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.

Keywords: Amana; Erythronium; Liliaceae; Tulipa; chloroplast genome; genomic structure; phylogenomics.

Figure 1

Distribution map of all six currently recognized Amana species. One of the species, A. edulis, is widespread and found primarily at low elevations (yellow-shaded areas). The other five species are narrow endemics restricted to disjunct montane habitats (filled symbols).

Figure 2

Gene map of the Amana edulis chloroplast genome. Genes shown on the outside of the circle are transcribed clockwise, and genes inside are transcribed counter-clockwise. Genes belonging to different functional groups are color-coded. The darker gray in the inner corresponds to the GC content, and the lighter gray to the AT content. The cp genomes of other five Amana species are slightly different with that of A. edulis in nucleotide composition, but do not vary in terms of gene content or order.

Figure 3

Comparison of the LSC, IR, and SSC junction positions among six Amana chloroplast genomes.

Figure 4

Nucleotide variability (Pi) values of six Amana chloroplast genomes.

Figure 5

Phylogenetic relationships among Amana, Erythronium, Tulipa and within Amana inferred from maximum likelihood (ML) and Bayesian inference (BI) based on complete genome sequences (162,505 bp). Numbers above the lines represent ML bootstrap values and BI posterior probabilities. A phylogenetic tree resulting from analysis of 74 protein-coding genes (78,815 bp) was fully congruent with this topology.