崖壁植物太行菊与长裂太行菊全基因组大小及特征分析
码上扫一扫！崖壁植物太行菊与长裂太行菊全基因组大小及特征分析王祎玲*, 臧 恩, 张 昊, 刘志霞, 兰亚飞, 何 珊, 郝伟丽, 曹艳玲山西师范大学 生命科学学院, 太原 030031 摘要: 太行菊(Opisthopappus taihangensis)、长裂太行菊(O. longilobus),为太行山特有多年生崖壁草本植物,菊科(Compositae)重要野生资源,具有较高的经济与生态价值。为确定适合两物种的全基因组测序策略,该研究利用流式细胞法和高通量测序技术,分析两物种基因组大小、杂合率、重复序列及GC含量等信息。结果表明:(1)流式细胞法估算太行菊基因组大小约为2.1 Gb,长裂太行菊基因组大小约为2.4 Gb。(2)高通量测序修正后太行菊基因组大小为3.13 Gb,重复序列比例为84.35%,杂合度为0.99%,GC含量为36.56%; 长裂太行菊基因组为3.18 Gb,重复序列比例为83.83%,杂合度为1.17%,GC含量为36.62%。(3)初步组装后GC含量分布及平均深度存在异常,出现分层现象,可能是两物种基因组杂合率较高所致。综上结果表明,太行菊、长裂太行菊均属于高重复、高杂合、大基因组的复杂基因组,建议使用Illumina + PacBio测序组装策略,进行全基因组测序分析。关键词: 太行菊, 长裂太行菊, 基因组调查, 基因组大小, 高通量测序 DOI：10.11931/guihaia.gxzw202106054 分类号:Q75 文章编号:1000-3142(2022)09-1582-08 基金项目:国家自然科学基金(31970358); 山西省回国留学人员科研项目(2020-090); 山西省研究生教育创新项目(2020SY323)[Supported by National Natural Science Foundation of China(31970358); Research Project of Shanxi Scholarship Council(2020-090); Graduate Education Innovation Project of Shanxi(2020SY323)]。 Genome sizes and characteristics of cliff plants Opisthopappus taihangensis and O. longilobus on Taihang MountainsWANG Yiling*, ZANG En, ZHANG Hao, LIU Zhixia, LAN Yafei, HE Shan, HAO Weili, CAO YanlingCollege of Life Sciences, Shanxi Normal University, Taiyuan 030031, ChinaCollege of Life Sciences, Shanxi Normal University, Taiyuan 030031, China Abstract: Opisthopappus taihangensis and O. longilobus, being perennial cliff herbs and endemic to Taihang Mountains, are important wild germplasm resources of Compositae, and have high economic and ecological values. To determine the appropriate sequencing strategy for the whole genome of O. taihangensis and O. longilobus, in this study, the genome sizes, heterozygosity, GC content, and repeatability were analyzed through the flow cytometry and high-throughput sequencing methods. The results were as follows:(1)Using maize of known genome size as controls, the genome size of O. taihangensis was approximately 2.1 Gb, while that of O. longilobus was approximately 2.4 Gb.(2)For O. taihangensis, the revised genome size was 3.13 Gb, and the repetitive sequences proportion, heterozygosity and GC content in the whole genome were estimated to be 84.35%, 0.99% and 36.56% respectively. Within O. longilobus, the revised genome size, the repetitive sequences proportion, heterozygosity and GC content were 3.18 Gb, 83.83%, 1.17% and 36.62% respectively.(3)The initial depth and content distribution of GC appeared abnormal after initial assembly, which might be related to the relatively high heterozygous rate of the two species. Above all, the whole genomes of O. taihangensis and O. longilobus were both large and complex genomes with high heterozygosity and repetitiveness. Therefore, it suggests that the use of Illumina + PacBio sequencing assembly strategy for the whole genome sequencing analysis of two Opisthopappus species in the future. Key words: Opisthopappus taihangensis, O. longilobus, genome survey, genome size, high-throughput sequencing 相似文献(共20条):[1] 唐 其,马小军,莫长明,潘丽梅,韦荣昌,赵 欢.罗汉果全基因组Survey分析[J].广西植物,2015,35(6):786-791.[2] 甘薯属耐盐植物马鞍藤基因组大小及特征分析[J].植物遗传资源学报[3] 伍艳芳,肖复明,徐海宁,章挺,江香梅.樟树全基因组调查[J].植物遗传资源学报,2014,15(1):150-153.[4] 宽边黄粉蝶(Eurema hecabe)基因组Survey分析[J].基因组学与应用生物学[5] 张露,李世峰,宋杰,解玮佳,彭绿春,李树发,王继华.木本高山花卉马缨杜鹃的全基因组扫描分析[J].基因组学与应用生物学,2018(1).[6] 大麻状罗布麻的全基因组分析和SSR标记开发[J].植物遗传资源学报[7] 晋家正,李午佼,牟必琴,沈咏梅,耿福能,岳碧松,范振鑫.药用美洲大蠊全基因组测序分析[J].四川动物,2018(2).[8] 王雪,周佳熠,孙会改,禹瑞敏,高飞,周宜君.新疆沙冬青基因组调查测序与基因组大小预测[J].植物遗传资源学报,2018,19(1):143-149.[9] 张太奎,苑兆和.植物古基因组学研究进展[J].遗传,2018(1).[10] 蒙古沙冬青基因组调查及SSR分析[J].基因组学与应用生物学[11] 复杂基因组测序技术研究进展[J].遗传[12] 王志明,潘元龙,吴俊,朱宝利.卡介苗美国株全基因组测序缺口修补及序列[J].微生物学报,2012,52(10):1219-1227.[13] 刘玉萍,吕婷,朱迪,周勇辉,刘涛,苏旭.青藏高原特有种—藏扇穗茅叶绿体基因组测序及序列分析[J].植物研究,2018(4).[14] 线粒体基因组的高通量测序策略[J].生命科学[15] 五味子叶绿体基因组结构解析与比较分析[J].中国科学:生命科学[16] 万仁鹏,李翔,杨慧林,朱笃,颜日明,张志斌,汪涯.卡奇霉素产生菌棘孢小单胞菌ATCC 15837的全基因组测序及序列分析[J].基因组学与应用生物学,2019(1).[17] 高洁云,万仁鹏,李浩,郑瑞,颜日明,汪涯,张志斌.小单孢菌(Micromonospora wenchangensis DSM 45709)全基因组测序及分析[J].基因组学与应用生物学,2018(6).[18] 李西文,高欢欢,王一涛,宋经元,Henry Robert,吴和珍,胡志刚,姚辉,罗红梅,罗焜,潘宏林,陈士林.荷花玉兰叶绿体全基因组高通量测序及结构解析[J].中国科学:生命科学,2012(12):947-956.[19] 小单孢菌(Micromonospora rifamycinica)AM105全基因组测序及分析[J].基因组学与应用生物学[20] 小单孢菌(Micromonospora rosaria)DSM803全基因组测序及分析[J].基因组学与应用生物学
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