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BMC Genomics

Ashok Kumar Sharma, Barbora Pafčo, Klára Vlčková, Barbora Červená, Jakub Kreisinger, Samuel Davison, Karen Beeri, Terence Fuh, Steven R Leigh, Michael B Burns, Ran Blekhman, Klára J Petrželková, Andres Gomez
BACKGROUND: Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in field conditions. To explore solutions to this limitation, we have used a noninvasive approach via fecal RNA-seq, for the quantification of gene expression markers in gastrointestinal cells of free-range primates and a forager human population. Thus, a combination of poly(A) mRNA enrichment and rRNA depletion methods was used in tandem with RNA-seq to quantify and compare gastrointestinal gene expression patterns in fecal samples of wild Gorilla gorilla gorilla (n = 9) and BaAka hunter-gatherers (n = 10) from The Dzanga Sangha Protected Areas, Central African Republic...
June 14, 2019: BMC Genomics
Shyam Solanki, Jonathan Richards, Gazala Ameen, Xue Wang, Atiya Khan, Harris Ali, Alex Stangel, Prabin Tamang, Thomas Gross, Patrick Gross, Thomas G Fetch, Robert S Brueggeman
BACKGROUND: Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance locus (RMRL), the only effective resistance to virulent Pgt races in the TTKSK lineage. The RMRL contains two nucleotide-binding domain and leucine-rich repeat (NLR) resistance genes, Rpg5 and HvRga1, which are required for resistance. The two NLRs have head-to-head genome architecture with one NLR, Rpg5, containing an integrated C-terminal protein kinase domain, characteristic of an "integrated sensory domain" resistance mechanism...
June 14, 2019: BMC Genomics
Lingyang Xu, Liu Yang, Bo Zhu, Wengang Zhang, Zezhao Wang, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, George E Liu, Junya Li
BACKGROUND: Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. RESULTS: We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China...
June 14, 2019: BMC Genomics
Sanjay Mallikarjunappa, Mounir Adnane, Paul Cormican, Niel A Karrow, Kieran G Meade
BACKGROUND: Mycobacterium avium subsp. paratuberculosis (MAP), the etiologic agent of Johne's disease is spread between cattle via the fecal-oral route, yet the functional changes in the salivary gland associated with infection remain uncharacterized. In this study, we hypothesized that experimental challenge with MAP would induce stable changes in gene expression patterns in the salivary gland that may shed light on the mucosal immune response as well as the regional variation in immune capacity of this extensive gland...
June 13, 2019: BMC Genomics
Siriluck Ponsuksili, Nares Trakooljul, Sajjanar Basavaraj, Frieder Hadlich, Eduard Murani, Klaus Wimmers
BACKGROUND: Epigenetic variation may result from selection for complex traits related to metabolic processes or appear in the course of adaptation to mediate responses to exogenous stressors. Moreover epigenetic marks, in particular the DNA methylation state, of specific loci are driven by genetic variation. In this sense, polymorphism with major gene effects on metabolic and cell signaling processes, like the variation of the ryanodine receptors in skeletal muscle, may affect DNA methylation...
June 13, 2019: BMC Genomics
Muhammad Arslan, Upendra Kumar Devisetty, Martin Porsch, Ivo Große, Jochen A Müller, Stefan G Michalski
BACKGROUND: Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction with co-occurring plants as well as microbes being involved in major biogeochemical cycles. J. effusus has biotechnological value as component of Constructed Wetlands where the plant has been employed in phytoremediation of contaminated water...
June 13, 2019: BMC Genomics
Lei Li, Lifang Yuan, Yanxia Shi, Xuewen Xie, Ali Chai, Qi Wang, Baoju Li
BACKGROUND: Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading enzymes is usually critical for Pectobacterium infection. However, other virulence factors and the mechanisms of genetic adaptation still need to be studied in detail. RESULTS: In this study, the complete genome of P. carotovorum subsp. brasiliense strain SX309 isolated from cucumber was compared with eight other pathogenic bacteria belonging to the Pectobacterium genus, which were isolated from various host plants...
June 13, 2019: BMC Genomics
Juan Pablo A Ortiz, Olivier Leblanc, Cristian Rohr, Mauricio Grisolia, Lorena A Siena, Maricel Podio, Carolina Colono, Celeste Azzaro, Silvina C Pessino
BACKGROUND: Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested that this trait could be modulated by epigenetic mechanisms involving small RNAs (sRNAs). Here we profiled floral sRNAs originated from apomictic and sexual Paspalum notatum genotypes in order to identify molecular pathways under epigenetic control that might be involved in the transition from sexuality to agamospermy...
June 13, 2019: BMC Genomics
Bijay K Khajanchi, Joshua Xu, Christopher J Grim, Andrea R Ottesen, Padmini Ramachandran, Steven L Foley
BACKGROUND: Salmonella enterica possess several iron acquisition systems, encoded on the chromosome and plasmids. Recently, we demonstrated that incompatibility group (Inc) FIB plasmid-encoded iron acquisition systems (Sit and aerobactin) likely play an important role in persistence of Salmonella in human intestinal epithelial cells (Caco-2). In this study, we sought to determine global transcriptome analyses of S. enterica in iron-rich (IR) and iron-depleted (ID) growth conditions. RESULTS: The number of differentially-expressed genes were substantially higher for recipient (SE819) (n = 966) and transconjugant (TC) (n = 945) compared to the wild type (WT) (SE163A) (n = 110) strain in ID as compared to IR growth conditions...
June 13, 2019: BMC Genomics
Sridhar Ravichandran, Raja Ragupathy, Tara Edwards, Michael Domaratzki, Sylvie Cloutier
BACKGROUND: With rising global temperature, understanding plants' adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post-transcriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed. RESULTS: Sequencing of 24 small RNA libraries produced 55...
June 13, 2019: BMC Genomics
Ehsan Hajiramezanali, Mahdi Imani, Ulisses Braga-Neto, Xiaoning Qian, Edward R Dougherty
BACKGROUND: Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty. RESULTS: The goal of this paper is to develop optimal classification of single-cell trajectories accounting for potential model uncertainty. Partially-observed Boolean dynamical systems (POBDS) are used for modeling gene regulatory networks observed through noisy gene-expression data...
June 13, 2019: BMC Genomics
Rasha Elhesha, Aisharjya Sarkar, Christina Boucher, Tamer Kahveci
BACKGROUND: Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the evolving topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time...
June 13, 2019: BMC Genomics
Christian P Kubicek, Andrei S Steindorff, Komal Chenthamara, Gelsomina Manganiello, Bernard Henrissat, Jian Zhang, Feng Cai, Alexey G Kopchinskiy, Eva M Kubicek, Alan Kuo, Riccardo Baroncelli, Sabrina Sarrocco, Eliane Ferreira Noronha, Giovanni Vannacci, Qirong Shen, Igor V Grigoriev, Irina S Druzhinina
BACKGROUND: The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma...
June 12, 2019: BMC Genomics
Huyen-Trang Tran, Hao-Chu Wang, Tsai-Wen Hsu, Rakesh Sarkar, Chao-Li Huang, Tzen-Yuh Chiang
BACKGROUND: Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan...
June 11, 2019: BMC Genomics
Chaokun Li, Longxin Chen, Xuefeng Liu, Xiaoqian Shi, Yu Guo, Rui Huang, Fangyuan Nie, Changming Zheng, Chenglin Zhang, Runlin Z Ma
BACKGROUND: The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is available for any of the wild ruminant species in the world. RESULTS: The high-density physical map is composed of two contigs of 47 overlapping bacterial artificial chromosome (BAC) clones, with an average of 115 Kb for each BAC, covering the entire addax MHC genome...
June 11, 2019: BMC Genomics
Adam Scheidegger, Carissa J Dunn, Ann Samarakkody, Nii Koney-Kwaku Koney, Danielle Perley, Ramendra N Saha, Sergei Nechaev
BACKGROUND: Global RNA sequencing technologies have revealed widespread RNA polymerase II (Pol II) transcription outside of gene promoters. Small 5'-capped RNA sequencing (Start-seq) originally developed for the detection of promoter-proximal Pol II pausing has helped improve annotation of Transcription Start Sites (TSSs) of genes as well as identification of non-genic regulatory elements. However, apart from the most well studied genomes of human and mouse, mammalian transcription has not been profiled with sufficiently high precision...
June 11, 2019: BMC Genomics
Diego Crespo, Jan Bogerd, Elisabeth Sambroni, Florence LeGac, Eva Andersson, Rolf B Edvardsen, Elisabeth Jönsson Bergman, Björn Thrandur Björnsson, Geir Lasse Taranger, Rüdiger W Schulz
BACKGROUND: When puberty starts before males reach harvest size, animal welfare and sustainability issues occur in Atlantic salmon (Salmo salar) aquaculture. Hallmarks of male puberty are an increased proliferation activity in the testis and elevated androgen production. Examining transcriptional changes in salmon testis during the transition from immature to maturing testes may help understanding the regulation of puberty, potentially leading to procedures to modulate its start. Since differences in body weight influence, via unknown mechanisms, the chances for entering puberty, we used two feed rations to create body weight differences...
June 11, 2019: BMC Genomics
Timothy A Clay, Michael A Steffen, Michael L Treglia, Carolyn D Torres, Ana Lilia Trujano-Alvarez, Ronald M Bonett
BACKGROUND: Global biodiversity is decreasing at an alarming rate and amphibians are at the forefront of this crisis. Understanding the factors that negatively impact amphibian populations and effectively monitoring their health are fundamental to addressing this epidemic. Plasma glucocorticoids are often used to assess stress in amphibians and other vertebrates, but these hormones can be extremely dynamic and impractical to quantify in small organisms. Transcriptomic responses to stress hormones in amphibians have been largely limited to laboratory models, and there have been few studies on vertebrates that have evaluated the impact of multiple stressors on patterns of gene expression...
June 11, 2019: BMC Genomics
Hong-Rui Zhang, Xian-Chun Zhang, Qiao-Ping Xiang
BACKGROUND: It is hypothesized that the highly conserved inverted repeats (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organization, whereas the mechanism of the occurrence and stability maintenance of the recently reported direct repeats (DR) structure is yet awaiting further exploration. Here we describe the DR structure of the Selaginella vardei (Selaginellaceae) plastome, to elucidate the mechanism of DR occurrence and stability maintenance...
June 11, 2019: BMC Genomics
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
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