摘要
为了解疣吻沙蚕(Tylorrhynchus heterochaetus)基因组信息并高效地开发微卫星标记,指导其种质资源保护与新品种的遗传改良研究,采用低深度高通量测序开展全基因组survey,k-mer分析估计疣吻沙蚕基因组大小为759.53 Mb,杂合率1.41%,重复序列比例45.92%;初步组装获得2181621条scaffold,全长为840375821 bp。在基因组序列中检测到130216个微卫星位点,丰度为154.9个·Mb^(−1)。微卫星重复次数集中在4~18拷贝;单碱基重复比例最高(35.00%),二碱基(32.48%)、三碱基(14.42%)次之;二碱基、三碱基优势基序分别是AT/AT、AAT/ATT,表现出A/T碱基优势。从随机挑选的50对引物中筛选到15对多态标记,在30尾样本中共检测到87个等位基因,等位基因数(N_(a))为2.000~12.000(平均5.800),有效等位基因数(Ne)为1.164~6.713(平均3.328),期望杂合度(H_(e))为0.141~0.789(平均0.561),多态信息含量(PIC)为0.136~0.776(平均0.511);其中13个为高度或中度多态性位点,在遗传分析中有较高的实用价值。结果表明,疣吻沙蚕基因组为复杂基因组,其微卫星位点类型丰富且具备良好的多态性潜能,可为种质资源评价、群体遗传学及分子育种研究提供有效的标记资源。
In order to understand the genomic information of Tylorrhynchus heterochaetus and efficiently develop microsatellite markers,so as to guide the conservation of its germplasm resources and genetic improvement of new varieties,we conducted a whole-genome survey by using low depth high-throughput sequencing.A total of 57.48 Gb of clean data were generated after the quality control of raw data.K-mer analysis estimates that the genome size of T.heterochaetus was 759.53 Mb;the heterozy-gosity rate was 1.41%;the proportion of repetitive sequences was 45.92%.Preliminary assembly obtained 2181621 scaffolds with a total length of 840375821 bp.A total of 130216 microsatellite loci were detected with a density of 154.9 loci per Mb.The repeated number of microsatellite units largely ranged from 4 to 18.The ratio of mononucleotide loci was the highest(35.00%),followed by those of dinucleotide(32.48%)and trinucleotide(14.42%)loci.AT/AT and AAT/ATT motifs were dominant in dinucleotide and trinucleotide loci,respectively,indicating an A/T dominance.Fifteen polymorphic loci were identified from 50 randomly selected primers,and 87 alleles were amplified in a T.heterochaetus population containing 30 individuals.The number of alleles per locus ranged from 2.000 to 12.000,with an mean of 5.800.The effective allele number(N_(e))and expected heterozygosity(H_(e))ranged from 1.164 to 6.713 and from 0.141 to 0.789,with means of 3.328 and 0.561,respectively.The polymorphic information content(PIC)ranged from 0.136 to 0.776,with a mean of 0.511.Thirteen loci were found to be highly or moderately polymorphic,having high practical value in genetic analysis.In conclusion,T.heterochaetus genome is a complex genome,and its microsatellites have a rich variety and high polymorphic potential.The results can provide effective marker resources for germplasm resource evaluation,population genetics and molecular breeding research.
作者
杨尉
司圆圆
许瑞雯
陈兴汉
YANG Wei;SI Yuanyuan;XU Ruiwen;CHEN Xinghan(Yangjiang Polytechnic,Yangjiang 529566,China)
出处
《南方水产科学》
CAS
CSCD
北大核心
2023年第5期123-133,共11页
South China Fisheries Science
基金
广东省自然科学基金项目(2022A1515011231)
广东省普通高校创新团队项目(2021KCXTD054)
广东省农业科技社会化服务与成果集成示范项目(2023B0202010011)
广东省农业农村厅农业科研类及技术推广示范类项目(0202020014)
阳江职业技术学院自然科学重点项目(2022kjzd01)。
