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The rps4 locus as an alternative marker for barcoding bryophytes: evaluation based on data mining from GenBank

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Author(s): Yan Liu | Jianxiu Wang | Xuejun Ge | Tong Cao

Journal: Biodiversity Science
ISSN 1005-0094

Volume: 19;
Issue: 3;
Start page: 311;
Date: 2011;

Keywords: cryptogamic plants | land plant barcoding | plastid DNA | species identification

ABSTRACT
Among the candidate DNA barcoding loci suggested for land plants, only rbcL and trnH-psbA are available for barcoding bryophytes. However, both loci have limitations in discriminating among species.The present study evaluated the feasibility of using the cpDNA rps4 locus as an additional marker to complement other candidate barcodes for bryophytes. We analyzed 3,365 rps4 sequences retrieved from Gen-Bank using pair-wise distance and phylogenetic methods. Our results demonstrated the universality of rps4 in bryophytes; the locus covers 96% of moss families and 88% of liverwort families. The rps4 locus resolved 73.0% of the species we tested. The discriminatory ability of rps4 is better than that of rbcL-a in each of the six bryophyte genera (i.e. Plagiochila, Tortula, Plagiomnium, Pyrrhobryum, Pogonatum, Grimmia) most commonly represented in the database. Moreover, large numbers of rps4 sequences from individuals of known bryophyte identities have been compiled in GenBank, thereby providing a reference for species identification. Therefore, we propose rps4 as an additional barcode, especially when rbcL and trnH-psbA do not perform well in certain bryophyte taxa.

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