Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)

Abstract

The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629–25,859 bp) separated by the large single-copy (81,482–82,218 bp) and small single-copy (17,366–17,465 bp) regions. Each cp genome equivalently contains 112 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 78 protein coding genes. Gene content, gene order, AT content, and IR/SC boundary structure are nearly identical among all Amana cp genomes. However, the relative contraction and expansion of the IR/SC borders among the six Amana cp genomes results in length variation among them. Simple sequence repeat (SSR) analyses of these Amana cp genomes indicate that the richest SSRs are A/T mononucleotides. The number of repeats among the six Amana species varies from 54 (A. anhuiensis) to 69 (Amana kuocangshanica) with palindromic (28–35) and forward repeats (23–30) as the most common types. Phylogenomic analyses based on these complete cp genomes and 74 common protein-coding genes strongly support the monophyly of the genus, and a sister relationship between Amana and Erythronium, rather than a shared common ancestor with Tulipa. Nine DNA markers (rps15–ycf1, accD–psaI, petA–psbJ, rpl32–trnL, atpH–atpI, petD–rpoA, trnS–trnG, psbM–trnD, and ycf4–cemA) with number of variable sites greater than 0.9% were identified, and these may be useful for future population genetic and phylogeographic studies of Amana species.

Structural and Comparative Analysis of the Complete Chloroplast Genome of a Mangrove Plant: Scyphiphora hydrophyllacea Gaertn. f. and Related Rubiaceae Species

“…Overall, the comparative genomic analysis showed that nine Rubiaceae cp genomes were relatively conserved. In agreement with similar studies in other plants, the IR region appeared to be more conserved than the LSC and SSC regions [15,34]. The noncoding regions appeared to be more variable globally than the coding regions in the cp genomes of Rubiaceae species.…”

Comparative genomics of figworts (Scrophularia, Scrophulariaceae), with implications for the evolution of Scrophularia and Lamiales

“…Such conservatism is expected considering the low substitution rate in chloroplasts and the presumed recent age of divergence among them. Similar findings have also been detected in many other closely related taxa, such as genera or tribes (Choi et al, 2016;Huang et al, 2016;Kaila et al, 2016;Yang et al, 2016;Li et al, 2017;Zeng et al, 2017).…”

Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

“…Of these regions, ndh F– rpl 32 has long been a popular region in phylogenetic studies of angiosperms [44,45]. Meanwhile, psb M– trn D and trn S– trn G are also noted as highly variable in Liliaceae [46] and occasionally used in low-level phylogenetic analyses ( Scabiosa : [47]; Solms-laubachia : [48]). The resolution of recent divergences in monocots would benefit considerably by the inclusion of any or all of these highly variable regions.…”