Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae

被引:28
作者
Han, Chenyang [1 ]
Ding, Rui [2 ]
Zong, Xiaoyan [1 ]
Zhang, Lijie [3 ]
Chen, Xuhui [1 ]
Qu, Bo [1 ]
机构
[1] Shenyang Agr Univ, Coll Biosci & Biotechnol, Shenyang 110161, Peoples R China
[2] Shenyang Agr Univ, Coll Land & Environm, Shenyang 110161, Peoples R China
[3] Shenyang Agr Univ, Coll Forestry, Shenyang 110161, Peoples R China
基金
中国国家自然科学基金;
关键词
Platanthera ussuriensis; Orchidaceae; Chloroplast genome; Molecular evolution; Phylogenetic analysis; SSR markers; RNA editing site; RNA EDITING SITES; PLANT MITOCHONDRIAL; COMPLETE PLASTOME; DNA; SEQUENCE; PRIMERS; GENES; SET; MICROSATELLITES; IDENTIFICATION;
D O I
10.1186/s12864-022-08319-9
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background The genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera. Platanthera ussuriensis, formerly named as Tulotis ussuriensis, is a small terrestrial orchid species and has been listed as wild plant under State protection (category II) in China. An improved understanding of the genomic information will enable future applications of conservation strategy as well as phylogenetic studies for this rare orchid species. The objective of this research was to characterize and compare the chloroplast genome of P. ussuriensis with other closely related species of Orchidaceae. Results The chloroplast genome sequence of P. ussuriensis is 155,016 bp in length, which included a pair of inverted repeats (IRs) of 26,548 bp that separated a large single copy (LSC) region of 83,984 bp and a small single copy (SSC) region of 17,936 bp. The annotation contained a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The simple sequence repeat (SSR) analysis showed that there were 104 SSRs in the chloroplast genome of P. ussuriensis. RNA editing sites recognition indicated 72 RNA editing events occurred, and all codon changes were C to T conversions. Comparative genomics showed that the chloroplast sequence of Platanthera related species were relatively conserved, while there were still some high variation regions that could be used as molecular markers. Moreover, Platanthera related species showed similar IR/SSC and IR/LSC borders. The phylogenetic analysis suggested that P. ussuriensis had a closer evolutionary relationship with P. japonica followed by the remaining Platanthera species. Conclusion Orchidaceae is a key group of biodiversity protection and also a hot spot group in the plant taxonomy and evolution studies due to their characteristics of high specialization and rapid evolution. This research determined the complete chloroplast genome of P. ussuriensis for the first time, and compared the sequence with other closely related orchid species. These results provide a foundation for future genomic and molecular evolution of the Orchidaceae species, and provide insights into the development of conservation strategy for Platanthera species.
引用
收藏
页数:13
相关论文
共 81 条
[1]   IRscope: an online program to visualize the junction sites of chloroplast genomes [J].
Amiryousefi, Ali ;
Hyvonen, Jaakko ;
Poczai, Peter .
BIOINFORMATICS, 2018, 34 (17) :3030-3031
[2]   Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes [J].
Angioi, S. A. ;
Desiderio, F. ;
Rau, D. ;
Bitocchi, E. ;
Attene, G. ;
Papa, R. .
PLANT BIOLOGY, 2009, 11 (04) :598-612
[3]   MISA-web: a web server for microsatellite prediction [J].
Beier, Sebastian ;
Thiel, Thomas ;
Muench, Thomas ;
Scholz, Uwe ;
Mascher, Martin .
BIOINFORMATICS, 2017, 33 (16) :2583-2585
[4]   Tandem repeats finder: a program to analyze DNA sequences [J].
Benson, G .
NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580
[5]   HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching [J].
Bi, Guiqi ;
Mao, Yunxiang ;
Xing, Qikun ;
Cao, Min .
GENOMICS, 2018, 110 (01) :18-22
[6]   Sense from nonsense: How the genetic information of chloroplasts is altered by RNA editing [J].
Bock, R .
BIOCHIMIE, 2000, 82 (6-7) :549-557
[7]   RNA editing [J].
Brennicke, A ;
Marchfelder, A ;
Binder, S .
FEMS MICROBIOLOGY REVIEWS, 1999, 23 (03) :297-316
[8]   Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis [J].
Castresana, J .
MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (04) :540-552
[9]   The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae):: Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications [J].
Chang, CC ;
Lin, HC ;
Lin, IP ;
Chow, TY ;
Chen, HH ;
Chen, WH ;
Cheng, CH ;
Lin, CY ;
Liu, SM ;
Chang, CC ;
Chaw, SM .
MOLECULAR BIOLOGY AND EVOLUTION, 2006, 23 (02) :279-291
[10]   An updated classification of Orchidaceae [J].
Chase, Mark W. ;
Cameron, Kenneth M. ;
Freudenstein, John V. ;
Pridgeon, Alec M. ;
Salazar, Gerado ;
Van den Berg, Cassio ;
Schuiteman, Andre .
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, 2015, 177 (02) :151-174