinyue Gao, Yonghong Ma, Jing Rao, Hengyun Wang, Touming Liu
BACKGROUND: The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop. RESULTS: We obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed...
June 11, 2019: BMC Genomics
Dan Long, Lan-Lan Zhu, Fang-Ling Du, Tian-Xin Xiang, La-Gen Wan, Dan-Dan Wei, Wei Zhang, Yang Liu
BACKGROUND: Plasmids play an vital role in driving the rapid global spread of antimicrobial resistance and adaptation to changing ambient conditions. It has been suggested that the presence of plasmids can pose tremendous impacts on the host physiology. However, little is known regarding the contributions of carbapenemase-encoding plasmid carriage on the physiology and pathogenicity of hypervirulent K. pneumoniae (hvKP). RESULTS: Here we performed a transcriptomic analysis of hvKP with or without carbapenemase-encoding plasmid p24835-NDM5...
June 11, 2019: BMC Genomics
Bryan P Brown, Jennifer J Wernegreen
BACKGROUND: Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety of relationships, occasionally persisting over evolutionary timescales. Ants are a diverse group of animals that engage in many types of associations with taxonomically distinct groups of bacterial associates. Here, we bring into culture and characterize two closely-related strains of gut associated Acetobacteraceae (AAB) of the red carpenter ant, Camponotus chromaiodes...
June 10, 2019: BMC Genomics
Emmanuel Avila de Dios, Luis Delaye, June Simpson
BACKGROUND: Reliable indicators for the onset of flowering are not available for most perennial monocarpic species, representing a drawback for crops such as bamboo, agave and banana. The ability to predict and control the transition to the reproductive stage in A. tequilana would represent an advantage for field management of agaves for tequila production and for the development of a laboratory model for agave species. RESULTS: Consistent morphological features could not be determined for the vegetative to reproductive transition in A...
June 10, 2019: BMC Genomics
George S Long, Mohammed Hussen, Jonathan Dench, Stéphane Aris-Brosou
BACKGROUND: A critical goal in biology is to relate the phenotype to the genotype, that is, to find the genetic determinants of various traits. However, while simple monofactorial determinants are relatively easy to identify, the underpinnings of complex phenotypes are harder to predict. While traditional approaches rely on genome-wide association studies based on Single Nucleotide Polymorphism data, the ability of machine learning algorithms to find these determinants in whole proteome data is still not well known...
June 10, 2019: BMC Genomics
Andrii Slonchak, Brian Clarke, Jason Mackenzie, Alberto Anastacio Amarilla, Yin Xiang Setoh, Alexander A Khromykh
BACKGROUND: Extracellular vesicles (EVs) are small membrane vesicles secreted by the cells that mediate intercellular transfer of molecules and contribute to transduction of various signals. Viral infection and action of pro-inflammatory cytokines has been shown to alter molecular composition of EV content. Transfer of antiviral proteins by EVs is thought to contribute to the development of inflammation and antiviral state. Altered incorporation of selected host RNAs into EVs in response to infection has also been demonstrated for several viruses, but not for WNV...
June 10, 2019: BMC Genomics
Sushil Raj Subedi, Nitika Sandhu, Vikas Kumar Singh, Pallavi Sinha, Santosh Kumar, S P Singh, Surya Kant Ghimire, Madhav Pandey, Ram Baran Yadaw, Rajeev K Varshney, Arvind Kumar
BACKGROUND: Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system...
June 10, 2019: BMC Genomics
Meng Xu, Jing Huang, Yu Shi, Hua Zhang, Maoxian He
BACKGROUND: The pearl oyster Pinctada fucata martensii (Pfu.), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of artificial breeding. To identify differentially expressed genes between yellow shell and normal black shell pearl oysters, we performed transcriptomic sequencing and proteomic analyses using mantle edge tissues. RESULTS: A total of 56,969 unigenes were obtained from transcriptomic, of which 21,610 were annotated, including 385 annotated significant up-regulated genes and 227 significant down-regulated genes in yellow shell oysters (| log2 (fold change) | ≥2 and false discovery rate < 0...
June 8, 2019: BMC Genomics
J Blommaert, S Riss, B Hecox-Lea, D B Mark Welch, C P Stelzer
BACKGROUND: The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale...
June 7, 2019: BMC Genomics
Wei Xue, Jiong-Tang Li, Ya-Ping Zhu, Guang-Yuan Hou, Xiang-Fei Kong, You-Yi Kuang, Xiao-Wen Sun
Following the publication of this article [1], the authors reported that the link to the software described in the article is no longer valid.
June 7, 2019: BMC Genomics
Yubang Shen, Le Wang, Jianjun Fu, Xiaoyan Xu, Gen Hua Yue, Jiale Li
BACKGROUND: Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture...
June 7, 2019: BMC Genomics
Chaoling Xue, Hongtai Li, Zhiguo Liu, Lili Wang, Yitong Zhao, Ximeng Wei, Hu Fang, Mengjun Liu, Jin Zhao
BACKGROUND: The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube (Ziziphus jujuba Mill.) is the largest type of dried fruit tree in China in terms of production, but its production is largely limited by phytoplasma infection, and the information about the role of WRKY genes under phytoplasma stress was still limited. RESULTS: We identified 54 ZjWRKYs in the jujube genome and classified them into three subgroups according to conserved WRKY domains and zinc-finger structure...
June 7, 2019: BMC Genomics
Marius Bredon, Benjamin Herran, Baptiste Lheraud, Joanne Bertaux, Pierre Grève, Bouziane Moumen, Didier Bouchon
BACKGROUND: Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especially plant biomass, might be one of the reasons of their successful spread. All isopods, which feed on plants and their by-products, must be capable of lignocellulose degradation. This complex composite is the main component of plants and is therefore an important nutrient source for many living organisms...
June 7, 2019: BMC Genomics
Qian Zhao, Weimin Zhong, Weiyi He, Yiying Li, Yaqing Li, Tianpu Li, Liette Vasseur, Minsheng You
BACKGROUND: The diamondback moth (DBM), Plutella xylostella (L.), is a major pest of cruciferous crops worldwide. While the species has become a model for genomics, post-transcriptional mechanisms associated with development and sex determination have not been comprehensively studied and the lack of complete structure of mRNA transcripts limits further research. RESULTS: Here, we combined the methods of single-molecule long-read sequencing technology (IsoSeq) and RNA-seq to re-annotate the published DBM genome and present the genome-wide identification of alternative splicing (AS) associated with development and sex determination of DBM...
June 7, 2019: BMC Genomics
Guilherme C Baião, Daniela I Schneider, Wolfgang J Miller, Lisa Klasson
BACKGROUND: The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer...
June 7, 2019: BMC Genomics
Alexander Capraro, Denis O'Meally, Shafagh A Waters, Hardip R Patel, Arthur Georges, Paul D Waters
BACKGROUND: Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many stress response pathways modulated to tolerate physiological challenges that might otherwise be lethal. Many studies have sought to elucidate the molecular mechanisms of mammalian hibernation, but detailed analyses are lacking in reptiles. Here we examine gene expression in the Australian central bearded dragon (Pogona vitticeps) using mRNA-seq and label-free quantitative mass spectrometry in matched brain, heart and skeletal muscle samples from animals at late hibernation, 2 days post-arousal and 2 months post-arousal...
June 6, 2019: BMC Genomics
Harsh G Shukla, Pushpinder Singh Bawa, Subhashini Srinivasan
BACKGROUND: The most widely used human genome reference assembly hg19 harbors minor alleles at 2.18 million positions as revealed by 1000 Genome Phase 3 dataset. Although this is less than 2% of the 89 million variants reported, it has been shown that the minor alleles can result in 30% false positives in individual genomes, thus misleading and burdening downstream interpretation. More alarming is the fact that, significant percentage of variants that are homozygous recessive for these minor alleles, with potential disease implications, are masked from reporting...
June 6, 2019: BMC Genomics
Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xingchu Yan, Xinxin Geng
BACKGROUND: Ricinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis at the transcriptional level are limited. RESULTS: In this study, we combined PacBio single-molecule long read isoform and Illumina RNA sequencing to identify the alternative splicing (AS) events, novel isoforms, fusion genes, long non-coding RNAs (lncRNAs) and alternative polyadenylation (APA) sites to unveil the transcriptomic complexity of castor beans and identify critical genes related to ricinoleic acid biosynthesis...
June 6, 2019: BMC Genomics
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