Plastome structure and adaptive evolution ofCalanthes.l. species

Abstract

Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants.

Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

“…These changes in length may affect the size of the cp genome and gene expression. Moreover, trnK -UUU gene containing the longest intron, and rps12 are considered as a trans-splicing gene (Table S2), this identical phenomenon were consistent with those of most other members of Orchidaceae species [54,62].…”

“…The length of the LSC, SSC, and IRs varied in the range of 84,046-89,021 bp, 16,914-18,821 bp, and 23,902-25,914 bp, respectively. Chloroplast genome size variation among different species, or even within different individuals of the same species, which has been reported in other species, such as Camptotheca acuminate [48,49], Eucommia ulmoides [50], Rosa rugosa [51][52][53] and Calanthe davidii [54]. This, besides polyploidy of plant material, has been shown to be due to the expansion/contraction of IR [55].…”

“…Statistical analysis of the locations of all identi ed SSRs showed that the number of SSRs located in the LSC region, SSC region and IR regions were 44-52, 8-12 and 4-14, respectively. Furthermore, we found that these SSRs were mainly distributed in IGS (38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54), and some in the CDS region (9)(10)(11)(12) and introns (8)(9)(10)(11)(12). A/T (no C/G) is the only mononucleotide SSRs type in the six species (Figures 6A and 7), and the repeat units of the other ve SSRs were also mainly composed of A or T (Figures 6A and 7).…”

Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis

“…Asia, Australia, Madagascar, Africa, Central and South America, and the Caribbean [2][3][4]. Calanthe species are evergreen or deciduous plants, terrestrial (rarely epipetric or epiphytic) with thick roots, small oval pseudobulbs, highly ridged leaves, and upright, occasionally arching flowering stems [5].…”

Comparative chloroplast genomes and phylogenetic analyses of Pinellia

“…4 Positive selection sites logo of four Pinellia plastomes polymerase gene (rpoC1), one gene for ribosome small subunit protein (rps12) and ycf1 gene. All these genes were also detected in other plants [51][52][53][54], and these genes may have played a significant role in the adaptive evolution of Pinellia. The specific role needs to be further studied.…”