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

【目的】阐明熊蜂全基因组SSR分布规律,为熊蜂SSR分子标记筛选及遗传进化分析提供参考依据。【方法】利用MSDB v2.4.3和Krait搜索15种已完成测序组装熊蜂(每个种代表1个亚属)基因组中的SSR序列,采用Excel 2019统计全基因组大小、GC含量、SSR类型、序列总数、相对丰度、相对密度、碱基重复类型及各重复类型相对丰度等相关信息,以Origin 2021进行绘图。【结果】基因组最大(262.4 Mb)的是西伯熊蜂;GC含量最高(39.40%)的是稳纹熊蜂,且其SSR序列总数最多(74676条)、相对丰度最高(323.53 loci/Mb)、相对密度最大(7094.37 bp/Mb)、及SSR占比最高(0.71%)。SSR类型中以纯合微卫星(P-SSR)最丰富,均占总SSR的92.00%以上,以卡氏熊蜂的占比最高(95.45%)、稳纹熊蜂的占比最低(92.07%)。除猛熊蜂和亲熊蜂外,其余13种熊蜂全基因组SSR的二碱基重复类型相对密度均最高(1362.789~2986.958 bp/Mb);除猛熊蜂、亲熊蜂和图氏熊蜂外,其余12种熊蜂全基因组SSR的二碱基重复类型总数和相对丰度均最高。15种熊蜂全基因组SSR出现频率较高的优势碱基序列有A、AG、AT、AAT、AAAT、AAAG、AATAT及AAAAG等,单碱基至五碱基重复类型的优势碱基序列相对丰度随着碱基数的增多而逐渐减小,而六碱基重复类型的优势碱基序列存在明显差异。【结论】15种熊蜂全基因组SSR总数与基因组大小不成正比,单碱基和二碱基重复类型在全基因组SSR中的占比均较高,三碱基、四碱基、五碱基和六碱基重复类型的占比则随着碱基数的增多而依次降低,即碱基重复次数越高其稳定性及多态性越低。每种熊蜂全基因组SSR都显示出特有的碱基重复类型相对丰度及优势碱基序列,今后可考虑以SSR分子标记为桥梁开展熊蜂遗传发育模式及其调控机制等相关研究。

【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 highest 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.difficillimus,B.con‐sobrinus,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 signifi‐cant.【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 increase in the number of bases in turn,the higher the number of base repeats,the lower the stability and polymorphism.Each bumblebee whole genome SSR shows unique relative abundance of base repeat types and dominant base sequences.In the future,SSR molecular markers can be considered as an intermediate bridge to carry out related studies on the genetic de‐velopment pattern of bumblebees and their regulatory mechanisms.