Insight into infrageneric circumscription through complete chloroplast genome sequences of two Trillium species

Abstract

Genomic events including gene loss, duplication, pseudogenization and rearrangement in plant genomes are valuable sources for exploring and understanding the process of evolution in angiosperms. The family Melanthiaceae is distributed in temperate regions of the Northern Hemisphere and divided into five tribes (Heloniadeae, Chionographideae, Xerophylleae, Melanthieae and Parideae) based on the molecular phylogenetic analyses. At present, complete chloroplast genomes of the Melanthiaceae have been reported from three species. In the previous genomic study of Liliales, atrnI-CAU gene duplication event was reported fromParis verticillata, a member of Parideae. To clarify the significant genomic events of the tribe Parideae, we analysed the complete chloroplast genome sequences of twoTrilliumspecies representing two subgenera:TrilliumandPhyllantherum InTrillium tschonoskii(subgenusTrillium), the circular double-stranded cpDNA sequence of 156 852 bp consists of two inverted repeat (IR) regions of 26 501 bp each, a large single-copy (LSC) region of 83 981 bp and a small single-copy (SSC) region of 19 869 bp. The chloroplast genome sequence ofT. maculatum(subgenusPhyllantherum) is 157 359 bp in length, consisting of two IRs (25 535 bp), one SSC (19 949 bp) and one LSC (86 340 bp), and is longer than that ofT. tschonoskii The results showed that the cpDNAs of Parideae are highly conserved across genome structure, gene order and contents. However, the chloroplast genome ofT. maculatumcontained a 3.4-kb inverted sequence betweenndhCandrbcLin the LSC region, and it was a unique feature for subgeneraPhyllantherum In addition, we found three different types of gene duplication in the intergenic spacer betweenrpl23andycf2containingtrnI-CAU, which were in agreement with the circumscription of subgenera and sections in Parideae excludingT. govanianum These genomic features provide informative molecular markers for identifying the infrageneric taxa ofTrilliumand improve our understanding of the evolution patterns of Parideae in Melanthiaceae.

Keywords: Chloroplast genome; Trillium maculatum; Trillium tschonoskii, trnI-CAU; comparative genomics; gene duplication; single inversion.

Figure 1.

Gene maps and summary of the T. tschonoskii Maxim. and T. maculatum Raf. chloroplast genomes. IR, inverted repeat; LCS, large single-copy region; SSC, small single-copy region.

Figure 2.

Comparison of the IR boundaries among five species within Melanthiaceae.

Figure 3.

Confirmation of inversion (3492 bp) between ndhC and rbcL in the genus Trillium. (A) Design of primer to amplify junction regions between atpB and rbcL regions. The positions of atpB and rbcL genes in LSC regions are drawn based on the sequence assembly results of T. tschonoskii, T. maculatum in this study (red text). *The data downloaded from the NCBI. The forward primer I1F contains the sequence in atpB region. The sequence of the reverse primer (I1R) is located in the rbcL gene. Polymerase chain reaction amplification of IGS between atpB and rbcL. Relationships of Parideae lineages followed the phylogenetic trees of S. C. Kim, J. S. Kim, W. C. Mark, F. F. Michael and J. H. Kim (unpublished data). (B) Primers were designed to amplify junction regions between trnV-UAC and rbcL regions. The positions of trnV-UAC and rbcL genes in LSC regions are drawn based on the sequence assembly results of T. tschonoskii, T. maculatum in this study (red text). *The data downloaded from the NCBI. The forward primer I2R contains the sequence in trnV-UAC region. The sequence of the reverse primer I1R is located in the rbcL gene. Polymerase chain reaction amplification of IGS between trnV-UAC and rbcL. Relationships of Parideae lineages followed the phylogenetic trees of S. C. Kim, J. S. Kim, W. C. Mark, F. F. Michael and J. H. Kim (unpublished data).

Figure 4.

Average p-distance across five classes of genomic regions between two Trillium.

Figure 5.

Summary of three types of trnI-CAU gene duplication in the tribe Parideae. *Including tandem repeats.