Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae)

• DOI: 10.1371/journal.pone.0227991
• Publication Date: 2020-01-28T16:25:57Z
• Authors: Eric de Camargo S...; Michelle Zavala Páez; Leila do Nascimen...; Juan Viruel; Valter Antônio de...; Eduardo Balsanelli; Emanuel Maltempi ...; Mark W. Chase
• Keywords: NdhF; Nucleotide diversity

This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification the most variable regions (hotspots) in this group orchids. These structure these plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC average typical quadripartite arrangement (LSC, SSC two IRs). Variation detected LSC/IR SSC/IR junctions explained by loss ndhF ycf1 length variation. For genera epiphytic clade Spiranthinae, almost whole sets ndh-gene family were missing. Eight mutation hotspots identified based nucleotide diversity, sequence variability parsimony-informative sites. Three them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem be universal family, other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, rps15-ycf1) are described first time as orchid molecular hotspots. have much more variation than all those used previously phylogenetics offer useful plastid markers phylogenetic, barcoding population genetic studies. The use or exclusive no-gap matrices also positioned high support holomycotrophic Rhizanthella among Orchidoideae model-based analyses, showing utility phylogenetic placement unusual genus.