干旱区生态环境知识资源中心(Arid): Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification

Arid

DOI	10.1186/s12870-022-03682-x
	Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
	Miao, Yujing; Chen, Haimei; Xu, Wanqi; Yang, Qiaoqiao; Liu, Chang; Huang, Linfang
通讯作者	Liu, C ; Huang, LF
来源期刊	BMC PLANT BIOLOGY
ISSN	1471-2229
出版年	2022
卷号	22 期号:1
英文摘要	Background Cistanche is an important genus of Orobanchaceae, with critical medicinal, economic, and desertification control values. However, the phylogenetic relationships of Cistanche genus remained obscure. To date, no effective molecular markers have been reported to discriminate effectively the Cistanche closely related species reported here. In this study, we obtained and characterized the plastomes of four Cistanche species from China, to clarify the phylogenetic relationship within the genus, and to develop molecular markers for species discrimination. Results Four Cistanche species (Cistanche deserticola, Cistanche salsa, Cistanche tubulosa and Cistanche sinensis), were deep-sequenced with Illumina. Their plastomes were assembled using SPAdes and annotated using CPGAVAS2. The plastic genomes were analyzed in detail, finding that all showed the conserved quadripartite structure (LSC-IR-SSC-IR) and with full sizes ranging from 75 to 111 Kbp. We observed a significant contraction of small single copy region (SSC, ranging from 0.4-29 Kbp) and expansion of inverted repeat region (IR, ranging from 6-30 Kbp), with C. deserticola and C. salsa showing the smallest SSCs with only one gene (rpl32). Compared with other Orobanchaceae species, Cistanche species showed extremely high rates of gene loss and pseudogenization, as reported for other parasitic Orobanchaceae species. Furthermore, analysis of sequence divergence on protein-coding genes showed the three genes (rpl22, clpP and ycf2) had undergone positive selection in the Cistanche species under study. In addition, by comparison of all available Cistanche plastomes we found 25 highly divergent intergenic spacer (IGS) regions that were used to predict two DNA barcode markers (Cis-mk01 and Cis-mk02 based on IGS region trnR-ACG-trnN-GUU) and eleven specific DNA barcode markers using Ecoprimer software. Experimental validation showed 100% species discrimination success rate with both type of markers. Conclusion Our findings have shown that Cistanche species are an ideal model to investigate the structure variation, gene loss and pseudogenization during the process of plastome evolution in parasitic species, providing new insights into the evolutionary relationships among the Cistanche species. In addition, the developed DNA barcodes markers allow the proper species identification, ensuring the effective and safe use of Cistanche species as medicinal products.
英文关键词	Cistanche Plastome Structural variation Gene loss Pseudogenization Molecular marker
类型	Article
语种	英语
开放获取类型	Green Published, gold
收录类别	SCI-E
WOS记录号	WOS:000844809700002
WOS关键词	CHEMICAL-CONSTITUENTS ; PHYLOGENETIC ANALYSIS ; CHLOROPLAST GENOME ; MULTIPLE ALIGNMENT ; GENE LOSSES ; SEQUENCE ; MODEL ; REDUCTION ; TOOL ; DNA
WOS类目	Plant Sciences
WOS研究方向	Plant Sciences
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/392011
推荐引用方式 GB/T 7714	Miao, Yujing,Chen, Haimei,Xu, Wanqi,et al. Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification[J],2022,22(1).
APA	Miao, Yujing,Chen, Haimei,Xu, Wanqi,Yang, Qiaoqiao,Liu, Chang,&Huang, Linfang.(2022).Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification.BMC PLANT BIOLOGY,22(1).
MLA	Miao, Yujing,et al."Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification".BMC PLANT BIOLOGY 22.1(2022).