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Accurate identification of species is an important prerequisite and guarantee
for biodiversity conservation, sustainable use of resources and systematic evolution research.
Orchid (Cymbidium) plants, especially national orchids, including spring orchids, Whelan, Jianlan, Molan, lotus orchids, etc.
, have beautiful leaves and strong sweet fragrance, which are deeply loved by the people of East Asian countries, many of which have been cultivated in China for more than 2,000 years, and have high economic, cultural, protection and research value
.
The genus has China as its distribution center and contains about 70 species
.
The accurate identification of its species is conducive to the selection of new varieties and the protection and monitoring of wild species, but the taxonomic identification of species of this genus has been controversial
for a long time.
The Chinese plant DNA barcoding research team, relying on the Southwest China Wildlife Germplasm Resource Bank of the Kunming Institute of Botany, Chinese Academy of Sciences, proposed to incorporate ITS into plant core barcoding in 2011 in 2013 In the past year, he also took orchid plants as the research object and proposed the concept of "organelle barcode", which has received extensive attention
from domestic and foreign counterparts.
Recently, researchers in the bank, together with the team of Zhang Shibao of the Key Laboratory of Resource Plant and Biotechnology, with the support of the Germplasm Resource Bank Collection Department, the Jin Xiaohua team of the Institute of Botany, Chinese Academy of Sciences, and the Yu Wenbin team of Xishuangbanna Tropical Botanical Garden, extensively sampled the plants of this genus and obtained 237 species using second-generation genome sequencing technology The shallow sequencing data of the genome of each individual carried out in-depth research on the species identification of orchids, and accumulated a relatively complete DNA barcode reference data
for the identification of orchids.
Researchers are based on sequence analysis (Barcoding gaps and ABGD), tree building analysis (ML, BI, and mPTP).
) and genomic genetic distance analysis (Skmer) and other methods have carried out in-depth research
on the barcoding of Orchid DNA.
The results showed that the species recognition rate of organelle barcodes (plastid genomes) increased from 58% to 68% compared with standard DNA barcoding (rbcL+matK+trnH-psbA).
The species recognition rate analyzed by Skmer can reach 72%.
According to the species recognition rate of three subgenera of Orchid plants in different data sets and analysis methods, an optimal identification strategy of Orchid species was proposed, namely: 1) for Orchid subgenus, standard DNA barcoding can be selected; 2) For the subgenus Macrophyllum macrophylla, organelle barcodes can be selected; 3) For the subgenus Jianlan, new identification techniques and methods
are needed.
Incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture have led to the inability of the plastid genome to fully identify orchid species
.
The Skmer method has the highest species recognition rate, mainly due to the increase in nuclear gene (possibly single/low copy nuclear genes) data, suggesting that nuclear genomic data can play an important role in species identification of difficult taxa such as the subgenus Jianlan, and is expected to become the next generation of nuclear barcodes
.
The results of the research were published in the international journal Molecular Ecology under the title DNA barcoding ofCymbidiumby genome skimming: call for next-generation nuclear barcodes Resources
.
Zhang Le, a master's student, is the first author of the paper, and researcher Li Debao, researcher Li Hongtao and senior engineer Yang Junbozheng are the corresponding authors
of the paper.
The research was supported by the Strategic Leading Science and Technology Project of the Chinese Academy of Sciences (XDB31000000), the Open Research Project of Large Scientific Installations of the Chinese Academy of Sciences (2017-LSF-GBOWS-2), the Key R&D Project of Yunnan Province (202103AC100003) and the Innovation Team Project of Yunnan Province (202105AE160012).
。
Link to the article
ML phylogenetic tree of the plastid genome of Orchids, where the numbers on the nodes indicate the ML tree support rate; A red star indicates a species that organelle barcodes can identify but cannot be identified by standard DNA barcodes (rbcL+matK+trnH-psbA); In the red rectangle is the type species
of the subgenus.
