The complete chloroplast genome of the endangered species garra de león [Bomarea ovallei (Phil.) Ravenna] from Chile

IF 1 4区 生物学 Q3 PLANT SCIENCES
R. Diaz, W. H. Mamani, Liesbeth van den Brink, Maria N. Fuentes, M. A. Aburto
{"title":"The complete chloroplast genome of the endangered species garra de león [Bomarea ovallei (Phil.) Ravenna] from Chile","authors":"R. Diaz, W. H. Mamani, Liesbeth van den Brink, Maria N. Fuentes, M. A. Aburto","doi":"10.31742/isgpb.82.3.14","DOIUrl":null,"url":null,"abstract":"Bomarea ovallei (Phil.) Ravenna (2n=2x=18) is an endangered endemic species that inhabits only a small part of the coast of the Atacama region. We describe the structure, gene composition and phylogeny of the complete chloroplast sequence of this elusive species. The chloroplast genome consists of 155,018 bp, with typical quadripartite structures: a large single copy region (LSC) of 84,132 bp, a small single copy region (SSC) of 17,794 bp, and two inverted repeat regions (IRs) contain 26,546 bp. One hundred and thirty-four genes were identified out of which 84 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. B. ovallei chloroplast resembles chloroplasts from seven species of the order Liliales in length and structure and is most similar to Bomarea edulis (BP=100). The average nucleotide variability (Pi) of 0.00254 between these two Bomarea species is moderate. Nine loci with increased variability were identified: rps16-trnQ, atpF, trnL, ndhC-trnV, rbcL, psbJ, rpl32-trnL, ndhD and ycf1. These loci could be used as DNA markers for classification and evaluation studies in Bomarea populations.","PeriodicalId":13321,"journal":{"name":"Indian Journal of Genetics and Plant Breeding","volume":" ","pages":""},"PeriodicalIF":1.0000,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Indian Journal of Genetics and Plant Breeding","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.31742/isgpb.82.3.14","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0

Abstract

Bomarea ovallei (Phil.) Ravenna (2n=2x=18) is an endangered endemic species that inhabits only a small part of the coast of the Atacama region. We describe the structure, gene composition and phylogeny of the complete chloroplast sequence of this elusive species. The chloroplast genome consists of 155,018 bp, with typical quadripartite structures: a large single copy region (LSC) of 84,132 bp, a small single copy region (SSC) of 17,794 bp, and two inverted repeat regions (IRs) contain 26,546 bp. One hundred and thirty-four genes were identified out of which 84 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. B. ovallei chloroplast resembles chloroplasts from seven species of the order Liliales in length and structure and is most similar to Bomarea edulis (BP=100). The average nucleotide variability (Pi) of 0.00254 between these two Bomarea species is moderate. Nine loci with increased variability were identified: rps16-trnQ, atpF, trnL, ndhC-trnV, rbcL, psbJ, rpl32-trnL, ndhD and ycf1. These loci could be used as DNA markers for classification and evaluation studies in Bomarea populations.
智利濒危物种garra de león[Bomarea ovallei(Phil.)Ravenna]的完整叶绿体基因组
蛋形区(菲尔)拉文纳(2n=2x=18)是一种濒临灭绝的地方性物种,仅栖息在阿塔卡马地区海岸的一小部分地区。我们描述了这个难以捉摸的物种的完整叶绿体序列的结构,基因组成和系统发育。叶绿体基因组全长155,018 bp,具有典型的四部结构:大单拷贝区(LSC)长度为84,132 bp,小单拷贝区(SSC)长度为17,794 bp,两个反向重复区(IRs)长度为26,546 bp。共鉴定出134个基因,其中编码基因84个,rRNA 8个,tRNA 38个,假基因4个。卵形叶的叶绿体在长度和结构上与百合目7种植物的叶绿体相似,与Bomarea edulis最相似(BP=100)。平均核苷酸变异率(Pi)为0.00254,为中等。鉴定出9个变异增加的位点:rps16-trnQ、atpF、trnL、ndhC-trnV、rbcL、psbJ、rpl32-trnL、ndhD和ycf1。这些基因座可作为Bomarea群体分类和评价研究的DNA标记。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
CiteScore
1.80
自引率
10.00%
发文量
0
审稿时长
6-12 weeks
期刊介绍: Advance the cause of genetics and plant breeding and to encourage and promote study and research in these disciplines in the service of agriculture; to disseminate the knowledge of genetics and plant breeding; provide facilities for association and conference among students of genetics and plant breeding and for encouragement of close relationship between them and those in the related sciences; advocate policies in the interest of the nation in the field of genetics and plant breeding, and facilitate international cooperation in the field of genetics and plant breeding.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信