Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar

Abstract

The study showed that NGS can be used to generate abundant phylogenetic information rapidly, opening new avenues for grass phylogenetics. These data clearly showed that Lecomtella forms an isolated lineage, which, in combination with its morphological peculiarities, justifies its treatment as a separate tribe: Lecomtelleae. New descriptions of the tribe, genus and species are presented with a typification, a distribution map and an IUCN conservation assessment.

Phylogenetic relationships of Echinolaena and Ichnanthus within Panicoideae (Poaceae) reveal two new genera of tropical grasses

“…We selected five chloroplast DNA regions from the large single copy (LSC), the small single copy (SSC) and the inverted repeat B (IR-B) regions of the genome: ndhF (coding region, SSC), rpl16 (coding region, intron, LSC), trnH-psbA (coding region, spacer, IR-B/LSC junction), encompassing the rps19 gene (Hiratsuka et al, 1989;Chang et al, 2006), trnL-trnF (coding region, intron, spacer, LSC) and trnS-trnG (coding region, spacer, LSC), encompassing the psbZ gene (e.g., see Fig. S1 in Besnard et al, 2013); and one nuclear DNA region: ITS (18S, 5.8S and 26S ribosomal RNA genes, and internal transcribed spacers 1 and 2). Primers used for amplification and sequencing, and PCR conditions are shown in Table 2. PCR products were cleaned using PEG 20% (polyethylene glycol; Paithankar and Prasad, 1991) and then sequenced in both directions using the Big Dye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Austin, Texas, USA) according to the following protocol: a hot start with 3 min of initial denaturation at 96°C, 30 cycles of 96°C denaturation for 20 s, 50°C annealing for 15 s, and 60°C extension for 4 min.…”

“…These morphological peculiarities and the phylogenetic placement of L. madagascariensis motivated Besnard et al (2013) to treat it separatelly in the tribe Lecomtelleae.…”

“…They are both included within Paspaleae, one of the major tribes of the Panicoideae, and comprise plants mostly of the Americas, with the base chromosome number x = 10 as its potential synapomorphy (Morrone et al, 2012). Paspaleae is among the 13 tribes currently recognized for Panicoideae, the second largest subfamily in Poaceae with 220-250 genera and approximately 3300 species, part of the PACMAD clade which encompasses about half of the diversity of the family (Sánchez-Ken and Clark 2010; GPWG II, 2012;Morrone et al, 2012;Besnard et al, 2013).…”

The recent and rapid spread of Themeda triandra

“…A complete chloroplast genome (hereafter plastome) was assembled de novo for one sample using the genome-walking method described in Besnard et al (2013). In brief, a combination of extractread2 (included in the OBITools package, http://metabarcoding.org/obitools) and velvet (Zerbino and Birney 2008) was used to identify overlapping chloroplast reads in the raw data and subsequently assemble them.…”

VIII. Subfamily Panicoideae Link (1827)

“…Lecomtella was provisionally placed sister to Gerritea in Paspalinae by Morrone et al (2012) based on morphological data, but molecular data (Besnard et al 2013) place it in an unresolved position at the base of Panicoideae. The tribal name Lecomtelleae Pilg.…”