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Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification

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...

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Autores principales: Miao, Yujing, Chen, Haimei, Xu, Wanqi, Yang, Qiaoqiao, Liu, Chang, Huang, Linfang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9404617/
https://www.ncbi.nlm.nih.gov/pubmed/36008757
http://dx.doi.org/10.1186/s12870-022-03682-x
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author Miao, Yujing
Chen, Haimei
Xu, Wanqi
Yang, Qiaoqiao
Liu, Chang
Huang, Linfang
author_facet Miao, Yujing
Chen, Haimei
Xu, Wanqi
Yang, Qiaoqiao
Liu, Chang
Huang, Linfang
author_sort Miao, Yujing
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03682-x.
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spelling pubmed-94046172022-08-26 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 BMC Plant Biol Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03682-x. BioMed Central 2022-08-25 /pmc/articles/PMC9404617/ /pubmed/36008757 http://dx.doi.org/10.1186/s12870-022-03682-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Miao, Yujing
Chen, Haimei
Xu, Wanqi
Yang, Qiaoqiao
Liu, Chang
Huang, Linfang
Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
title Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
title_full Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
title_fullStr Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
title_full_unstemmed Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
title_short Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
title_sort structural mutations of small single copy (ssc) region in the plastid genomes of five cistanche species and inter-species identification
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9404617/
https://www.ncbi.nlm.nih.gov/pubmed/36008757
http://dx.doi.org/10.1186/s12870-022-03682-x
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