Indel patterns of the plastid DNA trnL–trnF region within the genus Poa (Poaceae)

Abstract

The use of insertion/deletion (indel) patterns from sequences of the trnL intron and trnL-F intergenic spacer (IGS) in finding plastid genome types of the genus Poa L. was studied. New sequences for 23 taxa ( P. alpina, P. badensis, P. bulbosa, P. crassipes, P. molinerii, P. annua, P. chaixii, P. granitica, P. pratensis, P. sibirica, P. remota, P. botryoides, P. cenisia, P. compressa, P. laxa, P. margilicola, P. media, P. nemoralis, P. palustris, P. pannonica, P. pirinica, P. riphaea, and P. sejuncta) and 18 previously published sequences, which represent 11 of the 13 sections listed for Poa in Flora Europaea, were investigated. Collections were made primarily in central Europe. Indel patterns, despite sampling less than 0.7% of the plastid genome, produced four taxa groupings that were congruent with the major divisions obtained in intensive, previously published restriction-site studies. Insertion/deletion events in the trnL intron and trnL-trnF IGS were in nearly all cases unique to a single pattern group and thus provided almost no information about relationships among these groups. Indels did, however, provide a meaningful infrageneric classification criterion for Poa. They can serve as useful tools in studying relationships within this genus.

Taxonomy of the Poa laxa group, including two new taxa from Arctic Canada and Greenland, and Oregon, and a re‐examination of P. sect. Oreinos (Poaceae)

“…unnamed clades within a larger SPOSTA or subg. Stenopoa clade; Soreng 1990 (noted as unpublished data), Stoneberg et al 2004, Gillespie and Soreng 2005, Gillespie et al 2007, 2008, 2009).…”

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

“…Despite these difficulties with repeat indels, researchers have examined intergenic spacers in various plant species using improved indel coding and find that indel information is consistent with substitution information and largely reinforces it, improving phylogenetic resolution and support [9,10]. In some analyses, indels are useful only in distinguishing larger groups [36]. Despite the utility of indels in phylogeny estimation, most researchers note difficulties in indel coding that result from alignment ambiguity [35].…”

Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification

“…Indel in the trnL-F region has been widely used as a universal DNA barcode for species classification [22]. Phylogenetic relationships among 41 Poa species have been determined using indels in trnL-F and trnL introns, clustering these species into four major groups [23]. Indels in trnL-F , trnG-trnS , and trnL introns have been used for the analysis of the CP genomes of Silene latifolia and S. vulgaris .…”