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      Genome-Wide Identification and Expression Analysis of the Biotin Carboxyl Carrier Subunits of Heteromeric Acetyl-CoA Carboxylase in Gossypium

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          Abstract

          Acetyl-CoA carboxylase is an important enzyme, which catalyzes acetyl-CoA’s carboxylation to produce malonyl-CoA and to serve as a committed step for de novo fatty acid biosynthesis in plastids. In this study, 24 putative cotton BCCP genes were identified based on the lately published genome data in Gossypium. Among them, 4, 4, 8, and 8 BCCP homologs were identified in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. These genes were divided into two classes based on a phylogenetic analysis. In each class, these homologs were relatively conserved in gene structure and motifs. The chromosomal distribution pattern revealed that all the BCCP genes were distributed equally on corresponding chromosomes or scaffold in the four cotton species. Segmental duplication was a predominant duplication event in both of G. hirsutum and G. barbadense. The analysis of the expression profile showed that 8 GhBCCP genes expressed in all the tested tissues with changed expression levels, and GhBCCP genes belonging to class II were predominantly expressed in developing ovules. Meanwhile, the expression analysis for the 16 cotton BCCP genes from G. raimondii, G. arboreum and G. hirsutum showed that they were induced or suppressed by cold or salt stress, and their expression patterns varied among different tissues. These findings will help to determine the functional and evolutionary characteristics of the BCCP genes in Gossypium species.

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          Most cited references48

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          Evolution by gene duplication: an update

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            SMART: recent updates, new developments and status in 2015

            SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de/) providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. In the current version, SMART contains manually curated models for more than 1200 protein domains, with ∼200 new models since our last update article. The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million. SMART's ‘Genomic’ mode, which annotates proteins from completely sequenced genomes was greatly expanded and now includes 2031 species, compared to 1133 in the previous release. SMART analysis results pages have been completely redesigned and include links to several new information sources. A new, vector-based display engine has been developed for protein schematics in SMART, which can also be exported as high-resolution bitmap images for easy inclusion into other documents. Taxonomic tree displays in SMART have been significantly improved, and can be easily navigated using the integrated search engine.
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              The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

              Background Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. Results Our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions. Conclusions Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                01 May 2017
                2017
                : 8
                : 624
                Affiliations
                [1] 1Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University Beijing, China
                [2] 2Research Institute of Cash Crop, Hubei Academy of Agricultural Sciences Wuhan, China
                [3] 3Oil Crops Research Institute, Chinese Academy of Agricultural Sciences Wuhan, China
                Author notes

                Edited by: Takeshi Fukao, Virginia Tech, USA

                Reviewed by: Hak Soo Seo, Seoul National University, South Korea; Umesh K. Reddy, West Virginia State University, USA

                *Correspondence: Jinping Hua, jinping_hua@ 123456cau.edu.cn

                This article was submitted to Plant Abiotic Stress, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2017.00624
                5410604
                28507552
                a0028664-0081-469d-9fe1-48e05a966605
                Copyright © 2017 Cui, Zhao, Wang, Liu, Ijaz, Huang and Hua.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 24 January 2017
                : 06 April 2017
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 71, Pages: 14, Words: 0
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                biotin carboxyl carrier subunit (bccp),gene family,expression profile,gossypium,phylogenetic analysis

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