曼氏无针乌贼转录组微卫星特征分析

Deep Sequence-Based Transcriptome Analysis of Microsatellites in the Cuttlefish (Sepiella japonica)

中文关键词: 曼氏无针乌贼  微卫星  转录组  高通量测序  重复基元

英文关键词: Sepiella japonica  Microsatellite  Transcriptome  High-throughput sequencing  Repeat motif

中文摘要:

      本研究基于高通量测序获得的曼氏无针乌贼(Sepiella japonica)转录组数据，采用MISA (MIcroSAtellite)软件对其简单序列重复(Simple sequence repeat, SSR)位点进行了高通量发掘。组装并去冗余后，得到127575个Unigene，序列拼接的总长度为103104058 bp。对Unigene序列进行SSR分析，共得到62124个SSR(完整型SSR 36813个)，分布在50626条Unigene序列当中，SSR出现频率为48.70%，平均16.6 kb出现1个SSR。微卫星序列主要以二碱基重复类型为主(31227, 50.27%)，其次为三碱基重复(16230, 26.13%)。共发现122种碱基重复基元，在所有重复基元中(AT/AT)n占的比例最高为23.33%，其次为(AAAG/CTTT)n (17.42%)。曼氏无针乌贼SSR(完整型)的平均长度为25.87 bp，微卫星主要为重复长度大于20 bp的长序列，长度大于20 bp的微卫星序列占总数的51%。本研究发现，曼氏无针乌贼微卫星出现的频率和其长度呈极显著负相关(P<0.01)，相关系数为–0.594。该研究结果为开发高度多态性微卫星引物进行曼氏无针乌贼亲缘关系鉴定、种群遗传多样性和增殖放流效果评估等研究奠定了基础。

英文摘要:

      According to the transcriptome database of Sepiella japonica, the microsatellites have been explored at a high-throughput scale using a MIcroSAtellite identification tool. In total, 127575 unigenes were obtained after assembly and removal of redundant sequences. The total length of unigenes after sequence splicing was 103104058 bp. The microsatellites in the unigenes were analyzed, and a total of 62124 simple sequence repeats (SSR) (complete SSR, 36813) was identified in 50626 unigenes, accounting for 48.70% of the total unigenes, with one SSR per 16.6 kb. In addition, the microsatellite sequences mainly composed of dinucleotide repeats (31227, 50.27%), followed by trinucleotide repeats (16230, 26.13%). Furthermore, 122 types of repeat motifs were classified in all SSR motifs, (AT/AT)n was the most frequent repeat motif (23.33%), followed by (AAAG/CTTT)n (17.42%). The average length of microsatellites (complete SSR) was 25.87 bp, while that of the microsatellites over 20 bp was 51%. There was a significant negative correlation (P<0.01) between the frequency of microsatellites and the length, the correlation coefficient was ‒0.594. The results of the present study lay a foundation for the development of highly polymorphic microsatellite primers to identify parentage relationship and population genetic diversity, and to evaluate the effect of enhancement and release of S. japonica.