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

Abstract

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

Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae)

“…Molecular markers relative to these regions serve for the identification of valuable herbal medicinal plants (Cho et al, 2015;Hong et al, 2017;Park et al, 2018a,b). In terms of nucleotide diversity, most divergent regions were non-coding, which is again consistent with other cp genomes (Schroeder et al, 2016;Zhitao et al, 2017;Liu E. et al, 2019;Smidt et al, 2020). Other cp genomes were reported to have highly variable non-coding regions at trnS-GCU-trnG-UCC, trnC-GCA-petN, psaA-ycf3, trnI-CAU-ycf2, psbE-petL, and rps15-ycf1.…”

Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

“…A full reading frame for ndhG was observed only in B. exaltatum . Loss of ndh genes has been previously reported in orchids ( Chang et al, 2006 ; Yang et al, 2013 ; Luo et al, 2014 ; Kim et al, 2015 ; Zhitao et al, 2017 ; Kim and Chase, 2017 ; Mauad et al, 2019 ; Smidt et al, 2020 ) and is useful in comparative analyses but not in phylogenetics owing to high levels of homoplasy depicted by the independent loss of some ndh genes in a number of species of Orchidaceae ( Kim et al, 2015 ; Kim and Chase, 2017 ).…”

“…In recent years, numerous orchid plastid genomes have been sequenced. As a result, various plastid markers have been proposed for Orchidaceae ( Yang et al, 2013 ; Niu et al, 2017a , c ; Zhitao et al, 2017 ; Dong et al, 2018 ; Zhu et al, 2018 ; Li et al, 2019 ; Smidt et al, 2020 ). For instance, Niu et al (2017c) suggested that trnK-rps16 , trnS-trnG , and rps16-trnQ IGSs could be used for genera within Epidendroideae, and clpP-psbB and rps16-trnQ for Cypripedioideae.…”

“…Previous research ( Zhitao et al, 2017 ) has demonstrated that the plastid genome can be an effective tool in population genetics, but ancestral polymorphisms can be problematic in some taxa ( Dodsworth et al, 2020 ). In addition, the study of the plastid genome for phylogeographical analyses has great potential ( Mariac et al, 2014 ; Smidt et al, 2020 ). In Orchidaceae, with the exception of several mycoheterotrophic species ( Feng et al, 2016 ; Yuan et al, 2018 ), the plastid genome has the typical angiosperm quadripartite structure: two inverted repeated (IR) regions separated by a small (SSC) and large single-copy (LSC) regions ( Chang et al, 2006 ; Delannoy et al, 2011 ; Pan et al, 2012 ; Yang et al, 2013 ; Luo et al, 2014 ; Zhitao et al, 2017 ; Smidt et al, 2020 ).…”

“…In addition, the study of the plastid genome for phylogeographical analyses has great potential ( Mariac et al, 2014 ; Smidt et al, 2020 ). In Orchidaceae, with the exception of several mycoheterotrophic species ( Feng et al, 2016 ; Yuan et al, 2018 ), the plastid genome has the typical angiosperm quadripartite structure: two inverted repeated (IR) regions separated by a small (SSC) and large single-copy (LSC) regions ( Chang et al, 2006 ; Delannoy et al, 2011 ; Pan et al, 2012 ; Yang et al, 2013 ; Luo et al, 2014 ; Zhitao et al, 2017 ; Smidt et al, 2020 ). The size of the plastid genome within orchids is relatively small, ranging from 0.01 to 0.17 Mb ( Lin et al, 2015 ; Schelkunov et al, 2015 ).…”