Abstract:
BACKGROUND:Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. RESULTS:We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. CONCLUSION:These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Lescot M,Piffanelli P,Ciampi AY,Ruiz M,Blanc G,Leebens-Mack J,da Silva FR,Santos CM,D'Hont A,Garsmeur O,Vilarinhos AD,Kanamori H,Matsumoto T,Ronning CM,Cheung F,Haas BJ,Althoff R,Arbogast T,Hine E,Pappas GJ Jr,Sasdoi
10.1186/1471-2164-9-58subject
Has Abstractpub_date
2008-01-30 00:00:00pages
58issn
1471-2164pii
1471-2164-9-58journal_volume
9pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:It is unclear whether improving feed efficiency by selection for low residual feed intake (RFI) compromises pigs' immunocompetence. Here, we aimed at investigating whether pig lines divergently selected for RFI had different inflammatory responses to lipopolysaccharide (LPS) exposure, regarding to clinical p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6127-x
更新日期:2019-10-11 00:00:00
abstract:BACKGROUND:Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract infection in young children. The degree of disease severity is determined by the host response to infection. Lung macrophages play an important early role in the host response to infection and we have used a systems-based appr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-190
更新日期:2013-03-18 00:00:00
abstract:BACKGROUND:Sterol esterases and lipases are enzymes able to efficiently catalyze synthesis and hydrolysis reactions of both sterol esters and triglycerides and due to their versatility could be widely used in different industrial applications. Lipases with this ability have been reported in the yeast Candida rugosa tha...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-712
更新日期:2013-10-18 00:00:00
abstract:BACKGROUND:A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5364-8
更新日期:2018-12-27 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:Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2047-6
更新日期:2015-11-05 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are an abundant class of small single-stranded non-coding RNA molecules ranging from 18 to 24 nucleotides. They negatively regulate gene expression at the post-transcriptional level and play key roles in many biological processes, including skeletal development and cartilage maturation. In...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-798
更新日期:2014-09-17 00:00:00
abstract:BACKGROUND:The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found in fast neutron populations has been hindered, however, by the wide range of mutations generated and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5998-1
更新日期:2019-08-06 00:00:00
abstract:BACKGROUND:Transporter proteins are one of an organism's primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S1-S8
更新日期:2011-06-15 00:00:00
abstract:BACKGROUND:Extra-cellular components, such as serum and exosome, have drawn great attention as a readily accessible source of biomarkers for mammalian health. However, the contribution of different blood components to the signature of respective microRNAs (miRNAs) remains unknown, especially in cattle. In this study we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2962-1
更新日期:2016-08-12 00:00:00
abstract:BACKGROUND:Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07359-3
更新日期:2021-01-20 00:00:00
abstract:BACKGROUND:Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4783-x
更新日期:2018-05-30 00:00:00
abstract::The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catal...
journal_title:BMC genomics
pub_type: 杂志文章,评审
doi:10.1186/s12864-018-4963-8
更新日期:2018-08-08 00:00:00
abstract:BACKGROUND:The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07287-2
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1496-2
更新日期:2015-04-15 00:00:00
abstract:BACKGROUND:Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and int...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-243
更新日期:2006-09-22 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:The complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-281
更新日期:2012-06-24 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:The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome. In this new study, we used complementary methods to identify additional Zap1 ta...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-370
更新日期:2008-08-01 00:00:00
abstract:BACKGROUND:Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6056-8
更新日期:2019-09-02 00:00:00
abstract:BACKGROUND:The Abeta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10) is an enzyme involved in pivotal metabolic processes and in the mitochondrial dysfunction seen in the Alzheimer's disease. Here we use comparative genomic analyses to study the evolution of the HADH2 gene encodin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-202
更新日期:2006-08-09 00:00:00
abstract:BACKGROUND:Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visuali...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3195-z
更新日期:2016-11-07 00:00:00
abstract:BACKGROUND:Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-536
更新日期:2012-10-06 00:00:00
abstract:BACKGROUND:Malaria, caused by the parasitic protist Plasmodium falciparum, represents a major public health problem in the developing world. The P. falciparum genome has been sequenced, which provides new opportunities for the identification of novel drug targets. Eukaryotic protein kinases (ePKs) form a large family o...
journal_title:BMC genomics
pub_type: 杂志文章,评审
doi:10.1186/1471-2164-5-79
更新日期:2004-10-12 00:00:00
abstract:BACKGROUND:Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation. RESULTS:The analyses show that neighbou...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-42
更新日期:2009-01-22 00:00:00
abstract:BACKGROUND:Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearra...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-561
更新日期:2014-07-04 00:00:00
abstract:BACKGROUND:Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geog...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5453-3
更新日期:2019-01-24 00:00:00
abstract:BACKGROUND:Histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3) are widely perceived to be opposing and often mutually exclusive chromatin modifications. However, both are needed for certain light-activated genes in Neurospora crassa (Neurospora), including frequency (frq) and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5729-7
更新日期:2019-05-08 00:00:00
abstract:BACKGROUND:Stress responses provide valuable models for deciphering the transcriptional networks controlling the adaptation of the cell to its environment. We analyzed the transcriptome response of yeast to toxic concentrations of selenite. We used gene network mapping tools to identify functional pathways and transcri...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-333
更新日期:2008-07-15 00:00:00