Abstract:
BACKGROUND:Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the majority of genes for ecologically tractable species, and by subsequently developing microarray platforms from which to investigate gene regulatory networks that function in natural systems. We used GS-FLX Titanium Sequencing (Roche/454-Sequencing) of two normalized libraries of pooled RNA samples to characterize a transcriptome of the dark-eyed junco (Junco hyemalis), a North American sparrow that is a classically studied species in the fields of photoperiodism, speciation, and hormone-mediated behavior. RESULTS:From a broad pool of RNA sampled from tissues throughout the body of a male and a female junco, we sequenced a total of 434 million nucleotides from 1.17 million reads that were assembled de novo into 31,379 putative transcripts representing 22,765 gene sets covering 35.8 million nucleotides with 12-fold average depth of coverage. Annotation of roughly half of the putative genes was accomplished using sequence similarity, and expression was confirmed for the majority with a preliminary microarray analysis. Of 716 core bilaterian genes, 646 (90 %) were recovered within our characterized gene set. Gene Ontology, orthoDB orthology groups, and KEGG Pathway annotation provide further functional information about the sequences, and 25,781 potential SNPs were identified. CONCLUSIONS:The extensive sequence information returned by this effort adds to the growing store of genomic data on diverse species. The extent of coverage and annotation achieved and confirmation of expression, show that transcriptome sequencing provides useful information for ecological model systems that have historically lacked genomic tools. The junco-specific microarray developed here is allowing investigations of gene expression responses to environmental and hormonal manipulations - extending the historic work on natural history and hormone-mediated phenotypes in this system.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Peterson MP,Whittaker DJ,Ambreth S,Sureshchandra S,Buechlein A,Podicheti R,Choi JH,Lai Z,Mockatis K,Colbourne J,Tang H,Ketterson EDdoi
10.1186/1471-2164-13-305subject
Has Abstractpub_date
2012-07-09 00:00:00pages
305issn
1471-2164pii
1471-2164-13-305journal_volume
13pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6002-9
更新日期:2019-08-22 00:00:00
abstract:BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1321-y
更新日期:2015-02-15 00:00:00
abstract:BACKGROUND:Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris/trypanosome Crithidia bombi model system (two bumblebee colonies by two Crithidia strains), we have ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1031
更新日期:2014-11-27 00:00:00
abstract:BACKGROUND:Although an adverse early-life environment has been linked to an increased risk of developing the metabolic syndrome, the molecular mechanisms underlying altered disease susceptibility as well as their relevance to humans are largely unknown. Importantly, emerging evidence suggests that these effects operate...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-509
更新日期:2011-10-16 00:00:00
abstract:BACKGROUND:Chronic Allograft Nephropathy (CAN) is a clinical entity of progressive kidney transplant injury. The defining histology is tubular atrophy with interstitial fibrosis (IFTA). Using a meta-analysis of microarrays from 84 kidney transplant biopsies, we revealed growth factor and integrin adhesion molecule path...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-14-275
更新日期:2013-04-23 00:00:00
abstract:BACKGROUND:Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6738-2
更新日期:2020-04-23 00:00:00
abstract:BACKGROUND:In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy. RESULTS:Radiosensiti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-348
更新日期:2012-07-30 00:00:00
abstract:BACKGROUND:Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS:Existing algorithms are largely optimized for speed and coverage; in con...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-461
更新日期:2010-08-05 00:00:00
abstract:BACKGROUND:The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3946-5
更新日期:2017-07-21 00:00:00
abstract:BACKGROUND:Scaleless (sc/sc) chickens carry a single recessive mutation that causes a lack of almost all body feathers, as well as foot scales and spurs, due to a failure of skin patterning during embryogenesis. This spontaneous mutant line, first described in the 1950s, has been used extensively to explore the tissue ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-257
更新日期:2012-06-19 00:00:00
abstract::An amendment to this paper has been published and can be accessed via the original article. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-020-6754-2
更新日期:2020-06-03 00:00:00
abstract:BACKGROUND:NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads. The other k-mers are called weak k-mers. A solid k-mer does not likely contain errors, while a weak k-...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5272-y
更新日期:2018-12-31 00:00:00
abstract:BACKGROUND:Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the embryo-to-hatchling transition. Furthermore, we know very little about the metabolic and regulatory fac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5080-4
更新日期:2018-09-21 00:00:00
abstract:BACKGROUND:Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1066
更新日期:2014-12-04 00:00:00
abstract:BACKGROUND:It is well understood that distinct communities of bacteria are present at different sites of the body, and that changes in the structure of these communities have strong implications for human health. Yet, challenges remain in understanding the complex interconnections between the bacterial taxa within thes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S11-S6
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using thre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-319
更新日期:2013-05-10 00:00:00
abstract:BACKGROUND:Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insigh...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3885-1
更新日期:2017-06-28 00:00:00
abstract:BACKGROUND:Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-555
更新日期:2010-10-11 00:00:00
abstract:BACKGROUND:Although primarily known as the site of ribosome subunit production, the nucleolus is involved in numerous and diverse cellular processes. Recent large-scale proteomics projects have identified thousands of human proteins that associate with the nucleolus. However, in most cases, we know neither the fraction...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-74
更新日期:2011-01-27 00:00:00
abstract:BACKGROUND:Repetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6517-0
更新日期:2020-01-30 00:00:00
abstract:BACKGROUND:Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epig...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4814-7
更新日期:2018-06-04 00:00:00
abstract:BACKGROUND:Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; however the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. In this study, global transcriptome profiles of trifoliate orange under cold conditions (4 °C) ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1629-7
更新日期:2015-07-29 00:00:00
abstract:BACKGROUND:Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the com...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-96
更新日期:2012-03-19 00:00:00
abstract:BACKGROUND:Our previous study had proved that nigericin could reduce colorectal cancer cell proliferation in dose- and time-dependent manners by targeting Wnt/β-catenin signaling. To better elucidate its potential anti-cancer mechanism, two pancreatic cancer (PC) cell lines were exposed to increasing concentrations of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6032-3
更新日期:2019-09-18 00:00:00
abstract:BACKGROUND:Gene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication of specific genes in E. coli, a detailed analysis of the extent of gene duplications in this microorg...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5683-4
更新日期:2019-04-24 00:00:00
abstract:BACKGROUND:New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-501
更新日期:2009-10-29 00:00:00
abstract:BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and thre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6619-8
更新日期:2020-03-04 00:00:00
abstract:BACKGROUND:RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4933-1
更新日期:2018-07-13 00:00:00
abstract:BACKGROUND:Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and dis...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4035-5
更新日期:2017-08-16 00:00:00
abstract:BACKGROUND:Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.). RESULT:Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6111-5
更新日期:2019-10-15 00:00:00