A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales)

Abstract

The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 454 sequencing system and Sanger sequencing method to trace the evolutionary pattern in the tribe Parideae of the family Melanthiaceae (Liliales). The circular double-stranded cpDNA of P. verticillata (157,379 bp) consists of two inverted repeat regions each of 28,373 bp, a large single copy of 82,726 bp, and a small single copy of 17,907 bp. Gene content and order are generally similar to the previously reported cpDNA sequences within the order Liliales. However, we found that trnI_CAU was triplicated in P. verticillata. In addition, cemA is suspected to be a pseudogene due to the presence of internal stop codons created by poly(A) insertion and single small CA repeats. Such changes were not found in previously examined cpDNAs of the Melanthiaceae or other families of the Liliales, suggesting that such features are unique to the tribe Parideae of Melanthiaceae. The characteristics of P. verticillata cpDNA will provide useful information for uncovering the evolution within Paris and for further research of plastid genome evolution and phylogenetic studies in Liliales.

Keywords: Liliales; Melanthiaceae; Paris verticillata; cemA pseudogenization; chloroplast genome; trnI_CAU triplication.

Fig. 1.—

Photographs of Paris verticillata. (A) Young plant, (B) plant with flower, and (C) close up of flower.

Fig. 2.—

Map of the Paris verticillata chloroplast genome. Genes shown outside of the outer circle are transcribed counterclockwise, whereas those shown inside are transcribed clockwise. The thick lines in small circles indicate the IR regions. The asterisks indicate those genes with introns. # indicates triplicated genes.

Fig. 3.—

Illustration of trnI_CAU composition in Paris verticillata. (A) Positions of the trnI_CAU copies. (B) The nucleotide sequence of the rpl23-ycf2 IGS of P. verticillata, in which three tandem repeat units are highlighted in different colors. The bold italic characters indicate the sequences of trnI_CAU.

Fig. 4.—

The alignment of partial cemA sequences among Paris verticillata and related taxa. (A) Alignment of partial nucleotide sequences of cemA. The poly(A) sequences are underlined. The colored boxes show the SSR. (B) Alignment of partial amino acid sequences of cemA. The asterisks indicate stop codons. The letters shaded in color show differences in the amino acid compositions of the cemA genes among species. The underlined characters show amino acid sequences that are similar among P. verticillata and other species.

Fig. 5.—

Phylogenetic tree inferred by RAxML using nucleotide sequences of 76 protein-encoding regions from 40 species. Bootstrap values (>50) are shown above the branches. The light green color box shows the eudicots group whereas the light gray color box indicates the monocots species. The names in the right side of phylogenetic tree represent the classification of species at order level.