毛竹微型颠倒重复序列的鉴定及分子标记开发

Identification of Miniature Inverted-Repeat Transposable Elements and Development of Molecular Markers in Phyllostachys edulis

MITEs(miniature inverted-repeat transposable elements)又称颠倒重复序列,是缺少转座酶序列的非自主型转座子,在真核生物基因组含量丰富,是基因组多态性形成的重要驱动力之一。该研究利用MITE Tracker软件,在毛竹(Phyllostachys edulis)新版基因组中鉴定到1579个MITEs家族,共包括18373个全长MITEs,占毛竹基因组的0.34%,被归入到7个超家族。超家族的插入时间跨度为0.5~16.5 mya,其中有3个超家族在2~4 mya经历过一次扩增事件;2个超家族分别在1~2 mya和3~5 mya经历两次扩增事件;2个超家族在0.5~16.5 mya经历一次长期扩增。MITEs偏好插入基因或基因附近,且Micron-like超家族偏好插入ATT与ATA之间。该研究开发了3个分子标记,可从12份雷竹变种变型材料中鉴定出4份。综上所述,该文主要分析了毛竹基因组中MITEs的分布、进化及插入情况,并获得了3对可以区分雷竹变种变型的分子标记,为下一步验证MITEs功能奠定基础。

MITEs(miniature inverted-repeat transposable elements)are non-autonomous transposons lacking transposable enzyme sequences.It is abundant in eukaryotes genomes and is one of the most important driving forces for the formation of genomic polymorphism.In the present study,MITE Tracker,a novel software program,was used to identify MITEs in large genomes.A total of 1579 MITEs families(18373 full-length MITEs)in the latest genome version of Phyllostachys edulis(version 2018)were identified,accounting for 0.34%of the total genome of Ph.edulis.These MITEs families were clustered into seven super-families.The range of insertion time of the seven MITEs super-families was 0.5-16.5 mya.Three super-families might experience an expansion event during 2-4 mya.Two super-families might undergo two expansion events during 1-2 mya and 3-5 mya,respectively.Two super-families might experience a long expansion period during 0.5-16.5 mya.The MITEs in Ph.edulis genome preferred to insert into or near genes,and the Micron-like super-family preferred to insert between ATT and ATA regions.Furthermore,three pairs of primers were developed for the classification of the varieties and forms of Ph.violascens‘Prevernalis’.In conclusion,the distribution,evolution and insertion of MITEs in P.edulis genome were analyzed and three molecular markers were obtained,which laid the foundation for further verification of MITEs function.