Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis.
Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis.
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通过全基因组分析开发和鉴定柑橘基因组和表达的 SSR
DOI：
10.1371/journal.pone.0075149
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Zhang JZ
中科院分区：
文献类型：
--
作者：
Liu SR;Li WY;Long D;Hu CG;Zhang JZ
微卫星或简单序列重复序列(SSR)是最常用的遗传标记来源之一，在植物遗传学和育种中发挥着重要作用。在本研究中，我们在柑橘基因组中鉴定了柑橘SSR，并分析了它们在不同基因组区域的频率和分布。在基因组中共检测到80708个SSR，总密度为268个SSR/Mb。在基因组DNA序列中，二核苷酸重复序列是最常见的微卫星，而四核苷酸的累积序列长度最长，其重复单位比任何其他SSR类型都多。在33929个Clementine普通话转录本中，我们发现6834个转录本含有8989个SSR，其中三核苷酸基序最常见(36.0%)，其次是二核苷酸基序(26.9%)和六核苷酸基序(15.1%)。在这些SSR中，AG基序含量最高(16.7%)，AAG基序(6.6%)、AAT基序(5.0%)和Tag基序(2.2%)是最常见的三核苷酸。对含有SSR的转录本进行功能分类，发现5879个转录本(86.0%)与已知蛋白质有同源性，GO和KEGG注释表明，含有SSR的转录本参与了植物的多种生物学过程，包括结合、发育、转录和蛋白质降解。对27个基因组SSR和78个随机选择的SSR进行了测试，95个SSR表现出多态性。这95个SSR被进一步应用于芸香科3个属的18个基因类型上，用于遗传多样性评估，基因组SSR与从表达序列开发的SSR相比，可转移性普遍较低。这些转录本标记为柑橘遗传多样性研究、QTL定位、分子育种、比较定位等遗传研究和品种开发提供了有价值的遗传和基因组工具。
Microsatellites or simple sequence repeats (SSRs) are one of the most popular sources of genetic markers and play a significant role in plant genetics and breeding. In this study, we identified citrus SSRs in the genome of Clementine mandarin and analyzed their frequency and distribution in different genomic regions. A total of 80,708 SSRs were detected in the genome with an overall density of 268 SSRs/Mb. While di-nucleotide repeats were the most frequent microsatellites in genomic DNA sequence, tetra-nucleotides, which had more repeat units than any other SSR types, had the highest cumulative sequence length. We identified 6,834 transcripts as containing 8,989 SSRs in 33,929 Clementine mandarin transcripts, among which, tri-nucleotide motifs (36.0%) were the most common, followed by di-nucleotide (26.9%) and hexa-nucleotide motifs (15.1%). The motif AG (16.7%) was most abundant among these SSRs, while motifs AAG (6.6%), AAT (5.0%), and TAG (2.2%) were most common among tri-nucleotides. Functional categorization of transcripts containing SSRs revealed that 5,879 (86.0%) of such transcripts had homology with known proteins, GO and KEGG annotation revealed that transcripts containing SSRs were those implicated in diverse biological processes in plants, including binding, development, transcription, and protein degradation. When 27 genomic and 78 randomly selected SSRs were tested on Clementine mandarin, 95 SSRs revealed polymorphism. These 95 SSRs were further deployed on 18 genotypes of the three generas of Rutaceae for the genetic diversity assessment, genomic SSRs generally show low transferability in comparison to SSRs developed from expressed sequences. These transcript-markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in citrus, such as diversity study, QTL mapping, molecular breeding, comparative mapping and other genetic analyses.
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影响因子：
4.4
作者：
Luro, Francois L.;Costantino, Gilles;Terol, Javier;Argout, Xavier;Allario, Thierry;Wincker, Patrick;Talon, Manuel;Ollitrault, Patrick;Morillon, Raphael
通讯作者：
Morillon, Raphael
影响因子：
2.4
作者：
Coulibaly, I;Gharbi, K;Rexroad, CE
通讯作者：
Rexroad, CE
影响因子：
4.3
作者：
Amar, Mohamed Hamdy;Biswas, Manosh Kumar;Guo, Wen-Wu
通讯作者：
Guo, Wen-Wu
影响因子：
4.4
作者：
Cavagnaro PF;Senalik DA;Yang L;Simon PW;Harkins TT;Kodira CD;Huang S;Weng Y
通讯作者：
Weng Y
DOI：
10.1007/s004380050983
发表时间：
1999-03-01
期刊：
MOLECULAR AND GENERAL GENETICS
影响因子：
--
作者：
Dresselhaus, T;Cordts, S;Kranz, E
通讯作者：
Kranz, E