Characterization of the Complete Chloroplast Genome of Lour. 1790 (Helicteriodeae: Malvaceae)

Overview

Journal Mitochondrial DNA B Resour

Date 2024 May 6

PMID 38707209

Authors

Hoang Danh Nguyen

Minh Thiet Vu

Hoang Dang Khoa Do

Affiliations

Soon will be listed here.

Abstract

Lour. 1790 is a precious medicinal plant species, especially for treating chronic liver diseases. Genomic data on are limited. Therefore, this current study aimed to characterize the chloroplast genome of and reconstruct the phylogenetic relationship among Helicteroideae taxa. Consequently, the complete chloroplast genome of was 163,404 bp in length and contained 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). Notably, two introns of gene of were lost in comparison to that of other Helicteroideae species. The phylogenetic tree based on chloroplast genomes of eleven Helicteroideae species revealed that was closely related to species. In conclusion, our study described the first complete chloroplast genome of , which is essential for tracing evolutionary history in the Helicteroideae subfamily.

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PMID: 39359376 PMC: 11445884. DOI: 10.1080/23802359.2024.2410441.

References

Cauz-Santos L, Munhoz C, Rodde N, Cauet S, Santos A, Penha H . The Chloroplast Genome of (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales. Front Plant Sci. 2017; 8:334. PMC: 5345083. DOI: 10.3389/fpls.2017.00334. View

Wu L, Wu M, Cui N, Xiang L, Li Y, Li X . Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria. Chin Med. 2021; 16(1):52. PMC: 8256587. DOI: 10.1186/s13020-021-00460-z. View

Posada D . jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008; 25(7):1253-6. DOI: 10.1093/molbev/msn083. View

Zhang W, Sun Y, Liu J, Xu C, Zou X, Chen X . DNA barcoding of Oryza: conventional, specific, and super barcodes. Plant Mol Biol. 2020; 105(3):215-228. PMC: 7858216. DOI: 10.1007/s11103-020-01054-3. View

Huelsenbeck J, Ronquist F . MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001; 17(8):754-5. DOI: 10.1093/bioinformatics/17.8.754. View

Wang S, Ding S, Deng R, Shi W, Zhang H . The complete chloroplast genome of (Malvaceae). Mitochondrial DNA B Resour. 2021; 7(1):10-11. PMC: 8667874. DOI: 10.1080/23802359.2021.2005487. View

Dierckxsens N, Mardulyn P, Smits G . NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017; 45(4):e18. PMC: 5389512. DOI: 10.1093/nar/gkw955. View

Cai J, Ma P, Li H, Li D . Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications. PLoS One. 2015; 10(11):e0142705. PMC: 4643919. DOI: 10.1371/journal.pone.0142705. View

Dang V, Dang M, Hoang N . V.S.Dang (Malvaceae, Helicteroideae), a new species from southern Vietnam. PhytoKeys. 2020; 166:87-95. PMC: 7644645. DOI: 10.3897/phytokeys.166.57647. View

10.

Dugas D, Hernandez D, Koenen E, Schwarz E, Straub S, Hughes C . Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Sci Rep. 2015; 5:16958. PMC: 4655330. DOI: 10.1038/srep16958. View

11.

Wang J, Moore M, Wang H, Zhu Z, Wang H . Plastome evolution and phylogenetic relationships among Malvaceae subfamilies. Gene. 2020; 765:145103. DOI: 10.1016/j.gene.2020.145103. View

12.

Alverson W, Whitlock B, Nyffeler R, Bayer C, Baum D . Phylogeny of the core Malvales: evidence from ndhF sequence data. Am J Bot. 1999; 86(10):1474-86. View

13.

Lee H, Jansen R, Chumley T, Kim K . Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol. 2007; 24(5):1161-80. DOI: 10.1093/molbev/msm036. View

14.

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

15.

Tan F, Banerjee A, Deng J, Feng H, Feng Y, Shu Y . Characterization of the complete chloroplast genome of (Malvaceae), an endemic and vulnerable tree species of China. Mitochondrial DNA B Resour. 2023; 8(1):57-60. PMC: 9817124. DOI: 10.1080/23802359.2022.2160669. View

16.

Wong X, Law D, Wang Z, Ramaiya S, Lee S . The complete chloroplast genome sequence of (Malvaceae) and its phylogenetic position. Mitochondrial DNA B Resour. 2022; 7(9):1709-1712. PMC: 9518260. DOI: 10.1080/23802359.2022.2123256. View

17.

Geng L, Jiang T, Chen X, Li Q, Ma J, Hou W . Plastome structure, phylogeny and evolution of plastid genes in Reevesia (Helicteroideae, Malvaceae). J Plant Res. 2024; 137(4):589-604. DOI: 10.1007/s10265-024-01547-y. View

18.

Jin J, Yu W, Yang J, Song Y, dePamphilis C, Yi T . GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21(1):241. PMC: 7488116. DOI: 10.1186/s13059-020-02154-5. View

19.

Williams A, Friso G, van Wijk K, Sloan D . Extreme variation in rates of evolution in the plastid Clp protease complex. Plant J. 2018; 98(2):243-259. DOI: 10.1111/tpj.14208. View

20.

Ni Z, Ye Y, Bai T, Xu M, Xu L . Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion. Molecules. 2017; 22(9). PMC: 6151703. DOI: 10.3390/molecules22091528. View