Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Abstract

In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Fortytwo of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera (Amitostigma, Bulbophyllum, Dactylorhiza, Dipodium, Galearis, Gymnadenia, Hetaeria, Oreorchis, and Sedirea)-are new in this study. All orchid plastomes, except Aphyllorchis montana, Epipogium aphyllum, and Gastrodia elata, have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the A. montana and G. elata plastomes. The SSC is lost in the E. aphyllum plastome. The smallest plastome size was 19,047 bp, in E. roseum, and the largest plastome size was 178,131 bp, in Cypripedium formosanum. The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of rpl (14, 16, and 36), seven subunits of rps (2, 3, 4, 7, 8, 11, and 14), three subunits of rrn (5, 16, and 23), trnC-GCA, and clpP genes. Three stages of gene loss were observed among the orchid plastomes. The first was ndh gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes (atp, pet, psa, and psb) and rpo gene subunits, which are restricted to Aphyllorchis, Hetaeria, Hexalectris, and some species of Corallorhiza and Neottia. The third stage was gene loss related to prokaryotic gene expression (rpl, rps, trn, and others), which was observed in Epipogium, Gastrodia, Lecanorchis, and Rhizanthella. In addition, an intermediate stage between the second and third stage was observed in Cyrtosia (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in rpl16, rps16, and clpP(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

“…To construct the phylogeny tree and determine Coelogyne ’s systematic position, we ultimately chose 67, from 28 genera, out of 122 species in the Orchidaceae, for which the full cp genome sequencing had been accomplished and officially published in the database of the NCBI. The results showed that the main relationship was the same as other studies among Vanilloideae, Orchidoideae, and Epidendroideae [ 32 ]. Within Epidendroideae, the relationship among tribes was ultimately the same as other studies using chloroplast genome CDS (coding sequence) [ 32 ].…”

“…The results showed that the main relationship was the same as other studies among Vanilloideae, Orchidoideae, and Epidendroideae [ 32 ]. Within Epidendroideae, the relationship among tribes was ultimately the same as other studies using chloroplast genome CDS (coding sequence) [ 32 ]. These results showed that a systematic evolutionary relationship was robust using chloroplast genomes.…”

Plastome structure and adaptive evolution ofCalanthes.l. species

“…cemA encodes a chloroplast envelope membrane protein (Sasaki et al, 1993) and is inferred to indirectly influence CO 2 uptake in plastid (Rolland et al, 1997). In some non-photosynthetic orchids, cemA exists as pseudogene or is lost (Feng et al, 2016;Kim et al, 2020). infA is crucial for genetic information transmission that affects transcription of DNA into RNA and translation of RNA to protein; it is seen as a housekeeping gene (Schelkunov et al, 2015).…”

Comparative plastomics of Amaryllidaceae: Inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq

“…The expansion or contraction of the inverted repeats have been shown to occur in multiple land plant lineages (Wicke et al, 2011;Jansen & Ruhlman, 2012;Zhu et al, 2016) and can often be specific to a few genera within a family (Guisinger et al, 2011;Dugas et al, 2015;Tian et al, 2018;Thode & Lohmann, 2019). In Asparagales IR expansions have been reported in multiple genera in Orchidaceae incorporating genes from the SSC up to and including ccsA (Kim et al, 2015(Kim et al, , 2020, and in Eustrephus latifolius, Asparagaceae (Kim, Kim & Kim, 2016), where the IR expanded to include ycf1.…”