Abstract
Abstract
Background
Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.
Methods and results
We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.
Conclusions
The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.
Funder
Research Incubation Fund Project of Shandong Academy of Chinese Medicine
Major Special Project of Scientific and Technological Cooperation of Bijie City
Medical and Health Science and Technology Development Project of Shandong Province
Key Research and Development Program of Shandong Province
Publisher
Springer Science and Business Media LLC
Subject
Genetics,Molecular Biology,General Medicine
Reference56 articles.
1. Liu Y, Hui RK, Deng RN, Wang JJ, Wang M, Li ZY (2012) Abnormal male meiosis explains pollen sterility in the polyploid medicinal plant Pinellia ternata (Araceae). Genet Mol Res 11(1):112–120. https://doi.org/10.4238/2012.January.17.1
2. Zhu Y, Zhu G, Guo Q, Zhu Z, Wang C, Liu Z (2013) A comparative proteomic analysis of Pinellia ternata leaves exposed to heat stress. Int J Mol Sci 14(10):20614–20634. https://doi.org/10.3390/ijms141020614
3. Kozlov VA, Zhuravkin IN, Tsyrlova IG (1978) Comparative analysis of the migratory capacity of hematopoietic stem cells and of immunocompetent precursors after acute hypoxia and the administration of testosterone. Dokl Akad Nauk SSSR 239(3):747–749
4. Nauheimer L, Metzler D, Renner SS (2012) Global history of the ancient monocot family Araceae inferred with models accounting for past continental positions and previous ranges based on fossils. New Phytol 195(4):938–950. https://doi.org/10.1111/j.1469-8137.2012.04220.x
5. Renner SS, Zhang LB (2004) Biogeography of the Pistia clade (Araceae): based on chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference. Syst Biol 53(3):422–432. https://doi.org/10.1080/10635150490445904