Analysis of microsatellites in citrus unigenes
Analysis of microsatellites in citrus unigenes
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DOI：
10.1016/s0379-4172(06)60060-7
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发表时间：
2006-04-01
期刊：
影响因子：
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通讯作者：
Hong Qi-Bing
中科院分区：
文献类型：
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作者：
Jiang Dong;Zhong Guang-Yan;Hong Qi-Bing
研究了甜橙(Citrus Sinensis Osbeck)、三叶橙(PonCirus trifoliata Raf.)和其他柑橘品种和品种。共搜索了37 802个柑橘Unigene序列，分别对应于23.29 Mb，共鉴定出8218个SSR。其中单核苷酸SSR 4913个(59.8%)，二核苷酸SSR 1419个(17.3%)，TRI SSR 1709个(20.8%)，四核苷酸SSR 114个(1.39%)，五核苷酸SSR 23个(0.28%)，六核苷酸SSR 40个(0.49%)。估计SSR的频率约为1/2.8kb，可以外推到4.6个非基因中含有1个SSR的Unigene。根据SSR中基序的重复数不同，SSR的最大长度在40~105bp之间。SSR的总平均长度为20.9bp。甜橙和三叶橙不同SSR类型(二、三、四、五核苷酸重复)的频率非常相似。在甜橙和三叶橙中，单核苷酸重复似乎是最丰富的SSR，其次是三聚重复。A/T、AG、AT、AAG、AAAT、AAAG、AAAT、AAAAG、AAAAT、AAAAG、AAAAT等丰富的腺嘌呤重复序列在各种SSR(单、双、三、四、五)中占优势，而C/G、CG、CCG重复序列较少。在EST-SSR基因座两侧设计了25对引物，对甜橙和三叶橙等6个柑橘品种的遗传多样性进行了检测。这25对引物的扩增结果表明，6个柑橘品种间均存在多态性，表明柑橘EST数据库可以有效地用于基因衍生SSR标记的开发。
Simple sequence repeats (SSRs) were investigated in the unigene sequences from expressed sequence tags (EST) of sweet orange (Citrus sinensis osbeck), trifoliate orange (Poncirus trifoliata Raf.) and other citrus species and cultivars. A total of 37 802 citrus unigene sequences corresponding to 23.29 Mb were searched, resulting in the identification of 8 218 SSRs. Among them there were 4 913 (59.8%) mono-, 1 419 (17.3%) di-, 1 709 (20.8%) tri, 114 (1.39%) tetra-, 23 (0.28%) penta- and 40 (0.49%) hexa-nucleotide SSRs. The estimated frequency of SSRs was approximately 1/2.8 kb, which could be extrapolated to I SSR-containing unigene in 4.6 unigenes. The maximum length of the SSR ranged from 40 to 105 bp depending on the repeating numbers of the motif in the SSR. The overall average length of SSRs was 20.9 bp. The frequencies of different SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) were very similar between sweet orange and trifoliate orange. The mononucelotide repeats appeared to be the most abundant SSRs within sweet orange and trifoliate orange, followed by trimeric repeats. The adenine rich repeats such as A/T, AG, AT, AAG AAAT, AAAG, AAAT, AAAAG, AAAAT etc. were predominant in each type of SSRs (mono-, di-, tri-, tetra-, and penta-), whereas the C/G, CG, CCG repeats were less abundant. Twenty-five primer pairs flanking EST-SSR loci were designed to detect the possible polymorphism of six citrus cultivars including sweet orange and trifoliate orange. The PCR result with all these 25 primer pairs revealed the existence of polymorphism within six citrus cultivars confirming that citrus EST database could be efficiently exploited for the development of gene-derived SSR markers.