Abstract:
BACKGROUND:The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific transcripts (LSTs) from a cow term-placenta cDNA library, which are excellent candidates for adaptive placental functions acquired by the ruminant lineage. The aim of the present study was to infer functions of previously uncharacterized lineage-specific genes (LSGs) using co-expression, promoter, pathway and network analysis. RESULTS:Clusters of co-expressed genes preferentially expressed in liver, placenta and thymus were found using 49 previously uncharacterized LSTs as seeds. Over-represented composite transcription factor binding sites (TFBS) in promoters of clustered LSGs and known genes were then identified computationally. Functions were inferred for nine previously uncharacterized LSGs using co-expression analysis and pathway analysis tools. Our results predict that these LSGs may function in cell signaling, glycerophospholipid/fatty acid metabolism, protein trafficking, regulatory processes in the nucleus, and processes that initiate parturition and immune system development. CONCLUSIONS:The placenta is a rich source of lineage-specific genes that function in the adaptive evolution of placental architecture and functions. We have shown that co-expression, promoter, and gene network analyses are useful methods to infer functions of LSGs with heretofore unknown functions. Our results indicate that many LSGs are involved in cellular recognition and developmental processes. Furthermore, they provide guidance for experimental approaches to validate the functions of LSGs and to study their evolution.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Kumar CG,Everts RE,Loor JJ,Lewin HAdoi
10.1186/1471-2164-11-161subject
Has Abstractpub_date
2010-03-09 00:00:00pages
161issn
1471-2164pii
1471-2164-11-161journal_volume
11pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Genomic approaches provide unique opportunities to study interactions of insects with their pathogens. We developed a cDNA microarray to analyze the gene transcription profile of the lepidopteran pest Spodoptera frugiperda in response to injection of the polydnavirus HdIV associated with the ichneumonid wasp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-160
更新日期:2006-06-21 00:00:00
abstract::We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic var...
journal_title:BMC genomics
pub_type: 社论
doi:10.1186/s12864-017-3862-8
更新日期:2017-06-27 00:00:00
abstract:BACKGROUND:Intergenic splicing resulting in the combination of mRNAs sequences from distinct genes is a newly identified mechanism likely to contribute to protein diversity. Few cases have been described, most of them involving neighboring genes and thus suggesting a cotranscription event presumably due to transcriptio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-71
更新日期:2006-04-04 00:00:00
abstract:BACKGROUND:The Xanthomonas citri pv. citri (X. citri) is a phytopathogenic bacterium that infects different species of citrus plants where it causes canker disease. The adaptation to different habitats is related to the ability of the cells to metabolize and to assimilate diverse compounds, including sulfur, an essenti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1736-5
更新日期:2015-07-14 00:00:00
abstract:BACKGROUND:Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. RESULTS:In this study, we identified a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3502-3
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:Sacha Inchi (Plukenetia volubilis L., Euphorbiaceae) is a potential oilseed crop because the seeds of this plant are rich in unsaturated fatty acids (FAs). In particular, the fatty acid composition of its seed oil differs markedly in containing large quantities of α-linolenic acid (18C:3, a kind of ω-3 FAs)....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-716
更新日期:2012-12-20 00:00:00
abstract::The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...
journal_title:BMC genomics
pub_type: 社论
doi:10.1186/1471-2164-10-193
更新日期:2009-04-24 00:00:00
abstract:BACKGROUND:In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-646
更新日期:2013-09-23 00:00:00
abstract:BACKGROUND:V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS:We prop...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-409
更新日期:2014-05-28 00:00:00
abstract:BACKGROUND:Atlantic cod (Gadus morhua), is known to vary genetically across the North Atlantic, Greenland, and Newfoundland. This genetic variation occurs both spatially and temporally through decades of heavy fishing, and is concentrated in three linkage disequilibrium blocks, previously defined by pedigreed linkage m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3660-3
更新日期:2017-03-31 00:00:00
abstract:BACKGROUND:Transposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. The presence of an ORF coding for the DDE/DDD transposase, requi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-409
更新日期:2007-11-09 00:00:00
abstract:BACKGROUND:The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1533-1
更新日期:2015-05-08 00:00:00
abstract:BACKGROUND:Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on ho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6102-6
更新日期:2019-10-22 00:00:00
abstract:BACKGROUND:With the sequence of the Plasmodium falciparum genome and several global mRNA and protein life cycle expression profiling projects now completed, elucidating the underlying networks of transcriptional control important for the progression of the parasite life cycle is highly pertinent to the development of n...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-70
更新日期:2008-02-07 00:00:00
abstract:BACKGROUND:Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, most aspects of sand fly biology remain unknown including the molecular basis of their reproducti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5898-4
更新日期:2019-06-25 00:00:00
abstract:BACKGROUND:Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1287-9
更新日期:2015-02-06 00:00:00
abstract:BACKGROUND:To generate specific transcript profiles, one must isolate homogenous cell populations using techniques that often yield small amounts of RNA, requiring researchers to employ RNA amplification methods. The data generated by using these methods must be extensively evaluated to determine any technique dependen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-2
更新日期:2004-01-06 00:00:00
abstract:BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-271
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1259-0
更新日期:2015-02-14 00:00:00
abstract:BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4656-3
更新日期:2018-04-16 00:00:00
abstract:BACKGROUND:Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6221-0
更新日期:2019-11-15 00:00:00
abstract:BACKGROUND:Clock genes are considered to be the molecular core of biological clock in vertebrates and they are directly involved in the regulation of daily rhythms in vertebrate tissues such as skeletal muscles. Fish myotomes are composed of anatomically segregated fast and slow muscle fibers that possess different met...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3373-z
更新日期:2016-12-08 00:00:00
abstract:BACKGROUND:Lipopolysaccharide (LPS) from Gram-negative bacteria cause innate immune responses in animals and plants. The molecules involved in LPS signaling in animals are well studied, whereas those in plants are not yet as well documented. Recently, we identified Arabidopsis AtLBR-2, which binds to LPS from Pseudomon...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4372-4
更新日期:2017-12-29 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:The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obt...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-26
更新日期:2008-01-22 00:00:00
abstract:BACKGROUND:CRISPR-Cas9 is a revolutionary genome editing technique that allows for efficient and directed alterations of the eukaryotic genome. This relatively new technology has already been used in a large number of 'loss of function' experiments in cultured cells. Despite its simplicity and efficiency, screening for...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1002
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:Wood formation affects the chemical and physical properties of wood, and thus affects its utility as a building material or a feedstock for biofuels, pulp and paper. To obtain genome-wide insights on the transcriptome changes and regulatory networks in wood formation, we used high-throughput RNA sequencing t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1390-y
更新日期:2015-03-10 00:00:00
abstract:BACKGROUND:Flow cytometry has been widely used for the diagnosis of various hematopoietic diseases. Although there have been advances in the number of biomarkers that can be analyzed simultaneously and technologies that enable fast performance, the diagnostic data are still interpreted by a manual gating strategy. The ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S7-S1
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objective...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1376-9
更新日期:2015-03-25 00:00:00
abstract:BACKGROUND:Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. RESULTS:About 10% of the genes under study are overlapping ge...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-169
更新日期:2008-04-14 00:00:00