Skip to main content Skip to main navigation menu Skip to site footer
Responsive image
Issue: Vol. 737 No. 5: 21 Jan. 2026
Type: Article
Published: 2026-01-21
DOI: 10.11646/phytotaxa.737.5.1
Page range: 257-275
Abstract views: 23
PDF downloaded: 0

Plastid genome variation with phylogenetic implications within Anaphalis (Asteraceae: Gnaphalieae)

Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, School of Life Sciences, Jishou University, Jishou, Hunan 416000, China
Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, School of Life Sciences, Jishou University, Jishou, Hunan 416000, China
Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, School of Life Sciences, Jishou University, Jishou, Hunan 416000, China
Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, School of Life Sciences, Jishou University, Jishou, Hunan 416000, China
Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, School of Life Sciences, Jishou University, Jishou, Hunan 416000, China; Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013‐7012 U.S.A.
Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, School of Life Sciences, Jishou University, Jishou, Hunan 416000, China
Anaphalis Chloroplast genome Comparative analysis Phylogenomics Eudicots

Abstract

Anaphalis is the largest genus in tribe Gnaphalieae of Asteraceae in Asia, with more than 110 species distributed mainly in tropical to temperate Asia. The interspecific relationships and evolution within Anaphalis are complex and remain controversial, with little attention for their chloroplast evolution at the genomic level. In this study, we sequenced and assembled chloroplast genomes, performing comparative and phylogenetic analyses on 32 representative species of Anaphalis. Our results revealed that these chloroplast genomes exhibit a typically circular quadripartite structure ranging in length from 152,396 to 153,573 bp with a total of 131 to 132 genes, including 87 protein-coding, 36–37 tRNA, and 8 rRNA genes. The phylogenetic analyses suggested that Anaphalis is polyphyletic and nested with Helichrysum and Pseudognaphalium, which are clustered into two groups as clades I and II. The overall genome length of clade I was relatively smaller than that of clade II, possibly due to less insertion with more deletions in intergenic regions of the former. The trnT-GGU gene is presented as pseudogene in clade II but is absent in clade I. The rpl22 gene shows significantly higher positive selection from most species of clade I than those in clade II, probably related to environmental adaptations of species from clade I survived in high-altitude mountains. The results of the comparative and phylogenetic analyses provide valuable references for further research studies of classification, phylogenetic relationships and genomic adaptation of Anaphalis species.

References

  1. Abdullah, M.F., Heidari, P., Rahim, A., Ahmed, I. & Poczai, P. (2021) Pseudogenization of the chloroplast threonine (trnT-GGU) gene in the sunflower family (Asteraceae). Scientific Reports 11 (1): e21122. https://doi.org/10.1038/s41598-021-00510-4
  2. Abid, R. & Qaiser, M. (2007) Cypsela morphology of the genus Anaphalis DC. (Gnaphalieae—Asteraceae) from Pakistan. Pakistan Journal of Botany 39 (6): 1897–1906.
  3. Ahmed, I., Biggs, P.J., Matthews, P.J., Collins, L.J., Hendy, M.D. & Lockhart, P.J. (2012) Mutational dynamics of aroid chloroplast genomes. Genome Biology and Evolution 4: 1316–1323. https://doi.org/10.1093/gbe/evs110
  4. Anderberg, A.A. (1991) Taxonomy and phylogeny of the tribe Gnaphalieae (Asteraceae). Opera Botanica 104: 1–195. https://doi.org/10.1007/BF00937947
  5. Bao, J.Y., Lu, Y.C. & Bai, H.S. (2009) Quantitative and qualitative analysis on flavonoids in Anaphalis lactea Maxim. Journal of Molecular Science 25: 72–74.
  6. Bayer, R.J., Greber, D.G. & Bagnall, N.H. (2002) Phylogeny of Australian Gnaphalieae (Asteraceae) based on chloroplast and nuclear sequences, the trnL intron, trnL/trnF intergenic spacer, matK, and ETS. Systematic Botany 27 (4): 801–814. https://doi.org/10.1043/0363-6445-27.4.801
  7. Bayer, R.J., Breitwieser, I., Ward, J. & Puttock, C. (2007) Tribe Gnaphalieae. In: Kadereit, J.W. & Jeffrey, C. (eds.) The Families and Genera of Vascular Plants, vol. 8. Springer, Heidelberg, pp. 246–283.
  8. Beier, S., Thiel, T., Münch, T., Scholz, U. & Mascher, M. (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33 (16): 2583–2585. https://doi.org/10.1093/bioinformatics/btx198
  9. Bennetzen, J.L., Ma, J. & Devos, K.M. (2005) Mechanisms of recent genome size variation in flowering plants. Annals of Botany 95 (1): 127–132. https://doi.org/10.1093/aob/mci008
  10. Bergh, N.G. & Linder, H.P. (2009) Cape diversification and repeated out-of-southern-Africa dispersal in paper daisies (Asteraceae—Gnaphalieae). Molecular Phylogenetics and Evolution 51: 5–18. https://doi.org/10.1016/j.ympev.2008.09.001
  11. Bergh, N.G., Haiden, S.A. & Verboom, G.A. (2015) Molecular phylogeny of the ‘Cape snow’ genus Syncarpha (Asteraceae: Gnaphalieae) reveals a need for generic re-delimitation. South African Journal of Botany 100: 219–227. https://doi.org/10.1016/j.sajb.2015.05.023
  12. Birky, C.W. (1995) Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proceedings of the National Academy of Sciences of the United States of America 92 (25): 11331–11338. https://doi.org/10.1073/pnas.92.25.11331
  13. Blanco-Gavaldà, C., Galbany-Casals, M., Susanna, A., Andrés-Sánchez, S., Bayer, R.J., Brochmann, C., Cron, G.V., Bergh, N.G., Garcia-Jacas, N., Gizaw, A., Kandziora, M., Kolář, F., López-Alvarado, J., Leliaert, F., Letsara, R., Moreyra, L.D., Razafimandimbison, S.G., Schmickl, R. & Roquet, C. (2023) Repeatedly northwards and upwards: Southern African grasslands fuel the colonization of the African Sky Islands in Helichrysum (Compositae). Plants 12 (11): e2213. https://doi.org/10.3390/plants12112213
  14. Bolger, A.M., Lohse, M. & Usadel, B. (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
  15. Capella-Gutiérrez, S., Silla-Martínez, J.M. & Gabaldón, T. (2009) trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972–1973. https://doi.org/10.1093/bioinformatics/btp348
  16. Castle, J.C. (2011) SNPs occur in regions with less genomic sequence conservation. PloS One 6: e20660. https://doi.org/10.1371/journal.pone.0020660
  17. Chen, C., Chen, H., Zhang, Y., Thomas, H.R., Frank, M.H., He, Y. & Xia, R. (2020) TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Molecular Plant 13 (8): 1194–1202. https://doi.org/10.1016/j.molp.2020.06.009
  18. Chen, Y.S., Zhu, S.X. & Bayer, R.J. (2011) Gnaphalieae. In: Wu, C.Y., Raven, P.H. & Hong, D.Y. (eds.) Flora of China, vol. 20–21. Science Press, Beijing & Missouri Botanical Garden Press, St. Louis, pp. 774–818.
  19. Daniell, H., Lin, C.S., Yu, M. & Chang, W.J. (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology 17: e134. https://doi.org/10.1186/s13059-016-1004-2
  20. Dong, W.P., Liu, J., Yu, J., Wang, L. & Zhou, S. (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PloS One 7: e35071. https://doi.org/10.1371/journal.pone.0035071
  21. Doyle, J.J. & Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19 (1): 11–15.
  22. Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M. & Dubchak, I. (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Research 32 (suppl_2): W273–W279. https://doi.org/10.1093/nar/gkh458
  23. Galbany-Casals, M., Andrés-Sánchez, S., Garcia-Jacas, N., Susanna, A., Rico, E. & Martínez-Ortega, M.M. (2010) How many of Cassini anagrams should there be? Molecular systematics and phylogenetic relationships in the Filago group (Asteraceae, Gnaphalieae), with special focus on the genus Filago. Taxon 59: 1671–1689. https://doi.org/10.1002/tax.596003
  24. Galbany-Casals, M., Blanco-Moreno, J.M., Garcia-Jacas, N., Breitwieser, I. & Smissen, R.D. (2011) Genetic variation in Mediterranean Helichrysum italicum (Asteraceae; Gnaphalieae): do disjunct populations of subsp. microphyllum have a common origin? Plant Biology 13: 678–687. https://doi.org/10.1111/j.1438-8677.2010.00411.x
  25. Galbany-Casals, M., Garcia-Jacas, N., Sáez, L., Benedí, C. & Susanna, A. (2009) Phylogeny, biogeography, and character evolution in Mediterranean, Asiatic, and Macaronesian Helichrysum (Asteraceae, Gnaphalieae) inferred from nuclear phylogenetic analyses. International Journal of Plant Sciences 170 (3): 365–380. https://doi.org/10.1086/596332
  26. Galbany-Casals, M., Unwin, M., Garcia-Jacas, N., Smissen, R.D., Susanna, A. & Bayer, R.J. (2014) Phylogenetic relationships in Helichrysum (Compositae: Gnaphalieae) and related genera: Incongruence between nuclear and plastid phylogenies, biogeographic and morphological patterns, and implications for generic delimitation. Taxon 63 (3): 608–624. https://doi.org/10.12705/633.8
  27. Guan, B., Wen, J., Guo, H. & Liu, Y. (2024) Comparative and phylogenetic analyses based on the complete chloroplast genome of Cornus subg. Syncarpea (Cornaceae) species. Frontiers in Plant Science 15: e1306196. https://doi.org/10.3389/fpls.2024.1306196
  28. Guzmán-Díaz, S., Núñez, F.A.A., Veltjen, E., Asselman, P., Larridon, I. & Samain, M.S. (2022) Comparison of Magnoliaceae plastomes: Adding neotropical Magnolia to the discussion. Plants 11 (3): e448. https://doi.org/10.3390/plants11030448
  29. Huang, K., Li, B., Chen, X., Qin, C. & Zhang, X. (2024) Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis. Frontiers in Plant Science 15: e1430191. https://doi.org/10.3389/fpls.2024.1430191
  30. Huang, R., Xie, X., Chen, A., Li, F., Tian, E. & Chao, Z. (2021) The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences. BMC Genomics 22: e714. https://doi.org/10.1186/s12864-021-08008-z
  31. Jin, J.J., Yu, W.B., Yang, J.B., Song, Y., de Pamphilis, C.W., Yi, T.S. & Li, D.Z. (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21: e241. https://doi.org/10.1186/s13059-020-02154-5
  32. Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30 (4): 772–780. https://doi.org/10.1093/molbev/mst010
  33. Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P. & Drummond, A. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
  34. Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J. & Giegerich, R. (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29 (22): 4633–4642. https://doi.org/10.1093/nar/29.22.4633
  35. Lao, X.L., Meng, Y., Wu, J., Wen, J. & Nie, Z.L. (2024) Plastid genomes provide insights into the phylogeny and chloroplast evolution of the paper daisy tribe Gnaphalieae (Asteraceae). Gene 901: e148177. https://doi.org/10.1016/j.gene.2024.148177
  36. Lee, D.H., Cho, W.B., Choi, B.H. & Lee, J.H. (2017) Characterization of two complete chloroplast genomes in the tribe Gnaphalieae (Asteraceae): Gene loss or pseudogenization of trnT-GGU and implications for phylogenetic relationships. Horticultural Science and Technology 35 (6): 769–783. https://doi.org/10.12972/kjhst.20170081
  37. Li, D.M., Li, J., Wang, D.R., Xu, Y.C. & Zhu, G.F. (2021) Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). BMC Plant Biology 21: 1–24. https://doi.org/10.1186/s12870-021-03315-9
  38. Li, H., Guo, Q., Xu, L., Gao, H., Liu, L. & Zhou, X. (2023) CPJSdraw: analysis and visualization of junction sites of chloroplast genomes. PeerJ 11: e15326. https://doi.org/10.7717/peerj.15326
  39. Li, Q.Q., Zhang, Z.P., Aogan & Wen, J. (2024) Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications. Frontiers in Plant Science 15: e1349358. https://doi.org/10.3389/fpls.2024.1349358
  40. Li, W., Wang, L., Zuo, Y., Zhang, H., Zhang, X., Yang, L., Zhang, J., Zheng, F. & Deng, H. (2025) Organelle genomes reveal adaptive evolution and phylogenetic position of the endangered Primula mallophylla. Frontiers in Plant Science 16: e1653128. https://doi.org/10.3389/fpls.2025.1653128
  41. Li, Y., Zhang, L.N., Wang, T.X., Zhang, C.C., Wang, R.J., Zhang, D., Xie, Y.Q., Zhou, N.N., Wang, W.Z., Zhang, H.M., Hu, B., Li, W.H., Zhao, Q.Q., Wang, L.H. & Wu, X.W. (2022) The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses. Journal of Plant Research 135: 723–737. https://doi.org/10.1007/s10265-022-01417-5
  42. Ling, Y. (1979) Anaphalis DC. In: The editorial committee of Flora of China (eds.) Flora Reipublicae Popularis Sinicae, vol. 75. Science Press, Beijing, pp. 141–218.
  43. Liu, B.B., Campbell, C.S., Hong, D.Y. & Wen, J. (2020) Phylogenetic relationships and chloroplast capture in the Amelanchier-Malacomeles-Peraphyllum clade (Maleae, Rosaceae): Evidence from chloroplast genome and nuclear ribosomal DNA data using genome skimming. Molecular Phylogenetics and Evolution 147: e106784. https://doi.org/10.1016/j.ympev.2020.106784
  44. Lodhi, M.A., Ye, G.N., Weeden, N.F. & Reisch, B.I. (1994) A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Molecular Biology Reporter 12: 6–13. https://doi.org/10.1007/BF02668658
  45. Lyu, X. & Liu, Y. (2020) Nonoptimal codon usage is critical for protein structure and function of the master general amino acid control regulator CPC-1. mBio 11 (5): e2605–e2620. https://doi.org/10.1128/mBio.02605-20
  46. Nie, Z.L., Funk, V., Sun, H., Deng, T., Meng, Y. & Wen, J. (2013) Molecular phylogeny of Anaphalis (Asteraceae, Gnaphalieae) with biogeographic implications in the Northern Hemisphere. Journal of Plant Research 126 (1): 17–32. https://doi.org/10.1007/s10265-012-0506-6
  47. Nie, Z.L., Funk, V.A., Meng, Y., Deng, T., Sun, H. & Wen, J. (2016) Recent assembly of the global herbaceous flora: evidence from the paper daisies (Asteraceae: Gnaphalieae). New Phytologist 209 (4): 1795–1806. https://doi.org/10.1111/nph.13740
  48. Peden, J.F. (1999) Analysis of codon usage. PhD Thesis. University of Nottingham, 215 pp.
  49. Posada, D. (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25 (7): 1253–1256. https://doi.org/10.1093/molbev/msn083
  50. Rambaut, A., Drummond, A.J., Xie, D., Baele, G. & Suchard, M.A. (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67 (5): 901–904. https://doi.org/10.1093/sysbio/syy032
  51. Ramundo, S., Rahire, M., Schaad, O. & Rochaix, J.D. (2013) Repression of essential chloroplast genes reveals new signaling pathways and regulatory feedback loops in Chlamydomonas. Plant Cell 25: 167–186. https://doi.org/10.1105/tpc.112.103051
  52. Romero, H., Zavala, A. & Musto, H. (2000) Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Research 28 (10): 2084–2090. https://doi.org/10.1093/nar/28.10.2084
  53. Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D.L., Darling, A., Höhna, S. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61 (3): 539–542. https://doi.org/10.1093/sysbio/sys029
  54. Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E. & Sánchez-Gracia, A. (2017) DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution 34 (12): 3299–3302. https://doi.org/10.1093/molbev/msx248
  55. Sheng, J., Yan, M., Wang, J., Zhao, L., Zhou, F., Hu, Z., Jin, S. & Diao, Y. (2021) The complete chloroplast genome sequences of five Miscanthus species, and comparative analyses with other grass plastomes. Industrial Crops and Products 162: e113248. https://doi.org/10.1016/j.indcrop.2021.113248
  56. Sloan, D.B., Triant, D.A., Forrester, N.J., Bergner, L.M., Wu, M. & Taylor, D.R. (2013) A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae). Molecular Phylogenetics and Evolution 72: 82–89. https://doi.org/10.1016/j.ympev.2013.12.004
  57. Smissen, R.D. & Breitwieser, I. (2008) Species relationships and genetic variation in the New Zealand endemic Leucogenes (Asteraceae: Gnaphalieae). New Zealand Journal of Botany 46 (1): 65–76. https://doi.org/10.1080/00288250809509754
  58. Smissen, R.D., Bayer, R.J., Bergh, N.G., Breitwieser, I., Freire, S.E., Galbany-Casals, M. & Ward, J.M. (2020) A revised subtribal classification of Gnaphalieae (Asteraceae). Taxon 69 (4): 778–806. https://doi.org/10.1002/tax.12294
  59. Smissen, R.D., Breitwieser, I. & Ward, J.M. (2004) Phylogenetic implications of trans-specific chloroplast DNA sequence polymorphism in New Zealand Gnaphalieae (Asteraceae). Plant Systematics and Evolution 249: 37–53. https://doi.org/10.1007/s00606-004-0209-0
  60. Smissen, R.D., Galbany-Casals, M. & Breitwieser, I. (2011) Ancient allopolyploidy in the everlasting daisies (Asteraceae: Gnaphalieae): complex relationships among extant clades. Taxon 60 (3): 649–662. https://doi.org/10.1002/tax.603003
  61. Solís-Lemus, C., Yang, M. & Ané, C. (2016) Inconsistency of species tree methods under gene flow. Systematic Biology 65 (5): 843–851. https://doi.org/10.1093/sysbio/syw030
  62. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22 (21): 2688–2690. https://doi.org/10.1093/bioinformatics/btl446
  63. Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30 (9): 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
  64. Sun, B., Wang, H., Lu, M. & Tian, X. (2001) Volatile elements of Anaphalis margaritacea, a Chinese medicinal herb. Journal of Lanzhou University (Natural Sciences) 37: 66–71.
  65. Tillich, M., Lehwark, P., Pellizzer, T., Ulbricht-Jones, E.S., Fischer, A., Bock, R. & Greiner, S. (2017) GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45 (W1): W6–W11. https://doi.org/10.1093/nar/gkx391
  66. Wang, Y., Wen, F., Hong, X., Li, Z., Mi, Y. & Zhao, B. (2022) Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis. Frontiers in Plant Science 13: e1019831. https://doi.org/10.3389/fpls.2022.1019831
  67. Wu, J., Meng, Y., Huang, D.W., Liu, Z.H., Lao, X.L., Wen, J. & Nie, Z.L. (2025) Plastid genome variation with phylogenetic implications for the Helichrysum-Anaphalis-Pseudognaphalium (HAP) of the tribe Gnaphalieae (Asteraceae). Phytokeys 262: 203–221. https://doi.org/10.3897/phytokeys.262.153120
  68. Xu, X.M., Xu, H., Yang, Z., Wei, Z., Gu, J.Y., Liu, D.H., Liu, Q.R. & Zhu, S.X. (2024) Phylogeny, biogeography, and character evolution of Anaphalis (Gnaphalieae, Asteraceae). Frontiers in Plant Science 15: e1336229. https://doi.org/10.3389/fpls.2024.1336229
  69. Xu, X.M., Wei, Z., Sun, J.Z., Zhao, Q.F., Lu, Y., Wang, Z.L. & Zhu, S.X. (2023) Phylogeny of Leontopodium (Asteraceae) in China—with a reference to plastid genome and nuclear ribosomal DNA. Frontiers in Plant Science 14: e1163065. https://doi.org/10.3389/fpls.2023.1163065
  70. Yong, Q., Li, M., Li, Z., Luo, C., Zhang, J. & Bai, X. (2025) Complete chloroplast genomes of 13 species of the Impatiens genus for genomic features and phylogenetic relationships studies. Scientific Reports 15: e4258. https://doi.org/10.1038/s41598-025-87254-7
  71. Yuan, Y.P., Liu, Z. & Jin, D.Q. (2004) Study of curing tracheitis by Anaphalis lactea Maxim. on animals. Chinese Journal of Comparative Medicine 14: 172–175.
  72. Zhang, Z., Li, J., Zhao, X.Q., Wang, J., Wong, G.K. & Yu, J. (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics, Proteomics and Bioinformatics 4 (4): 259–263. https://doi.org/10.1016/S1672-0229(07)60007-2
  73. Zhao, S., Gao, X., Yu, X., Yuan, T., Zhang, G., Liu, C., Li, X., Wei, P., Li, X. & Liu, X. (2024) Comparative analysis of chloroplast genome of Meconopsis (Papaveraceae) provides insights into their genomic evolution and adaptation to high elevation. International Journal of Molecular Sciences 25: e2193. https://doi.org/10.3390/ijms25042193
  74. Zheng, S., Poczai, P., Hyvönen, J., Tang, J. & Amiryousefi, A. (2020) Chloroplot: an online program for the versatile plotting of organelle genomes. Frontiers in Genetics 11: e576124. https://doi.org/10.3389/fgene.2020.576124
  75. Zhou, M., Guo, J., Cha, J., Chae, M., Chen, S., Barral, J. M., Sachs, M. S. & Liu, Y. (2013) Nonoptimal codon usage affects expression, structure and function of clock protein FRQ. Nature 495: 111–115. https://doi.org/10.1038/nature11833
  76. Zou, X.H. & Ge, S. (2008) Conflicting gene trees and phylogenomics. Journal of Systematics and Evolution 46: 795–807. https://doi.org/10.3724/SP.J.1002.2008.08081

How to Cite

Huang, D.-W., Meng, Y., Wu, J., Liu, Z.-H., Wen, J. & Nie, Z.-L. (2026) Plastid genome variation with phylogenetic implications within Anaphalis (Asteraceae: Gnaphalieae). Phytotaxa 737 (5): 257–275. https://doi.org/10.11646/phytotaxa.737.5.1