NDLI: Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer

Content Provider	Springer Nature : BioMed Central
Author	Fu, Ning Xu, Yong Jin, Lu Xiao, Tian-Wen Song, Feng Yan, Hai-Fei Chen, You-Sheng Ge, Xue-Jun
Abstract	Background Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer. Result Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer. Conclusion Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.
Related Links	https://bmcplantbiol.biomedcentral.com/counter/pdf/10.1186/s12870-024-05073-w.pdf
Ending Page	15
Page Count	15
Starting Page	1
File Format	HTM / HTML
ISSN	14712229
DOI	10.1186/s12870-024-05073-w
Journal	BMC Plant Biology
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2024-05-23
Access Restriction	Open
Subject Keyword	Plant Sciences Agriculture Tree Biology Acer Plastome nrDNA Next-generation DNA barcodes Phylogeny
Content Type	Text
Resource Type	Article
Subject	Plant Science
Journal Impact Factor	4.3/2023
5-Year Journal Impact Factor	5.2/2023

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