1. Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae)
- Author
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Atsushi Ebihara, Jun Wen, Fan-Hong Wang, Jin-Mei Lu, and De-Zhu Li
- Subjects
0106 biological sciences ,0301 basic medicine ,Molecular biology ,lcsh:Medicine ,Evolutionary biology ,Artificial Gene Amplification and Extension ,01 natural sciences ,DNA barcoding ,Polymerase Chain Reaction ,Adiantum ,Sequencing techniques ,lcsh:Science ,Molecular systematics ,Multidisciplinary ,Computer and information sciences ,biology ,Sequence analysis ,Phylogenetic Analysis ,Genomics ,Plants ,Nuclear DNA ,Fern ,Research Article ,Species complex ,China ,Nuclear gene ,DNA, Plant ,Evolutionary systematics ,010603 evolutionary biology ,Data management ,DNA sequencing ,03 medical and health sciences ,Species Specificity ,Botany ,DNA, Ribosomal Spacer ,Genetics ,DNA Barcoding, Taxonomic ,Repeated Sequences ,DNA sequence analysis ,Taxonomy ,Molecular Biology Assays and Analysis Techniques ,lcsh:R ,Organisms ,Biology and Life Sciences ,biology.organism_classification ,Research and analysis methods ,030104 developmental biology ,Molecular biology techniques ,Pteridaceae ,Genetic Loci ,Ferns ,lcsh:Q ,Cloning - Abstract
DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.
- Published
- 2016