南方农业学报2023，Vol.54Issue(11)：3378-3387,10.DOI:10.3969/j.issn.2095-1191.2023.11.024
15种熊蜂全基因组SSR分布规律研究
Distribution regularities of SSR in the whole genomes of fifteen species of bumblebees
摘要
Abstract
[Objective]The purpose of the study was to elucidate the distribution regularities of SSR in the whole ge-nome of bumblebees,and to provide a reference for the screening of SSR molecular markers and the analysis of genetic evolution of bumblebees.[Method]SSR sequences in the genomes of 15 species of bumblebees(each species represented one subgenus)that had been sequenced and assembled using MSDB v2.4.3 and Krait.Excel 2019 was used to calculate the information related to whole genome size,GC content,SSR type,total number of sequences,relative abundance,relative density,base repeat type and relative abundance of each repeat type.Meanwhile,the results were plotted using the Origin 2021.[Rsesult]The largest genome(262.4 Mb)was found in Bombus sibiricus,the highest GC content(39.40%)was found in B.waltoni.It had the largest total number of SSR sequences(74676),the highest relative abun-dance(323.53 loci/Mb),the highest relative density(7094.37 bp/Mb)and the highest proportion of SSRs(0.71%).Pure microsatellite(P-SSRs)was the most abundant SSR type,accounting for more than 92.00%of the total SSRs.The high-est percentage(95.45%)was B.cullumanus and the lowest percentage(92.07%)was B.waltoni.The whole genome SSRs of the remaining 13 species of bumblebees had the highest relative density of dinucleotide repeat type(1362.789～2986.958 bp/Mb)except for B.difficillimus and B.consobrinus.The total number and relative abundance of dinucleotide repeat type of the whole genome SSRs of the remaining 12 species of bumblebees was the highest,except for B.difficilli-mus,B.consobrinus,and B.turneri.The dominance base sequences of the 15 bumblebees with a high frequency of whole genome SSR occurrences were A,AG,AT,AAT,AAAT,AAAG,AATAT and AAAAG,etc.The relative abundance of the dominant base sequences of the mononucleotide to pentanucleotide repeat types decreased gradually with the increase in the number of bases,while the differences in the dominant base sequences of the hexanucleotide repeat type were sig-nificant.[Conclusion]The total number of whole genome SSRs of 15 bumblebee species is not in direct proportion with the genome size.The proportion of mononucleotide and dinucleotide repeat types in whole genome SSRs is higher,and the proportion of trinucleotide,tetranucleotide,pentanucleotide and hexanucleotide repeat types decreases with the in-crease in the number of bases in turn,i.e.,the higher the number of base repeats,the lower the stability and polymor-phism.Each bumblebee whole genome SSR shows unique relative abundance of base repeat types and dominant base se-quences.In the future,SSR molecular markers can be considered as an intermediate bridge to carry out related studies on the genetic development pattern of bumblebees and their regulatory mechanisms.关键词
熊蜂/基因组/SSR/分布规律/碱基重复类型Key words
bumblebee/genome/SSR/distribution regularities/base repeat type分类
农业科技引用本文复制引用
孙国,梁程博,赵芳,张富东,闫京艳..15种熊蜂全基因组SSR分布规律研究[J].南方农业学报,2023,54(11):3378-3387,10.基金项目
中国科学院"西部之光"人才培养计划项目(人字[2022]4号) （人字[2022]4号）
江西省引进培养创新创业高层次人才"千人计划"项目(jxsq2020101050) "Light of the West"Talent Training Project of Chinese Academy of Sciences(Renzi[2022]4) （jxsq2020101050）
"Thousand Talents Plan"Project for Introducing and Cultivating High-level Talents for Innovation and Entrepreneurship in Jiangxi(jxsq2020101050) （jxsq2020101050）
