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Int. J. Mol. Sci. 2018, 19(7), 1962; https://doi.org/10.3390/ijms19071962

Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers

1
School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
2
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi’an 710069, China
*
Author to whom correspondence should be addressed.
Received: 16 May 2018 / Revised: 2 July 2018 / Accepted: 3 July 2018 / Published: 5 July 2018
(This article belongs to the Special Issue Chloroplast)
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Abstract

Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (G. dahurica, G. siphonantha and G. officinalis). We further compared them with the previously published plastomes from sect. Cruciata and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (accD, clpP, matK and ycf1) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. Cruciata and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication. View Full-Text
Keywords: Gentiana section Cruciata; chloroplast genome; molecular markers; species authentication Gentiana section Cruciata; chloroplast genome; molecular markers; species authentication
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Zhou, T.; Wang, J.; Jia, Y.; Li, W.; Xu, F.; Wang, X. Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers. Int. J. Mol. Sci. 2018, 19, 1962.

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