Full-length Transcriptome Sequencing and Bioinformatic Analysis of Psammochloa villosa (Poaceae)

doi:10.11733/j.issn.1007-0435.2023.06.009

Acta Agrestia Sinica ›› 2023, Vol. 31 ›› Issue (6): 1673-1681.DOI: 10.11733/j.issn.1007-0435.2023.06.009

Full-length Transcriptome Sequencing and Bioinformatic Analysis of Psammochloa villosa (Poaceae)

MAO Xuan-rui¹, SU Xu^1,2,3, LIU Yu-ping^1,2,4, LIU Tao¹, CHEN Jin-yuan^1,3, HU Xia-yu¹, YANG Ping¹, LI Xiao-li¹, YUAN Yuan¹

1. School of Life Sciences, Qinghai Normal University, Xining, Qinghai Province 810008, China;
2. Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai Province 810016, China;
3. Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, Qinghai Province 810008, China;
4. Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, Qinghai Province 810008, China

Received:2022-12-19 Revised:2023-02-10 Online:2023-06-15 Published:2023-06-30

沙鞭全长转录组测序及生物信息学分析

毛轩睿¹, 苏旭^1,2,3, 刘玉萍^1,2,4, 刘涛¹, 陈金元^1,3, 胡夏宇¹, 杨萍¹, 李小莉¹, 袁园¹

1. 青海师范大学生命科学学院, 青海西宁 810008;
2. 青海师范大学高原科学与可持续发展研究院, 青海西宁 810016;
3. 青海师范大学青海省青藏高原生物多样性形成机制与综合利用重点实验室, 青海西宁 810008;
4. 青海师范大学青海省青藏高原药用动植物资源重点实验室, 青海西宁 810008

通讯作者: 刘玉萍,E-mail:lyp8527970@126.com
作者简介:毛轩睿(1997-)，男，汉族，湖南长沙人，硕士研究生，主要从事高山植物遗传多样性和系统进化研究，E-mail：maoxaunrui@163.com
基金资助:
青海省自然科学基金面上项目(2022-ZJ-918)；国家自然科学基金项目(32160297)；2023年大学生创新创业训练计划项目(qhnucxcy2023052)资助

Abstract

Abstract: In order to explore the transcriptome characteristics of Psammochloa villosa (Poaceae),the full-length transcriptome was firstly sequenced,then the genomic library of P. villosa were established by using the PacBio Sequel platform in this study. The result showed that 323 309 clean reads were obtained from that transcriptome sequence,which could form 673 540 circular consensus reads (CCS) through self-correction and a total of 28 447 coding sequences (CDS) in prediction. Moreover,93 563 SSRs in the transcriptome of P. villosa were searched and found out by MISA software,which were distributed in 56 824 unigenes. The transcripts of P.villosa was matched to the counterparts in NR database for the gene function,and it was identified out that 166 541 unigenes of P. villosa were annotated and that P. villosa had the closest genetic relationship with Brachypodium distachyon. Based on KOG database,97 892 unigenes within the transcriptome of P. villosa were classified into 25 functional groups,most of which were annotated in the participation of the posttranslational modification,protein turnover and chaperones. Similarly,87 930 unigenes within that transcriptome were annotated to GO database,whose functions were divided into 62 subclades of three clades of the biological processes,cellular components,and molecular functions. Besides,the functional analysis of unigenes referred to the KEGG database indicated that the functions of annotated genes in that transcriptome were related with carbohydrate metabolism,signal transduction and energy metabolism. These results above enriched the genetic information of P. villosa,and could provide a theoretical basis for excavating the key drought-resistant genes of P. villosa in coming days.

Key words: Poaceae, Psammochloa villosa, Full-length transcriptome, Function annotation, SSR

摘要： 为了明晰沙鞭(Psammochloa villosa)的转录组特征，本研究利用PacBio Sequel测序平台首次对其进行全长转录组测序和数据分析，结果共获得323 309个clean reads，自我矫正产生环形一致性序列(CCS)673 540个，预测得到蛋白编码区(CDS)序列28 447个；MISA软件共搜索得到沙鞭93 563个简单重复序列(SSR)，分布于56 824条unigene上；转录本基因功能注释，共有166 541条序列得到NR注释，结果显示沙鞭与二穗短柄草(Brachypodium distachyon)亲缘最近；KOG数据库比对将97 892个unigene分为25个功能类别，其中注释较多的功能为翻译后修饰、蛋白质周转和分子伴侣；GO数据库比对共注释到87 930个unigene，分为生物过程、细胞组成和分子功能3大类及62个亚类分支；KEGG结果表明碳水化合物代谢、信号转导、能量代谢通路中注释基因较多。本研究结果丰富了沙鞭的遗传信息，为今后沙鞭关键耐旱基因的挖掘提供了理论依据。

关键词: 禾本科, 沙鞭, 全长转录组, 功能注释, SSR

CLC Number:

MAO Xuan-rui, SU Xu, LIU Yu-ping, LIU Tao, CHEN Jin-yuan, HU Xia-yu, YANG Ping, LI Xiao-li, YUAN Yuan. Full-length Transcriptome Sequencing and Bioinformatic Analysis of Psammochloa villosa (Poaceae)[J]. Acta Agrestia Sinica, 2023, 31(6): 1673-1681.

毛轩睿, 苏旭, 刘玉萍, 刘涛, 陈金元, 胡夏宇, 杨萍, 李小莉, 袁园. 沙鞭全长转录组测序及生物信息学分析[J]. 草地学报, 2023, 31(6): 1673-1681.

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References

[1] 郭本兆. 中国植物志[M]. 北京：科学出版社,1997:309
[2] YU F H,DONG M,BERTIL K. Clonal integration helps Psammochloa villosa survive sand burial in an inland dune [J]. New Phytologist,2004,162(3):697-904
[3] 刘峰,马子兰,刘涛,等. 不同生态环境条件沙生植物沙鞭的结实研究[J]. 广西植物,2021,41(9):1457-1464
[4] 马毓泉. 内蒙古植物志[M]. 呼和浩特:内蒙古人民出版社,1997:115-152
[5] 董鸣. 切断根茎对根茎禾草沙鞭和赖草克隆生长的影响[J]. 植物学报,1999(2):194-198
[6] 董鸣,阿拉腾宝,邢雪荣,等. 根茎禾草沙鞭的克隆基株及分株种群特征[J]. 植物生态学报,1999(4):15-23
[7] 吕婷,刘玉萍,周勇辉,等. 沙生植物沙鞭叶表皮微形态特征及其生态适应性研究[J]. 植物研究,2018,38(3):330-337
[8] 吕婷,刘涛,梁瑞芳,等. 沙生植物沙鞭不同居群形态变异研究[J]. 植物研究,2021,41(1):60-66
[9] 黄振英. 鄂尔多斯高原固沙禾草沙鞭种子休眠和萌发与环境的关系[J]. 西北植物学报,2003(7):72-77
[10] 黄振英,董鸣,张淑敏. 沙鞭(禾本科)种子在沙丘上的萌发策略及幼苗的耐干燥特性[J]. 生态学报,2005(2):298-303
[11] 贺学礼,李英鹏,赵丽莉,等. 毛乌素沙地克隆植物沙鞭生长对AM真菌生态分布的影响[J]. 生态学报,2010,30(3):751-758
[12] 徐翥骍,贺学礼,郭辉娟,等. 内蒙古农牧交错区沙鞭和羊柴AM真菌侵染及其土壤因子[J]. 河北农业大学学报,2011,34(1):56-61
[13] CHEN M Y,LIN L,ZHANG Y M. Genome sequence of Klebsiella oxytoca SA2,an endophytic nitrogen-fixing bacterium isolated from the pioneer grass Psammochloa villosa[J]. Genome Announcements,2013,1(4):e00601
[14] 王可青,葛颂,董鸣. 根茎禾草沙鞭的等位酶变异及克隆多样性[J]. 植物学报,1999,41(5):537-540
[15] LI A,GE S. Genetic variation and clonal diversity of Psammochloa villosa (Poaceae) detected by ISSR markers [J]. Annals of Botany,2001(87):585-590
[16] 吕婷. 沙生牧草沙鞭的遗传多样性研究[D]. 西宁:青海师范大学,2019:2-62
[17] 吕婷,刘玉萍,周勇辉,等. 荒漠植物沙鞭(Psammochloa villosa)种质资源收集及谱系遗传分化初探[J]. 草地学报,2018,26(3):733-740
[18] WANG Z,GERSTEIN M,SNYDER M. RNA-Seq:a revolutionary tool for transcriptomics [J]. Nature Reviews Genetics,2009,10(1):57-63
[19] LIAO X,LIU Y Q,HAN T Y,et al. Full-Length transcriptome sequencing reveals tissue-specific gene expression profile of mangrove clam Geloina erosa[J]. Frontiers in Physiology,2022(13):851957
[20] FRANSSEN S U,SHRESTHA R P,BRAUTIGAM A,et al. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing[J]. BMC Genomics,2011,12(1):227
[21] 刘春晓,黄小庆,刘自广,等. 十字花科植物种子低分子RNA提取方法比较[J]. 基因组学与应用生物学,2019,38(3):1236-1241
[22] 崔凯,吴伟伟,刁其玉. 转录组测序技术的研究和应用进展[J]. 生物技术通报,2019,35(7):1-9
[23] 孙铭阳,徐世强,顾艳,等. 穿心莲全长转录组测序及特性分析[J]. 中国农学通报,2021,37(27):82-89
[24] 潘敏,于旭东,蔡泽坪,等. 菠萝蜜茎叶全长转录组分析[J]. 热带作物学报,2020,41(7):1288-1297
[25] THIEL T,MICHALEK W,VARSHNEY R K,et al. Exploiting EST databases for the development and characterization of gene derived SSR-markers in barley (Hordeum vulgare L.) [J]. Theoretical and Applied Genetics,2003,106(3):411-422
[26] 毛轩睿,刘玉萍,苏旭,等. 沙鞭转录组简单重复序列(SSR)位点特征分析[J]. 草地学报,2022,30(8):1990-2001
[27] 富贵,刘玉萍,苏旭. 基于转录组数据的密花香薷SSR位点特征分析[J]. 西北植物学报,2021,41(4):654-663
[28] ALTSCHUL S F,GISH W,MILLER W,et al. Basic local alignment search tool[J]. Journal of Molecular Biology,1990,215(3):403-410
[29] 陈春光,米华玲. 天麻素生物合成途径相关基因的分析[J]. 植物生理学报,2021,57(9):1819-1828
[30] 周延清,邵露营,李慧敏,等. 地黄全长转录组分析及毛蕊花糖苷生物合成下游途径关键酶基因的挖掘与解析[J]. 植物生理学报,2022,58(1):197-206
[31] WIXON J,KELL D. The kyoto encyclopedia of genes and genomes-KEGG [J]. Yeast,2000,17(1):48-55
[32] MICHAEL A,CATHERINE A B,JUDITH A B,et al. Gene ontology:tool for the unification of biology [J]. Nature Genetics,2000,25(1):25-29
[33] TATUSOV R,FEDOROVA N,JACKSON J,et al. The COG database:an updated version includes eukaryotes [J]. BMC Bioinformatics,2003,4(1):41
[34] BATEMAN A,COIN L,DURBIN R,et al. The Pfam protein family’s database [J]. Nucleic Acids Research,2004,32(1):138-141
[35] BAIROCH A,APWEILER R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 2000 [J]. Nucleic Acids Research,2000,28(1):45-48
[36] 夏丽飞,孙云南,宋维希,等. 基于PacBio平台的紫娟茶树全长转录组分析[J]. 基因组学与应用生物学,2020,39(6):2646-2658
[37] 欧阳雨晴,李玲玲,石好宇,等. 薏苡转录组测序及基因功能注释[J]. 中南药学,2021,19(7):1286-1293
[38] 刘敏,黄炜忠,何孟璐,等. 大青转录组测序及生物信息学分析[J]. 广州中医药大学学报,2022,39(1):177-183
[39] 马玉金. 七个禾本科牧草转录组测序(RNA-Seq)及转录组数据分析与基因发掘[D]. 昆明:昆明理工大学,2016:33-38
[40] 庞丹丹,张亚真,徐礼羿,等. 基于转录组测序的茶树儿茶素合成调控相关基因的挖掘[J]. 分子植物育种,2019,17(17):5604-5612
[41] 徐金青,夏腾飞,王蕾,等. 青稞转录组SSR位点及其基因功能分析[J]. 麦类作物学报,2017,37(2):175-184
[42] 王恒波,祁舒婷,陈姝琦,等. 甘蔗栽培种单倍体基因组SSR位点的发掘与应用[J]. 作物学报,2020,46(4):631-642
[43] 朱永群,彭丹丹,林超文,等. 苏丹草转录组SSR分子标记开发及遗传多样性评价[J]. 草业学报,2018,27(5):178-189
[44] 陈渝,邓洁,陈君愉,等. 番茄FAR1/FHY3转录因子家族的全基因组鉴定及表达分析[J]. 植物生理学报,2021,57(10):1983-1995
[45] 袁娜,王彤,刘廷利,等. 棉花FAR1/FHY3基因家族的全基因组分析[J]. 棉花学报,2018,30(1):1-11
[46] 罗文巧. 二穗短柄草根中木栓质脂肪醇合成基因的克隆与功能验证[D]. 杨凌:西北农林科技大学,2018:46-49
[47] 陈柳君. bHLH转录因子在植物低温胁迫中的研究进展[J]. 江西农业学报,2022,34(1):79-87
[48] 何江峰,王力伟,房永雨,等. 干旱胁迫和复水处理后梭梭转录因子的转录组分析[J]. 华北农学报,2020,35(1):36-43
[49] 关淑艳,焦鹏,蒋振忠,等. MYB转录因子在植物非生物胁迫中的研究进展[J]. 吉林农业大学学报,2019,41(3):253-260

Full-length Transcriptome Sequencing and Bioinformatic Analysis of Psammochloa villosa (Poaceae)

沙鞭全长转录组测序及生物信息学分析

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