A case study of DNA barcoding in Chinese Grimmiaceae and a moss recorded in China for the first time

Abstract

Mosses are among the basal lineages of embryophytes and one of the three bryophyte lineages. In the present study, four regions of chloroplast DNA (rbcL‐a, rps4, trnH‐psbA, trnL intron) were used to investigate the applicability of DNA barcoding to four moss genera of Grimmiaceae (Racomitrium, Coscinodon, Grimmia, Schistidium) in China. The species resolution of the four loci examined was 65% (trnH‐psbA), 59% (rps4), 53% (rbcL‐a) and 29% (trnL intron). However, rps4 (59%) provided a higher value of monophyletic species with bootstrap support >50% than trnH‐psbA (47%), rbcL‐a (35%), and trnL intron (18%). No multi‐locus combinations could significantly increase the species resolution but they increased the percentages of monophyletic species with bootstrap support >50% compared to the best single locus. Species of the genus Racomitrium could be resolved completely by rps4 and mostly (>80%) by rbcL‐a or trnH‐psbA. The species of Coscinodon (i.e., C. cribrosus) showed distinct plastid region sequences in rbcL‐a, rps4, trnH‐psbA, and trnL intron. Inter‐specific sequence sharing or high intra‐specific variability led to large amounts of barcoding failure in Grimmia and Schistidium. Furthermore, using a combination of morphological characteristics and DNA barcoding for identification, a moss species, Racomitrium elongatum, was recorded for the first time in China. The results suggest that trnH‐psbA is potentially the best barcode in mosses and rps4 a good supplementary locus for future use, as standard plant barcodes (rbcL + matK) do not perform well in this taxonomic group.

Molecular Species Delimitation in the Racomitrium canescens Complex (Grimmiaceae) and Implications for DNA Barcoding of Species Complexes in Mosses

“…The suitability of these markers for discriminating closely related moss species in species complexes, however, remained difficult to assess, as only few species from selected genera were compared. The subsequent study focusing on Grimmiaceae [9] already showed that (partial) rbcL sequences did not perform well, and the discrimination capacity of the best marker ( psbA- trnH ) did not exceed 65% in the whole family. In Racomitrium , all 11 species included in Liu et al [9] could be distinguished by rps4 , and with >80% success by rbcL and psbA-trnH , but again the question arises whether these markers would provide sufficient information when further closely related species are compared.…”

“…In addition, pairwise nucleotide distances between all sequences were calculated according to the K2P model (cf. [8], [9]) for the combined dataset and all partitions, and compared between and within the species of the R. canescens complex.…”

“…A clade composed of two species, R. fasciculare and R. laevigatum , was resolved as sister group of the R. canescens complex [15], [19]. A first case study to evaluate molecular markers for species identification in Grimmiaceae indicated that DNA barcoding can facilitate species identification in the R. canescens complex [9]. However, the taxon sampling of these molecular studies was too limited to infer species delimitations within the R. canescens complex with confidence.…”

“…According to previous analyses [9], [14], [15], the plastid (cpDNA) rps4-trnT-trnL and nuclear ribosomal ITS regions were chosen as most promising markers in terms of potential sequence variability and sequencing success. We aim to infer whether (i) the morphological taxa of the R. canescens complex can be distinguished at the molecular level and whether the degree of genetic differentiation supports their recognition at the species level, (ii) morphological characters used for species identification are suitable in the light of the molecular data, and (iii) intraspecific molecular diversity corresponds to hitherto recognized intraspecific taxa.…”

The development of species-specific SCAR markers for delimitation ofCalypogeiaspecies

“…The usefulness of DNA barcodes for bryophytes has also been proved, but this group of plants requires further testing (Rowntree et al, 2010;Crä utlein et al, 2011;Liu et al, 2011;Stech et al, 2011). Hence, alternative markers for species delimitation may be needed.…”