http://orcid.org/0000-0003-4248-9943
Abstract
Iris tectorum (I. tectorum) has a high medicinal value that belongs to the family Iridaceae. Here, we reported the complete chloroplast (cp) genome sequences of I. tectorum, which was 153,199 bp in length. The cp genome was characterized by a typical quadripartite structure composed of an LSC (82,779 bp) and an SSC (18,562 bp) region interspersed by a pair of 25,929 bp IR regions, and it contained 87 protein-coding genes, 8 rRNAs, 38 tRNAs. A maximum-likelihood (ML) phylogenetic tree indicated that I. tectorum was closely related to Iris gatesii.
Keywords:
Iris tectorum is a perennial herb, which belongs to the family Iridaceae. It originated in central China and Japan and is mainly distributed in central and southern China. Its rhizome is frequently used to treat inflammation, cough, and pharyngitis in China (Yang et al. Citation2015). So far, no complete chloroplast (cp) genome of I. tectorum has been reported, hindering molecular research of I. tectorum based on cp genome. Therefore, we assembled and characterized the complete cp genome of I. tectorum. This study will provide genomic resources for species identification, molecular biology, and phylogenetic studies of I. tectorum.
Young fresh leaves of an individual plant of Ligustrum quihoui were collected from Tianjin City (117.06°E, 38.96°N), China. The voucher specimens were deposited in Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, under the voucher number of YW2019. DNA isolation was carried out according to the standard protocol of Extract Genomic DNA Kit. Then, the library was sequenced with a paired-end read length of 2 × 150 bp on Illumina HiSeq X Ten platform (Illumina, San Diego, CA). The paired-end reads were assembled into a circular contig using NOVOPlasty 2.6.3 (Dierckxsens et al. Citation2017) with k-mer length of 39. The cp genome of I. tectorum was annotated using GeSeq (Tillich et al. Citation2017), coupled with manual correction for start and stop codons of protein-coding genes. Finally, the complete cp genome was submitted to GenBank under accession number MT103435.
The cp genome of I. tectorum is 153,199 bp in length, including an LSC region of 82,779 bp, an SSC region of 18,562 bp, and a pair of IRs regions of 25,929 bp. In addition, a total of 133 genes were annotated, including 87 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. Overall, the cp genome features of I. tectorum were consistent with other land plants in terms of genomic structure (Cui et al. Citation2019; Yang et al. Citation2019; Yu et al. Citation2019).
To help us understand the phylogenetic position of I. tectorum in family Iridaceae, I. tectorum and other 6 Iridaceae cp genome sequences available in GenBank were used to reconstruct the phylogenetic tree. The protein-coding genes were extracted, aligned separately, and recombined to construct a matrix using PhyloSuite_v1.1.15 (Zhang et al. Citation2019). ML analyses were inferred using IQ-TREE (Nguyen et al. Citation2015) under the model automatically selected by IQ-TREE. The result indicated that I. tectorum was closely related to Iris gatesii ().
Figure 1. ML phylogenetic tree of Iridaceae inferred from protein-coding genes of cp genomes. The Scutellaria baicalensis was set as the outgroup. The numbers associated with each node are bootstrap support values for ML analyses.
Disclosure statement
No potential conflict of interest was reported by the author(s).
References
- Cui Y, Nie L, Sun W, Xu Z, Wang Y, Yu J, Yao H. 2019. Comparative and phylogenetic analyses of ginger (Zingiber officinale) in the family Zingiberaceae based on the complete chloroplast genome. Plants (Basel). 8(8):283.
- Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18.
- Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274.
- Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11.
- Yang Z, Huang Y, An W, Zheng X, Huang S, Liang L. 2019. Sequencing and structural analysis of the complete chloroplast genome of the medicinal plant Lycium chinense Mill. Plants (Basel). 8(4):87.
- Yang M, Yang X, An J, Xiao W, Wang Z, Huang W, Yang Z, Li F. 2015. Comparative pharmacokinetic profiles of tectorigenin in rat plasma by UPLC-MS/MS after oral administration of Iris tectorum Maxim extract and pure tectoridin. J Pharm Biomed Anal. 114:34–41.
- Yu X, Tan W, Zhang H, Gao H, Wang W, Tian X. 2019. Complete chloroplast genomes of Ampelopsis humulifolia and Ampelopsis japonica: molecular structure, comparative analysis, and phylogenetic analysis. Plants (Basel). 8(10):410.
- Zhang D, Gao F, Jakovlic I, Zou H, Zhang J, Li WX, Wang GT. 2019. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355.