Synteny mapping between common bean and soybean reveals extensive blocks of shared loci.


BACKGROUND:Understanding syntentic relationship between two species is critical to assessing the potential for comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively. Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species. RESULTS:Genetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was approximately 120 kb/cM. approximately 15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points. CONCLUSION:The collected evidence from this mapping strongly supports the duplicate history of soybean. It further provides evidence that the soybean genome was fractionated and reassembled at some point following the duplication event. These well mapped syntentic relationships between common bean and soybean will enable researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both species.


BMC Genomics


BMC genomics


McClean PE,Mamidi S,McConnell M,Chikara S,Lee R




Has Abstract


2010-03-18 00:00:00










  • Identification of functional regulatory elements in the human genome using pooled CRISPR screens.

    abstract:BACKGROUND:Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function. However, protein-coding genes comprise < 2% of the se...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Borys SM,Younger ST

    更新日期:2020-01-31 00:00:00

  • Chronic wounds alter the proteome profile in skin mucus of farmed gilthead seabream.

    abstract:BACKGROUND:Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers as external clinical signs. However, there is no information about the changes produced by the wounds...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cordero H,Brinchmann MF,Cuesta A,Esteban MA

    更新日期:2017-12-02 00:00:00

  • Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data.

    abstract:BACKGROUND:Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate-specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiological processes and ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cui W,Qian Y,Zhou X,Lin Y,Jiang J,Chen J,Zhao Z,Shen B

    更新日期:2015-01-01 00:00:00

  • Genome-wide transcriptional analysis of T cell activation reveals differential gene expression associated with psoriasis.

    abstract:BACKGROUND:Psoriasis is a chronic autoimmune disease in which T cells have a predominant role in initiating and perpetuating the chronic inflammation in skin. However, the mechanisms that regulate T cell activation in psoriasis are still incompletely understood. The objective of the present study was to characterize th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Palau N,Julià A,Ferrándiz C,Puig L,Fonseca E,Fernández E,López-Lasanta M,Tortosa R,Marsal S

    更新日期:2013-11-23 00:00:00

  • Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling.

    abstract:BACKGROUND:Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamica...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li S,Dong X,Su Z

    更新日期:2013-07-30 00:00:00

  • Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species.

    abstract:BACKGROUND:Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a criti...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Xia Y,Luo W,Yuan S,Zheng Y,Zeng X

    更新日期:2018-12-07 00:00:00

  • Correction to: Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line.

    abstract::An amendment to this paper has been published and can be accessed via the original article. ...

    journal_title:BMC genomics

    pub_type: 已发布勘误


    authors: Levin M,Scheibe M,Butter F

    更新日期:2020-11-12 00:00:00

  • The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.

    abstract:BACKGROUND:Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Natali L,Cossu RM,Barghini E,Giordani T,Buti M,Mascagni F,Morgante M,Gill N,Kane NC,Rieseberg L,Cavallini A

    更新日期:2013-10-06 00:00:00

  • Estimating survival time of patients with glioblastoma multiforme and characterization of the identified microRNA signatures.

    abstract:BACKGROUND:Though glioblastoma multiforme (GBM) is the most frequently occurring brain malignancy in adults, clinical treatment still faces challenges due to poor prognoses and tumor relapses. Recently, microRNAs (miRNAs) have been extensively used with the aim of developing accurate molecular therapies, because of the...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yerukala Sathipati S,Huang HL,Ho SY

    更新日期:2016-12-22 00:00:00

  • Regulation of gene expression by FSP27 in white and brown adipose tissue.

    abstract:BACKGROUND:Brown and white adipose tissues (BAT and WAT) play critical roles in controlling energy homeostasis and in the development of obesity and diabetes. The mouse Fat-Specific protein 27 (FSP27), a member of the cell death-inducing DFF45-like effector (CIDE) family, is expressed in both BAT and WAT and is associa...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li D,Zhang Y,Xu L,Zhou L,Wang Y,Xue B,Wen Z,Li P,Sang J

    更新日期:2010-07-22 00:00:00

  • dCaP: detecting differential binding events in multiple conditions and proteins.

    abstract:BACKGROUND:Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analysis of multiple epigenetic features in many samples can gain substantial power and specificity than a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen KB,Hardison R,Zhang Y

    更新日期:2014-01-01 00:00:00

  • Gene expression changes during caste-specific neuronal development in the damp-wood termite Hodotermopsis sjostedti.

    abstract:BACKGROUND:One of the key characters of social insects is the division of labor, in which different tasks are allocated to various castes. In termites, one of the representative groups of social insects, morphological differences as well as behavioral differences can be recognized among castes. However, very little is ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ishikawa Y,Okada Y,Ishikawa A,Miyakawa H,Koshikawa S,Miura T

    更新日期:2010-05-20 00:00:00

  • Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

    abstract:BACKGROUND:Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages. RESULTS:Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic se...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu GE,Matukumalli LK,Sonstegard TS,Shade LL,Van Tassell CP

    更新日期:2006-06-07 00:00:00

  • Gene expression profiles at different stages for formation of pearl sac and pearl in the pearl oyster Pinctada fucata.

    abstract:BACKGROUND:The most critical step in the pearl formation during aquaculture is issued to the proliferation and differentiation of outer epithelial cells of mantle graft into pearl sac. This pearl sac secretes various matrix proteins to produce pearls by a complex physiological process which has not been well-understood...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mariom,Take S,Igarashi Y,Yoshitake K,Asakawa S,Maeyama K,Nagai K,Watabe S,Kinoshita S

    更新日期:2019-03-25 00:00:00

  • Changes in Bacillus anthracis CodY regulation under host-specific environmental factor deprived conditions.

    abstract:BACKGROUND:Host-specific environmental factors induce changes in Bacillus anthracis gene transcription during infection. A global transcription regulator, CodY, plays a pivotal role in regulating central metabolism, biosynthesis, and virulence in B. anthracis. In this study, we utilized RNA-sequencing to assess changes...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim SK,Jung KH,Chai YG

    更新日期:2016-08-17 00:00:00

  • Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

    abstract:BACKGROUND:High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integrat...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hermida L,Poussin C,Stadler MB,Gubian S,Sewer A,Gaidatzis D,Hotz HR,Martin F,Belcastro V,Cano S,Peitsch MC,Hoeng J

    更新日期:2013-07-29 00:00:00

  • Methylome and transcriptome analyses of apple fruit somatic mutations reveal the difference of red phenotype.

    abstract:BACKGROUND:Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect the phenotype of mutation, there are large unknown of difference of the DNA methylation in plant and...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jiang SH,Sun QG,Chen M,Wang N,Xu HF,Fang HC,Wang YC,Zhang ZY,Chen XS

    更新日期:2019-02-07 00:00:00

  • Spontaneous preterm birth and single nucleotide gene polymorphisms: a recent update.

    abstract:BACKGROUND:Preterm birth (PTB), birth at <37 weeks of gestation, is a significant global public health problem. World-wide, about 15 million babies are born preterm each year resulting in more than a million deaths of children. Preterm neonates are more prone to problems and need intensive care hospitalization. Health ...

    journal_title:BMC genomics

    pub_type: 杂志文章,评审


    authors: Sheikh IA,Ahmad E,Jamal MS,Rehan M,Assidi M,Tayubi IA,AlBasri SF,Bajouh OS,Turki RF,Abuzenadah AM,Damanhouri GA,Beg MA,Al-Qahtani M

    更新日期:2016-10-17 00:00:00

  • A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification.

    abstract:BACKGROUND:RNA-Seq has become increasingly popular in transcriptome profiling. One aspect of transcriptome research is to quantify the expression levels of genomic elements, such as genes, their transcripts and exons. Acquiring a transcriptome expression profile requires genomic elements to be defined in the context of...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhao S,Zhang B

    更新日期:2015-02-18 00:00:00

  • The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus.

    abstract:BACKGROUND:Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic i...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Heitlinger E,Bridgett S,Montazam A,Taraschewski H,Blaxter M

    更新日期:2013-02-08 00:00:00

  • The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression.

    abstract:BACKGROUND:Understanding how plants and pathogens modulate gene expression during the host-pathogen interaction is key to uncovering the molecular mechanisms that regulate disease progression. Recent advances in sequencing technologies have provided new opportunities to decode the complexity of such interactions. In th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dobon A,Bunting DC,Cabrera-Quio LE,Uauy C,Saunders DG

    更新日期:2016-05-20 00:00:00

  • A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens.

    abstract:BACKGROUND:Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. However, the genomic information for this fungal pathogen is limited and the pathogenic mechanism of this disease is still not clear. To facilitate genetic, molecular...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang X,Liu Q,Wang H,Luo CX,Wang G,Luo M

    更新日期:2013-12-16 00:00:00

  • Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

    abstract:BACKGROUND:An estimated 15,000 children and adolescents under the age of 19 years are diagnosed with leukemia, lymphoma and other tumors in the USA every year. All children and adolescent acute leukemia patients will undergo chemotherapy as part of their treatment regimen. Fortunately, survival rates for most pediatric...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rajagopala SV,Yooseph S,Harkins DM,Moncera KJ,Zabokrtsky KB,Torralba MG,Tovchigrechko A,Highlander SK,Pieper R,Sender L,Nelson KE

    更新日期:2016-08-15 00:00:00

  • Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum.

    abstract:BACKGROUND:Sugarcane is an economically important crop contributing to about 80% of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane's complicated genomes, it is still...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhang Q,Hu W,Zhu F,Wang L,Yu Q,Ming R,Zhang J

    更新日期:2016-02-01 00:00:00

  • Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming.

    abstract:BACKGROUND:Human induced pluripotent stem cells (iPSCs) have a wide range of applications throughout the fields of basic research, disease modeling and drug screening. Epigenetic instable iPSCs with aberrant DNA methylation may divide and differentiate into cancer cells. Unfortunately, little effort has been taken to c...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Shao X,Zhang C,Sun MA,Lu X,Xie H

    更新日期:2014-11-18 00:00:00

  • Gene expression profiling of Spodoptera frugiperda hemocytes and fat body using cDNA microarray reveals polydnavirus-associated variations in lepidopteran host genes transcript levels.

    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


    authors: Barat-Houari M,Hilliou F,Jousset FX,Sofer L,Deleury E,Rocher J,Ravallec M,Galibert L,Delobel P,Feyereisen R,Fournier P,Volkoff AN

    更新日期:2006-06-21 00:00:00

  • A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection.

    abstract:BACKGROUND:Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS:To overcome these limitations, we developed a novel RoV capture and genome sequencing method combin...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dung TTN,Duy PT,Sessions OM,Sangumathi UK,Phat VV,Tam PTT,To NTN,Phuc TM,Hong Chau TT,Chau NNM,Minh NN,Thwaites GE,Rabaa MA,Baker S

    更新日期:2017-04-24 00:00:00

  • Early transcriptional responses of internalization defective Brucella abortus mutants in professional phagocytes, RAW 264.7.

    abstract:BACKGROUND:Brucella abortus is an intracellular zoonotic pathogen which causes undulant fever, endocarditis, arthritis and osteomyelitis in human and abortion and infertility in cattle. This bacterium is able to invade and replicate in host macrophage instead of getting removed by this defense mechanism. Therefore, und...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cha SB,Lee WJ,Shin MK,Jung MH,Shin SW,Yoo AN,Kim JW,Yoo HS

    更新日期:2013-06-27 00:00:00

  • Metabolite and transcriptome analysis during fasting suggest a role for the p53-Ddit4 axis in major metabolic tissues.

    abstract:BACKGROUND:Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Schupp M,Chen F,Briggs ER,Rao S,Pelzmann HJ,Pessentheiner AR,Bogner-Strauss JG,Lazar MA,Baldwin D,Prokesch A

    更新日期:2013-11-05 00:00:00

  • TICdb: a collection of gene-mapped translocation breakpoints in cancer.

    abstract:BACKGROUND:Despite the importance of chromosomal translocations in the initiation and/or progression of cancer, a comprehensive catalog of translocation breakpoints in which these are precisely located on the reference sequence of the human genome is not available at present. DESCRIPTION:We have created a database tha...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Novo FJ,de Mendíbil IO,Vizmanos JL

    更新日期:2007-01-26 00:00:00