Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

Abstract

Dendrobium is one of the largest genera in Orchidaceae, comprising about 800–1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots—trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ—should be used in the phylogenetic and identification studies of Dendrobium.

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

“…The LSC, SSC, and IR regions of D. loddigesii and D. devonianum ranged from 84,089 to 84,897 bp, 14,311 to 16,932 bp, and 25,736 to 25,800 bp, respectively. The overall GC content (37.38–37.56%) was similar with other Dendrobium plastomes [ 20 , 22 ], with 35.12–35.36% and 30.54–30.61% in LSC and SSC regions, respectively, and a higher content of 43.51–43.57% in the IR regions ( Table 1 ). The two Dendrobium plastomes contained 102 unique functional coding genes, including 30 tRNA genes, four rRNA genes, and 68 protein-coding genes.…”

“…Recently, plastome sequences have been made available for more than 20 orchid genera. However, in this study, we chose to focus on the Dendrobium genus because it is the only genus of orchids for which more than 30 plastome sequences have been sequenced [ 21 , 22 ]. Dendrobium is one of the largest genera in the orchid species.…”

Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum

“…All four rRNAs and the 68 selected plastid protein encoding genes were successfully mined from off-target reads. Regarding the ndh gene family, our results agree with previous studies (e.g., Kim et al, 2015;Lin et al, 2015;Kim et al, 2017;Niu et al, 2017;Zhitao et al, 2017;Dong et al, 2018) which have shown that this set of genes are commonly pseudogenized, lost, or translocated in orchids, since most ndh genes for most of the target species were recovered most likely as pseudogenes and very rarely as functional genes. The ndhA, ndhG, ndhH, and ndhI genes were missing in one or several species; however, this cannot be assumed with confidence to be the consequence of gene loss, because there is a possibility that they were simply not recovered among the off-target reads.…”

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

“…[63] reported mutational hotspots as genus-specific in orchid plastomes and proposed three markers for Epidendroideae (trnK-rps16, trnS-trnG, and rps16-trnQ) and two for Cypripedioideae (clpP-psbB and rps16-trnQ). In a study of plastome variation in Dendrobium, [64] proposed the combination of five markers (trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ) for phylogenetic and DNA barcoding studies of the genus. Here, we suggest eight hotspot markers for Cranichideae.…”