Abstract
The first complete mitochondrial genome (mt) of Paraprenanthes diversifolia (Vaniot) N. Kilian (Cichorieae; Asteraceae) was sequenced and successfully assembled in this study. The full length of the mt genome is 360,751 bp, containing 73 genes (33 protein-coding genes, 29 tRNA genes, 6 rRNA genes, and 5 protein-coding genes containing internal stop codons). There are two pairs of long (over 1000 bp) repeat regions in the mt genome of P. diversifolia. The phylogenetic analysis indicated that P. diversifolia has a close relationship with other Lactucinae species.
Keywords: Mitochondrial genome, Paraprenanthes diversifolia, Asteraceae, Cichorieae, phylogenetics
Paraprenanthes diversifolia (Vaniot) N. Kilian belongs to Lactucinae (Cichorieae, Asteraceae) and is an endemic herbaceous plant mainly distributed in south-central and southeast of China (Shih 1988). In order to identify the taxonomic position of P. diversifolia and provide phylogenetic evidence for further study of Lactucinae based on mt sequences, we sequenced and assembled the complete mitochondrial (mt) genome of P. diversifolia.
The P. diversifolia specimen (ZZU2012-1845) was collected from Chongqing, China (N29°2′122″, E107°8′255″) and stored at the herbarium of School of Life Sciences, Zhengzhou University, Zhengzhou, China. The total DNA of P. diversifolia was extracted from the leaves of specimen using modified CTAB method (Wei et al. 2017) and then was purified by Wizard DNA clean-up system (Promega Corp., Madison, USA). The DNA sample was sequenced using Illumina HiSeq X Ten platform at Novogene Biotech Co. (Beijing, China). About 10.7 GB paired-end clean reads were generated and assembled using NOVOPlasty (Dierckxsens et al. 2016) software with reference sequences Diplostephium hartwegii Hieron. (NCBI accession no. NC_034354), Chrysanthemum boreale B. Fedtsch. (NC_039757) and Helianthus annuus L. (NC_023337). The Kmer number was estimated and selected as 35 using KmerGenie (Chikhi and Medvedev 2014). Other parameters were default settings. The assembled contigs were annotated and adjusted manually in Geneious Prime 2019.1.1 (https://www.geneious.com) with previously mentioned references plus Lactuca saligna L. (MK759657), L. serriola L. (MK820672) and L. sativa ‘Salinas’ L. (MK642355). All borders of 11 contigs were verified by PCR amplification and Sanger sequencing. Repeat regions (over 100 bp) were detected using Repeat Finder v1.0 in Geneious Prime.
The complete mt genome of P. diversifolia (NCBI accession no. MN661146) is circular and 360,751 bp in length with a GC content of 45.2%. The mt genome contains 73 genes, including 33 protein-coding genes, 29 tRNA genes, 6 rRNA genes and 5 protein-coding genes containing internal stop codons. The protein-coding genes consist of 9 NADH dehydrogenase genes, 1 cytochrome b gene, 3 cytochrome c oxidase genes, 4 cytochrome c biogenesis genes, 5 ATP synthase genes, 8 ribosomal proteins genes and 3 other genes. Additionally, there are four protein-coding genes (nad4, ccmFc, rps3 and cox2) having one intron and three (nad1, nad2 and nad7) having four introns. There are 26 repeat regions (over 100 bp) in the mt genome of P. diversifolia, including two pairs of repeat regions over 1000 bp. The sequence (containing dpo gene, position 173,401–180,661 bp) between two inverted repeat regions was found also having its reverse complimentary sequence existing in the mt genome.
Phylogenetic relationships among P. diversifolia and other 7 Asteraceae species were studied based on 23 mt protein-coding genes. The phylogenetic tree was constructed using RAxML-HPC2 on XSEDE from CIPRES Science Gateway website (Miller et al. 2010). The results showed that P. diversifolia is closely related to Lactuca species (Cichorieae). Other Asteraceae species from Anthemideae, Astereae and Heliantheae are sister groups of the species of Cichorieae. The phylogenetic analysis supported previous research based on the nrITS and chloroplast DNA (Gao et al. 2009; Kilian et al. 2017) (Figure 1).
Figure 1.
Phylogenetic tree of P. diversifolia and other 7 Asteraceae species based on 23 mt protein-coding genes using RAxML method. Bupleurum falcatum L. (Bupleureae, Apiaceae), Platycodon grandiflorus (Jacq.) A. DC. (Campanuloideae, Campanulaceae) and Codonopsis lanceolata (Siebold & Zucc.) Benth. & Hook.f. ex Trautv. (Campanuloideae, Campanulaceae) were set as outgroups. The numbers above the branches are bootstrap values.
Funding Statement
This work was supported by [grant 31700175] of The National Natural Science Foundation of China (to ZW).
Disclosure statement
No potential conflict of interest was reported by the author(s).
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