[1]

Eurlings MCM, Gravendeel B. 2005. TrnL-trnF sequence data imply paraphyly of Aquilaria and Gyrinops (Thymelaeaceae) and provide new perspectives for agarwood identification. Plant Systematics and Evolution 254:1−12

doi: 10.1007/s00606-005-0312-x
[2]

Hashim YZHY, Kerr PG, Abbas P, Mohd Salleh H. 2016. Aquilaria spp. (agarwood) as source of health beneficial compounds: a review of traditional use, phytochemistry and pharmacology. Journal of Ethnopharmacology 189:331−60

doi: 10.1016/j.jep.2016.06.055
[3]

Takamatsu S, Ito M. 2020. Agarotetrol in agarwood: its use in evaluation of agarwood quality. Journal of Natural Medicines 74:98−105

doi: 10.1007/s11418-019-01349-w
[4]

López-Sampson A, Page T. 2018. History of use and trade of agarwood. Economic Botany 72:107−29

doi: 10.1007/s12231-018-9408-4
[5]

Adam AZ, Lee SY, Mohamed R. 2017. Pharmacological properties of agarwood tea derived from Aquilaria (Thymelaeaceae) leaves: an emerging contemporary herbal drink. Journal of Herbal Medicine 10:37−44

doi: 10.1016/j.hermed.2017.06.002
[6]

Liu Y, Chen H, Yang Y, Zhang Z, Wei J, et al. 2013. Whole-tree agarwood-inducing technique: an efficient novel technique for producing high-quality agarwood in cultivated Aquilaria sinensis trees. Molecules 183:3086−106

doi: 10.3390/molecules18033086
[7]

Ahmad Mokhtar AM, Mohd Zain HH, Mohammed Muayad TA. 2021. Overview of medicinal properties and toxicities of agarwood species. Educatum Journal of Science, Mathematics and Technology 8:1−16

doi: 10.37134/ejsmt.vol8.2.1.2021
[8]

Tsuyuki H, Roberts E. 1965. Zone electrophoretic comparison of muscle myogens and blood proteins of artificial hybrids of Salmonidae with their parental species. Journal of the Fisheries Board of Canada 22:767−73

doi: 10.1139/f65-067
[9]

Yin Y, Jiao L, Dong M, Jiang X, Zhang S. 2016. Wood resources, identification, and utilization of agarwood in China. In Agarwood, ed. Mohamed R. Singapore: Springer. pp. 21–38. doi:10.1007/978-981-10-0833-7_2

[10]

Wyn L, Anak N. 2010. Wood for the trees: a review of the agarwood (Gaharu) trade in Malaysia. Malaysia: Traffic Southeast Asia. 108 pp.

[11]

Uddin MS, Mukul SA, Khan MASA, Alamgir M, Harun MY, et al. 2008. Small-scale agar (Aquilaria agallocha Roxb.) based cottage enterprises in Maulvibazar district of Bangladesh: production, marketing and potential contribution to rural development. Small-scale Forestry 7:139−49

doi: 10.1007/s11842-008-9046-2
[12]

Sy EY, Melgar AGB. 2024. The online agarwood trade and seizure analysis in the philippines. Journal of Nature Studies 22(2):12−26

[13]

Eurlings MCM, van Beek HH, Gravendeel B. 2010. Polymorphic microsatellites for forensic identification of agarwood (Aquilaria crassna). Forensic Science International 197:30−34

doi: 10.1016/j.forsciint.2009.12.017
[14]

Naef R. 2011. The volatile and semi-volatile constituents of agarwood, the infected heartwood of Aquilaria species: a review. Flavour and Fragrance Journal 26:73−87

doi: 10.1002/ffj.2034
[15]

Dahham SS, Hassan LEA, Ahamed MBK, Majid ASA, Majid AMSA, et al. 2016. In vivo toxicity and antitumor activity of essential oils extract from agarwood (Aquilaria crassna). BMC Complementary and Alternative Medicine 16:236

doi: 10.1186/s12906-016-1210-1
[16]

Wu Z, Gu C, Tembrock LR, Zhang D, Ge S. 2017. Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species. PLoS One 12:e0177553

doi: 10.1371/journal.pone.0177553
[17]

Takamatsu T, Baslam M, Inomata T, Oikawa K, Itoh K, et al. 2018. Optimized method of extracting rice chloroplast DNA for high-quality plastome resequencing and de novo assembly. Frontiers in Plant Science 9:266

doi: 10.3389/fpls.2018.00266
[18]

Zhao J, Zhang X, Hong Y, Liu Y. 2016. Chloroplast in plant-virus interaction. Frontiers in Microbiology 7:1565

doi: 10.3389/fmicb.2016.01565
[19]

Ding H, Han S, Ye Y, Bi D, Zhang S, et al. 2022. Ten plastomes of Crassula (Crassulaceae) and phylogenetic implications. Biology 11:1779

doi: 10.3390/biology11121779
[20]

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 11:576124

doi: 10.3389/fgene.2020.576124
[21]

Sheng J, Yan M, Wang J, Zhao L, Zhou F, et al. 2021. The complete chloroplast genome sequences of five Miscanthus species, and comparative analyses with other grass plastomes. Industrial Crops and Products 162:113248

doi: 10.1016/j.indcrop.2021.113248
[22]

Xie C, An W, Liu S, Huang Y, Yang Z, et al. 2021. Comparative genomic study on the complete plastomes of four officinal Ardisia species in China. Scientific Reports 11:22239

doi: 10.1038/s41598-021-01561-3
[23]

Yan XL, Kan SL, Wang MX, Li YY, Tembrock LR, et al. 2024. Genetic diversity and evolution of the plastome in allotetraploid cotton (Gossypium spp.). Journal of Systematics and Evolution 00:Early View

doi: 10.1111/jse.13070
[24]

Zhang S, Han S, Bi D, Yang J, Ge W, et al. 2024. Intraspecific and intrageneric genomic variation across three Sedum species (Crassulaceae): a plastomic perspective. Genes 15:444

doi: 10.3390/genes15040444
[25]

Kan J, Zhang S, Wu Z, Bi D. 2024. Exploring plastomic resources in Sempervivum (Crassulaceae): implications for phylogenetics. Genes 15:441

doi: 10.3390/genes15040441
[26]

Wang J, Liao X, Li Y, Ye Y, Xing G, et al. 2023. Comparative plastomes of Curcuma alismatifolia (Zingiberaceae) reveal diversified patterns among 56 different cut-flower cultivars. Genes 14:1743

doi: 10.3390/genes14091743
[27]

Wang J, Kan S, Liao X, Zhou J, Tembrock LR, et al. 2024. Plant organellar genomes: much done, much more to do. Trends in Plant Science 29:754−69

doi: 10.1016/j.tplants.2023.12.014
[28]

Farah AH, Lee SY, Gao Z, Yao TL, Madon M, et al. 2018. Genome size, molecular phylogeny, and evolutionary history of the tribe Aquilarieae (Thymelaeaceae), the natural source of agarwood. Frontiers in Plant Science 9:712

doi: 10.3389/fpls.2018.00712
[29]

Lee SY, Turjaman M, Chaveerach A, Subasinghe S, Fan Q, et al. 2022. Phylogenetic relationships of Aquilaria and Gyrinops (Thymelaeaceae) revisited: evidence from complete plastid genomes. Botanical Journal of the Linnean Society 200:344−59

doi: 10.1093/botlinnean/boac014
[30]

Porebski S, Bailey LG, Baum BR. 1997. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter 15:8−15

doi: 10.1007/BF02772108
[31]

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
[32]

Shi L, Chen H, Jiang M, Wang L, Wu X, et al. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Research 47:W65−W73

doi: 10.1093/nar/gkz345
[33]

Greiner S, Lehwark P, Bock R. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47:W59−W64

doi: 10.1093/nar/gkz238
[34]

Li H, Guo Q, Xu L, Gao H, Liu L, et al. 2023. CPJSdraw: analysis and visualization of junction sites of chloroplast genomes. PeerJ 11:e15326

doi: 10.7717/peerj.15326
[35]

Darling ACE, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research 14:1394−403

doi: 10.1101/gr.2289704
[36]

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
[37]

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, et al. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34:3299−302

doi: 10.1093/molbev/msx248
[38]

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 29:4633−42

doi: 10.1093/nar/29.22.4633
[39]

Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−85

doi: 10.1093/bioinformatics/btx198
[40]

Xia X. 2017. DAMBE6: new tools for microbial genomics, phylogenetics, and molecular evolution. Journal of Heredity 108:431−37

doi: 10.1093/jhered/esx033
[41]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772−80

doi: 10.1093/molbev/mst010
[42]

Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24:1586−91

doi: 10.1093/molbev/msm088
[43]

Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312−13

doi: 10.1093/bioinformatics/btu033
[44]

Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539−42

doi: 10.1093/sysbio/sys029
[45]

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 37:291−94

doi: 10.1093/molbev/msz189
[46]

Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67:901−04

doi: 10.1093/sysbio/syy032
[47]

Hishamuddin MS, Lee SY, Ng WL, Ramlee SI, Lamasudin DU, et al. 2020. Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships. Scientific Reports 10:13034

doi: 10.1038/s41598-020-70030-0
[48]

Zheng G, Wei L, Ma L, Wu Z, Gu C, et al. 2020. Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships. Plant Molecular Biology 102:659−76

doi: 10.1007/s11103-020-00972-6
[49]

Abdullah, Mehmood F, Shahzadi I, Waseem S, Mirza B, et al. 2020. Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): comparative analyses and identification of mutational hotspots. Genomics 112:581−91

doi: 10.1016/j.ygeno.2019.04.010
[50]

Wang J, Fu GF, Tembrock LR, Liao XZ, Ge S, et al. 2023. Mutational meltdown or controlled chain reaction: The dynamics of rapid plastome evolution in the hyperdiversity of Poaceae. Journal of Systematics and Evolution 61:328−44

doi: 10.1111/jse.12854
[51]

Zhou J, Zhang S, Wang J, Shen H, Ai B, et al. 2021. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Scientific Reports 11:9471

doi: 10.1038/s41598-021-88160-4
[52]

He L, Zhang Y, Lee SY. 2021. Complete plastomes of six species of Wikstroemia (Thymelaeaceae) reveal paraphyly with the monotypic genus Stellera. Scientific Reports 11:13608

doi: 10.1038/s41598-021-93057-3
[53]

Qian S, Zhang Y, Lee SY. 2021. Comparative analysis of complete chloroplast genome sequences in Edgeworthia (Thymelaeaceae) and new insights into phylogenetic relationships. Frontiers in Genetics 12:643552

doi: 10.3389/fgene.2021.643552
[54]

Bakewell MA, Shi P, Zhang J. 2007. More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences of the United States of America 104:7489−94

doi: 10.1073/pnas.0701705104
[55]

Ai B, Gao Y, Zhang X, Tao J, Kang M, et al. 2015. Comparative transcriptome resources of eleven Primulina species, a group of 'stone plants' from a biodiversity hot spot. Molecular Ecology Resources 15:619−32

doi: 10.1111/1755-0998.12333
[56]

Hurst LD. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends in Genetics 18:486−87

doi: 10.1016/S0168-9525(02)02722-1
[57]

Zhang YH, Huang Y, Li ZM, Zhang SD. 2019. Characterization of the complete chloroplast genome of the vulnerable agarwood tree, Aquilaria yunnanensis (Thymelaeaceae). Conservation Genetics Resources 11:161−64

doi: 10.1007/s12686-018-0989-0
[58]

Guo L, Guo S, Xu J, He L, Carlson JE, et al. 2020. Phylogenetic analysis based on chloroplast genome uncover evolutionary relationship of all the nine species and six cultivars of tree peony. Industrial Crops and Products 153:112567

doi: 10.1016/j.indcrop.2020.112567
[59]

Sun J, Wang Y, Liu Y, Xu C, Yuan Q, et al. 2020. Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species. Scientific Reports 10:11466

doi: 10.1038/s41598-020-67943-1
[60]

Li E, Liu K, Deng R, Gao Y, Liu X, et al. 2023. Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae). BMC Plant Biology 23:32

doi: 10.1186/s12870-023-04034-z
[61]

Liang H, Zhang Y, Deng J, Gao G, Ding C, et al. 2020. The complete chloroplast genome sequences of 14 Curcuma species: insights into genome evolution and phylogenetic relationships within Zingiberales. Frontiers in Genetics 11:802

doi: 10.3389/fgene.2020.00802
[62]

Dong WL, Wang RN, Zhang NY, Fan WB, Fang MF, et al. 2018. Molecular evolution of chloroplast genomes of orchid species: insights into phylogenetic relationship and adaptive evolution. International Journal of Molecular Sciences 19:716

doi: 10.3390/ijms19030716
[63]

Du F, Li Y, Xu K. 2023. Phylogeny and evolution of Cocconeiopsis (Cocconeidaceae) as revealed by complete chloroplast and mitochondrial genomes. International Journal of Molecular Sciences 25:266

doi: 10.3390/ijms25010266
[64]

Ahmad S, Kaul T, Chitkara P, Raza K. 2023. Comparative insight into rice chloroplasts genome: mutational phylogenomics reveals Echinochloa oryzicola as the ongoing progenitor of rice. Genetic Resources and Crop Evolution 70:869−85

doi: 10.1007/s10722-022-01471-x
[65]

Tomitani A, Okada K, Miyashita H, Matthijs HCP, Ohno T, et al. 1999. Chlorophyll b and phycobilins in the common ancestor of cyanobacteria and chloroplasts. Nature 400:159−62

doi: 10.1038/22101
[66]

Li S, Duan W, Zhao J, Jing Y, Feng M, et al. 2022. Comparative analysis of chloroplast genome in Saccharum spp. and related members of 'Saccharum Complex'. International Journal of Molecular Sciences 23:7661

doi: 10.3390/ijms23147661
[67]

Yan L, Wang H, Huang X, Li Y, Yue Y, et al. 2022. Chloroplast genomes of genus Tilia: comparative genomics and molecular evolution. Frontiers in Genetics 13:925726

doi: 10.3389/fgene.2022.925726