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波纹唇鱼是一种极度濒危的珍贵观赏鱼和高价值食用鱼,全面了解其转录组中SSR和SNP位点的分布及序列特征,可有助于开展波纹唇鱼遗传资源的保存和合理开发利用。利用二代高通量RNA-seq测序技术对波纹唇鱼进行转录组测序,通过MISA和Samtools对所得Unigene进行SSR与SNP位点的发掘与分析。结果显示,在150 218条Unigene序列中共发现22 428个SSR,出现频率为14.93%,平均约5.35 kb出现1个SSR。波纹唇鱼SSR的主要重复单元类型为单碱基和二碱基重复,分别占SSR总数的61.32%和19.12%,除复合类型以外,所有重复基元共65种,其中(A/T)n所占比例最高(55.64%),(AG/CT)n和(AC/GT)n分别占8.31%和6.80%。22 427个SSR处于CDS中,其中1 773个位于编码区。SSR重复次数集中在5～15次,序列平均长度为13.3 bp。3 438个SSR位点共获得669对候选引物。随机选取50对验证,发现21对可扩增出与预期产物长度大小一致的特异性条带,其中5对在4个波纹唇鱼个体间具有多态性。在Unigene中共发现245 373个SNP位点,发生频率为1/490 bp,其中转换类型发生频率显著高于颠换类型,转换类型中A/G (33.61%)和C/T (32.51%)发生频率最高,颠换类型中则是A/T的最高(11.12%)。波纹唇鱼转录组中SSR和SNP位点非常丰富,可为波纹唇鱼遗传多样性分析、亲缘关系鉴定与遗传资源开发利用等方面提供丰富的基础数据信息。
Abstract：Cheilinus undulatus is an extremely endangered precious ornamental fish and high-value edible fish. A comprehensive understanding of the distribution and sequence characteristics of SSR and SNP loci in its transcriptome can help to preserve and utilize the genetic resources of C. undulatus. The second generation highthroughput RNA-seq sequencing technology was used to sequence the transcriptome of C. undulatus. The SSR and SNP loci were extracted and analyzed by MISA and Samtools. The results showed that a total of 22 428 SSRs were found in 150 218 Unigene sequences with a frequency of 14.93% and an average of about 1 SSR per 5.35 kb.Mononucleotide and dinucleotide repeat were the main SSR types, accounting for 61.32% and 19.12% of all SSRs,respectively. Except for the composite type, there were 65 repeating motifs, of which(A/T)n frequency is the highest(55.64%),(AG/CT)n and(AC/GT)n account for 8.31% and 6.80%, respectively. 22 427 SSRs were in the CDS, of which 1 773 were located in the coding area. The number of SSR repetitions was concentrated on 5-15 times, and the average length of the SSR sequence was 13.3 bp. A total of 669 pairs of candidate primers were obtained from 3 438 SSR loci. 50 pairs of validations were randomly selected and it was found that 21 pairs could amplify specific bands consistent with the expected product length, of which 5 pairs were polymorphic among 4 individuals.245 373 SNP loci were found in Unigene sequences, the frequency of SNP occurrence was 1/490 bp, and the frequency of conversion type was significantly higher than that of transversion type. The frequency of A/G(33.61%) and C/T(32.51%) were the highest in the conversion type, and the highest transversion type A/T was up to 11.12%. The SSR and SNP loci in the transcriptome of C. undulatus are very rich, which can provide rich basic data information for genetic diversity analysis, genetic relationship identification and genetic resources utilization of C. undulatus.
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基本信息:
DOI：10.13417/j.gab.039.002451
中图分类号:S917.4
引用信息:
[1]刘洪涛,刘金叶,杨明秋,等.基于转录组测序的波纹唇鱼SSR和SNP多态特征分析[J].基因组学与应用生物学,2020,39(06):2451-2461.DOI:10.13417/j.gab.039.002451.
基金信息:
海南省重点研发项目(ZDYF2018066);; 2017年海南省热带海水养殖技术重点实验室建设项目;; 2018年海南省热带海水养殖工程技术研究中心建设项目共同资助
2019-03-20
2019-03-20
2019-03-20