Corrigendum to "Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches".
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ABSTRACT:
SUBMITTER: Bi C
PROVIDER: S-EPMC6735218 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
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Corrigendum to "Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton <i>Gossypium raimondii</i> by Comparative Genomics Approaches".
Bi Changwei C Paterson Andrew H AH Wang Xuelin X Xu Yiqing Y Wu Dongyang D Qu Yanshu Y Jiang Anna A Ye Qiaolin Q Ye Ning N
BioMed research international 20190828
[This corrects the article DOI: 10.1155/2016/5040598.]. ...[more]
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Project description:Plant disease resistance genes are a key component of defending plants from a range of pathogens. The majority of these resistance genes belong to the super-family that harbors a Nucleotide-binding site (NBS). A number of studies have focused on NBS-encoding genes in disease resistant breeding programs for diverse plants. However, little information has been reported with an emphasis on systematic analysis and comparison of NBS-encoding genes in cotton. To fill this gap of knowledge, in this study, we identified and investigated the NBS-encoding resistance genes in cotton using the whole genome sequence information of Gossypium raimondii. Totally, 355 NBS-encoding resistance genes were identified. Analyses of the conserved motifs and structural diversity showed that the most two distinct features for these genes are the high proportion of non-regular NBS genes and the high diversity of N-termini domains. Analyses of the physical locations and duplications of NBS-encoding genes showed that gene duplication of disease resistance genes could play an important role in cotton by leading to an increase in the functional diversity of the cotton NBS-encoding genes. Analyses of phylogenetic comparisons indicated that, in cotton, the NBS-encoding genes with TIR domain not only have their own evolution pattern different from those of genes without TIR domain, but also have their own species-specific pattern that differs from those of TIR genes in other plants. Analyses of the correlation between disease resistance QTL and NBS-encoding resistance genes showed that there could be more than half of the disease resistance QTL associated to the NBS-encoding genes in cotton, which agrees with previous studies establishing that more than half of plant resistance genes are NBS-encoding genes.
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Project description:Cotton (Gossypium spp.) is one of the most important natural fiber and oil crops worldwide. Improvement of fiber yield and quality under changing environments attract much attention from cotton researchers; however, a functional analysis platform integrating omics data is still missing. The success of cotton genome sequencing and large amount of available transcriptome data allows the opportunity to establish a comprehensive analysis platform for integrating these data and related information. A comprehensive database, Platform of Functional Genomics Analysis in Gossypium raimondii (GraP), was constructed to provide multi-dimensional analysis, integration and visualization tools. GraP includes updated functional annotation, gene family classifications, protein-protein interaction networks, co-expression networks and microRNA-target pairs. Moreover, gene set enrichment analysis and cis-element significance analysis tools are also provided for gene batch analysis of high-throughput data sets. Based on these effective services, GraP may offer further information for subsequent studies of functional genes and in-depth analysis of high-throughput data. GraP is publically accessible at http://structuralbiology.cau.edu.cn/GraP/, with all data available for downloading.
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Project description:BackgroundGenetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing.ResultsA whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences.ConclusionSeveral lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence.
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