Amiryousefi A, Hyvönen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of chloroplast genomes. An online program to visualize the junction sites of chloroplast genomes. Bioinform 34:3030–3031. https://doi.org/10.1093/bioinformatics/bty220

Article  CAS  Google Scholar 

Bi G, Luan X, Yan J (2023) ORPA: a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes. J Genet Genomics 51:352–358. https://doi.org/10.1016/j.jgg.2023.08.006

Article  PubMed  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao Z, Qu Y, Song Y, Xin P (2024) Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae). Gene. https://doi.org/10.1016/j.gene.2024.148259

Article  PubMed  Google Scholar 

Darshetkar AM, Khedkar SM, Barvkar VT, Nadaf AB, Sardesai MM, Kotkar HM (2024) Chloroplast genome sequence of Tectaria coadunata (Tectariaceae), plastome features, mutational hotspots and comparative analysis. Braz J Bot. https://doi.org/10.1007/s40415-023-00979-5

Article  Google Scholar 

Dong W, Xu C, Cheng T, Lin K, Zhou S (2013) Sequencing angiosperm plastid genomes made easy: a complete set of universal primers and a case study on the phylogeny of Saxifragales. Genome Biol Evol 5:989–997. https://doi.org/10.1093/gbe/evt063

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 1987:10

Google Scholar 

Ge L, Shen L, Chen Q, Li X, Zhang L (2017) The complete chloroplast genome sequence of Hydrocotyle sibthorpioides (Apiales: Araliaceae). Mitochondrial DNA B 2:29–30. https://doi.org/10.1080/23802359.2016.1241676

Article  Google Scholar 

Govaerts R, Nic Lughadha E, Black N, Turner R, Paton A (2021) The World checklist of vascular plants, a continuously updated resource for exploring global plant diversity. Sci Data 8:215

Article  PubMed  PubMed Central  Google Scholar 

Greiner S, Lehwark P, Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res 47:W59–W64. https://doi.org/10.1093/nar/gkz238

Grierson AJC, Long DG (1999) Flora of Bhutan: including a record of plants from Sikkim. Volume 2, Part 2 [Angiospermae: Umberlliferae - Labiatae]. Royal Botanic Garden, Royal Government of Bhutan, Edinburgh, Thimphu

Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518–522. https://doi.org/10.1093/molbev/msx281

Article  CAS  PubMed  Google Scholar 

Kang JS, Giang VN, Park HS, Park YS, Cho W, Nguyen VB, Shim H, Waminal NE, Park JY, Kim HH, Yang TJ (2023) Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure. Sci Rep 13:22325. https://doi.org/10.1038/s41598-023-49830-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim K, Nguyen VB, Dong J, Wang Y, Park JY, Lee SC, Yang TJ (2017) Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species. Sci Rep 7:4917. https://doi.org/10.1038/s41598-017-05218-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kumari R, Brahma G, Rajak S, Singh M, Kumar S (2016) Antimicrobial activity of green silver nanoparticles produced using aqueous leaf extract of Hydrocotyle rotundifolia. Orient Pharm Exp Med 16:195–201. https://doi.org/10.1007/s13596-016-0236-8

Article  Google Scholar 

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29:4633–4642. https://doi.org/10.1093/nar/29.22.4633

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee B, Park J (2021) The complete chloroplast genome of Zoysia matrella (L.) Merr. isolated in Korea (Poaceae): investigation of intraspecific variations on chloroplast genomes. Mitochondrial DNA B 6:572–574. https://doi.org/10.1080/23802359.2021.1875907

Article  Google Scholar 

Li Q, Li Y, Song J, Xu H, Xu J, Zhu Y, Li X, Gao H, Dong L, Qian J, Sun C (2014) High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy. New Phytol 204:1041–1049. https://doi.org/10.1111/nph.12966

Article  CAS  PubMed  Google Scholar 

Maddison WP, Knowles LL (2006) Inferring Phylogeny despite incomplete lineage sorting. Syst Biol 55:21–30

Article  PubMed  Google Scholar 

Manzanilla V, Kool A, Nguyen Nhat L, Van Nong H, Le Thi TH, De Boer HJ (2018) Phylogenomics and barcoding of Panax: toward the identification of ginseng species. BMC Evol Biol 18:44. https://doi.org/10.1186/s12862-018-1160-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mao L, Zou Q, Sun Z, Dong Q, Cao X (2023) Insights into chloroplast genome structure, intraspecific variation, and Phylogeny of Cyclamen species (Myrsinoideae). Sci Rep 13:87. https://doi.org/10.1038/s41598-022-27163-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Ann Harikrishna J (2017) Codon usage and codon pair patterns in non-grass monocot genomes. Ann Bot 120:893–909. https://doi.org/10.1093/aob/mcx112

Article  CAS  PubMed  PubMed Central  Google Scholar 

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 32:268–274. https://doi.org/10.1093/molbev/msu300

Article  CAS  PubMed  Google Scholar 

Nguyen VB, Park HS, Lee SC, Lee J, Park JY, Yang TJ (2017) Authentication markers for five major Panax species developed via comparative analysis of complete chloroplast genome sequences. J Agric Food Chem 65:6298–6306. https://doi.org/10.1021/acs.jafc.7b00925

Article  CAS  PubMed  Google Scholar 

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34:3299–3302. https://doi.org/10.1093/molbev/msx248

Article  CAS  PubMed  Google Scholar 

Schwarz G (1978) Estimating the dimension of a model. Ann Stat 461–464

Senapati A, Chetri BK, Mitra S, Shelke RG, Rangan L (2023) Decoding the complete chloroplast genome of Cissus quadrangularis: insights into molecular structure, comparative genome analysis and mining of mutational hotspot regions. Physiol Mol Biol Plants. https://doi.org/10.1007/s12298-023-01312-w

Article  PubMed  PubMed Central  Google Scholar 

Shelke RG, Rangan L (2022) The whole chloroplast genome of Mesua ferrea: insight into the dynamic pattern of evolution and its comparison with species from recently diverged families. Gene 846:146866. https://doi.org/10.1016/j.gene.2022.146866

Article  CAS  PubMed  Google Scholar 

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:W6–W11. https://doi.org/10.1093/nar/gkx391

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang D, Zhang Y, Zhang Z, Zhu J, Yu J (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteom Bioinform 8:77–80. https://doi.org/10.1016/S1672-0229(10)60008-3

Article  CAS  Google Scholar 

Wang Y, Jiang D, Guo K, Zhao L, Meng F, Xiao J, Niu Y, Sun Y (2023) Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species. BMC Genom Data 24:3. https://doi.org/10.1186/s12863-023-01104-x

Article  CAS  PubMed