[1]

Chang X, Yang Z, Zhang X, Zhang F, Huang X, et al. 2022. Transcriptome-wide identification of WRKY transcription factors and their expression profiles under different stress in Cynanchum thesioides. PeerJ 10:e14436

doi: 10.7717/peerj.14436
[2]

Endress ME, Liede-Schumann S, Meve U. 2014. An updated classification for Apocynaceae. Phytotaxa 159:175−194
[3]

Yao X, Zhang ZR, Yang JB, Corlett RT, Li DZ, et al. 2025. An updated plastome phylogeny and molecular dating of Apocynaceae, with an emphasis on histories of biogeography and diversification in tropical and subtropical Asia. Journal of Systematics and Evolution 63:1519−1535

doi: 10.1111/jse.70014
[4]

Daniell H, Jin S, Zhu XG, Gitzendanner MA, Soltis DE, et al. 2021. Green giant—a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. Plant Biotechnology Journal 19:430−447

doi: 10.1111/pbi.13556
[5]

Chu X, Li L, Zhu G. 2025. A review of the molecular mechanisms of the crop cytoplasmic genome and maternal genetic effects. Resources Data Journal 4:357−372

doi: 10.50908/rdj.4.0_357
[6]

Wang M, Lin H, Lin H, Du P, Zhang S. 2025. From species to varieties: how modern sequencing technologies are shaping medicinal plant identification. Genes 16:16

doi: 10.3390/genes16010016
[7]

Qin HH, Cai J, Liu CK, Zhou RX, Price M, et al. 2023. The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution. BMC Plant Biology 23:9

doi: 10.1186/s12870-022-04027-4
[8]

Fishbein M, Livshultz T, Straub SCK, Simões AO, Boutte J, et al. 2018. Evolution on the backbone: Apocynaceae phylogenomics and new perspectives on growth forms, flowers, and fruits. American Journal of Botany 105:495−513

doi: 10.1002/ajb2.1067
[9]

Wang Y, Zhang CF, Ochieng Odago W, Jiang H, Yang JX, et al. 2023. Evolution of 101 Apocynaceae plastomes and phylogenetic implications. Molecular Phylogenetics and Evolution 180:107688

doi: 10.1016/j.ympev.2022.107688
[10]

Long JL, Zhang N, Wu Y, Zhang YP, Wu ZK. 2022. The complete chloroplast genome of Periploca forrestii (Apocynaceae), a traditional Chinese medicinal plant. Mitochondrial DNA Part B: Resources 7:468−470

doi: 10.1080/23802359.2022.2049459
[11]

Portis E, Comino C, Lanteri S, Lenzi A, Lombardi P, et al. 2004. Genetic relationships between oleander (Nerium oleander L.) accessions by means of AFLP profiling. Acta Horticulturae 651:173−180
[12]

Zibbu G, Batra A. 2014. In vivo and in vitro RAPD analysis in Apocynaceae family: population growing in different regions of Rajasthan, India. Journal of Pharmaceutical Sciences and Innovation 3:230−239

doi: 10.7897/2277-4572.033145
[13]

Lazzaro L, Sarracco E, Benesperi R, Coppi A. 2018. A probable anthropic origin of Nerium oleander L. (Apocynaceae) population in Montecristo island (Italy, Tuscany): evidence from loci polymorphism and ISSR analysis. Caryologia 71:50−57

doi: 10.1080/00087114.2017.1410634
[14]

Straub SCK, Parks M, Weitemier K, Fishbein M, Cronn RC, et al. 2012. Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. American Journal of Botany 99:349−364

doi: 10.3732/ajb.1100335
[15]

Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19:11−15
[16]

Jin JJ, Yu WB, Yang JB, Song Y, DePamphilis CW, et al. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21:241

doi: 10.1186/s13059-020-02154-5
[17]

Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31:3350−3352

doi: 10.1093/bioinformatics/btv383
[18]

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, et al. 2017. GeSeq—versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45:W6−W11

doi: 10.1093/nar/gkx391
[19]

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647−1649

doi: 10.1093/bioinformatics/bts199
[20]

Lohse M, Drechsel O, Kahlau S, Bock R. 2013. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research 41:W575−W581

doi: 10.1093/nar/gkt289
[21]

Huang L, Yu H, Wang Z, Xu W. 2024. CPStools: a package for analyzing chloroplast genome sequences. iMetaOmics 1:e25

doi: 10.1002/imo2.25
[22]

Gerdol M, De Moro G, Venier P, Pallavicini A. 2015. Analysis of synonymous codon usage patterns in sixty-four different bivalve species. PeerJ 3:e1520

doi: 10.7717/peerj.1520
[23]

Ji H, Liu J, Chen Y, Yu X, Luo C, et al. 2024. Bioinformatic analysis of codon usage bias of HSP20 genes in four cruciferous species. Plants 13:468

doi: 10.3390/plants13040468
[24]

Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, et al. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources 20:348−355

doi: 10.1111/1755-0998.13096
[25]

Zhang Z. 2022. KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences. Genomics, Proteomics & Bioinformatics 20:536−540

doi: 10.1016/j.gpb.2021.12.002
[26]

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29:4633−4642

doi: 10.1093/nar/29.22.4633
[27]

Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−2585

doi: 10.1093/bioinformatics/btx198
[28]

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. 2004. VISTA: computational tools for comparative genomics. Nucleic Acids Research 32:W273−W279

doi: 10.1093/nar/gkh458
[29]

Amiryousefi A, Hyvönen J, Poczai P. 2018. IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34:3030−3031

doi: 10.1093/bioinformatics/bty220
[30]

Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, et al. 2021. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. American Journal of Botany 108:1143−1165

doi: 10.1002/ajb2.1697
[31]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772−780

doi: 10.1093/molbev/mst010
[32]

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972−1973

doi: 10.1093/bioinformatics/btp348
[33]

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, et al. 2020. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Molecular biology and evolution 37:291−294

doi: 10.1093/molbev/msz189
[34]

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453−4455

doi: 10.1093/bioinformatics/btz305
[35]

Letunic I, Bork P. 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49:W293−W296

doi: 10.1093/nar/gkab301
[36]

Daniell H, Lin CS, Yu M, Chang WJ. 2016. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology 17:134

doi: 10.1186/s13059-016-1004-2
[37]

Menezes APA, Resende-Moreira LC, Buzatti RSO, Nazareno AG, Carlsen M, et al. 2018. Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences. Scientific Reports 8:2210

doi: 10.1038/s41598-018-20189-4
[38]

Hu Q, Wu J, Fan C, Luo Y, Liu J, et al. 2024. Comparative analysis of codon usage bias in the chloroplast genomes of eighteen Ampelopsideae species (Vitaceae). BMC Genomic Data 25:80
[39]

Dai J, Liu Q, Xu X, Tan Z, Lin Y, et al. 2023. Comparative and phylogenetic analysis of the complete chloroplast genomes of Uncaria (Rubiaceae) species. Frontiers in Plant Science 14:1271689

doi: 10.3389/fpls.2023.1271689
[40]

Yang X, Wang Y, Gong W, Li Y. 2024. Comparative analysis of the codon usage pattern in the chloroplast genomes of Gnetales species. International Journal of Molecular Sciences 25:10622

doi: 10.3390/ijms251910622
[41]

Zhang J, Feng M. 2025. Analysis of the codon usage bias pattern in the chloroplast genomes of Chloranthus species (Chloranthaceae). Genes 16:186

doi: 10.3390/genes16020186
[42]

Zhao X, Lan X, Wang Z, Li D, Sun W, et al. 2026. Comparative chloroplast genomics of Cypripedioideae: structural divergence, adaptive evolution, and phylogenomic insights. Frontiers in Plant Science 16:1723281

doi: 10.3389/fpls.2025.1723281
[43]

Zhang Y, Fan Y, Lv X, Zeng X, Zhang Q, et al. 2023. Deficiency in NDH-cyclic electron transport retards heat acclimation of photosynthesis in tobacco over day and night shift. Frontiers in Plant Science 14:1267191

doi: 10.3389/fpls.2023.1267191
[44]

Yamori W, Shikanai T. 2016. Physiological functions of cyclic electron transport around photosystem I in sustaining photosynthesis and plant growth. Annual Review of Plant Biology 67:81−106

doi: 10.1146/annurev-arplant-043015-112002
[45]

Tiller N, Bock R. 2014. The translational apparatus of plastids and its role in plant development. Molecular Plant 7:1105−1120

doi: 10.1093/mp/ssu022
[46]

Robbins EHJ, Kelly S. 2025. Widespread adaptive evolution in angiosperm photosystems provides insight into the evolution of photosystem II repair. The Plant Cell 37:koae281

doi: 10.1093/plcell/koae281
[47]

Shen L, Chen S, Liang M, Qu S, Feng S, et al. 2024. Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae. BMC Plant Biology 24:424

doi: 10.1186/s12870-024-04999-5
[48]

Wu L, Nie L, Wang Q, Xu Z, Wang Y, et al. 2021. Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae. Scientific Reports 11:14643

doi: 10.1038/s41598-021-94137-0
[49]

Zheng C, Fan J, Caraballo-Ortiz MA, Liu Y, Liu T, et al. 2022. The complete chloroplast genome and phylogenetic relationship of Apocynum pictum (Apocynaceae), a Central Asian shrub and second-class national protected species of western China. Gene 830:146517

doi: 10.1016/j.gene.2022.146517
[50]

Wei N, Pérez-Escobar OA, Musili PM, Huang WC, Yang JB, et al. 2021. Plastome evolution in the hyperdiverse genus Euphorbia (Euphorbiaceae) using phylogenomic and comparative analyses: large-scale expansion and contraction of the inverted repeat region. Frontiers in Plant Science 12:712064

doi: 10.3389/fpls.2021.712064
[51]

Chen X, Cheng Z, Duan Z, Xi D, Luo B. 2025. Characterization and phylogenetic analysis of the chloroplast genome of Vicia kulingana (Fabaceae). Mitochondrial DNA Part B 10:342−346

doi: 10.1080/23802359.2025.2485168
[52]

Li DM, Pan YG, Wu XY, Zou SP, Wang L, et al. 2024. Comparative chloroplast genomics, phylogenetic relationships and molecular markers development of Aglaonema commutatum and seven green cultivars of Aglaonema. Scientific Reports 14:11820

doi: 10.1038/s41598-024-62586-y
[53]

Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. 2011. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Molecular Biology 76:273−297

doi: 10.1007/s11103-011-9762-4
[54]

Sururi ZF, Nururrahmani A, Sihombing ME, Hidayat T. 2025. The role of chloroplast DNA markers (psbA) in maintaining the position of Lemnoideae. Biota: Jurnal Ilmiah Ilmu-Ilmu Hayat 10:71−79

doi: 10.24002/biota.v10i1.8906
[55]

Özdemir Değirmenci F. 2026. Evaluating SSR marker transferability and plastid barcode variation in native Populus and Salix species of Türkiye. PeerJ 14:e20936

doi: 10.7717/peerj.20936
[56]

Abdullah, Haram D, Yan R, Ma M, Naz I, et al. 2025. Inverted repeats dynamics shape Asclepiadoideae (Apocynaceae) chloroplast genomes: effects on genome size, gene content, structural arrangement, and mutation rate. BMC Genomics 26:697

doi: 10.1186/s12864-025-11839-9