[1] |
Mukherjee SK. 1949. The mango and its wild relatives. Science and Culture 26:5−9 |
[2] |
Singh NK, Mahato AK, Jayaswal PK, Singh A, Singh S, et al. 2016. Origin, diversity and genome sequence of mango ( Mangifera indica L.). Indian Journal of History of Science 51:1 doi: 10.16943/ijhs/2016/v51i2.2/48449 |
[3] |
Vasanthaiah HKN, Ravishankar KV, Mukunda GK. 2007. Mango. In Fruits and Nuts. Genome Mapping and Molecular Breeding in Plants, ed. Kole C. Berlin, Heidelberg: Springer. pp. 303−23. doi: 10.1007/978-3-540-34533-6_16 |
[4] |
FAOSTAT. 2022. Haosheng. www.fao.org/faostat/en/#data/QCL |
[5] |
Hou D. 1978. Florae Malesianae praecursores LVI. Anacardiaceae. Blumea: Biodiversity, Evolution and Biogeography of Plants 24:1−41 |
[6] |
Kostermans AJGH, Bompard JM. 1993. The mangoes: their botany, nomenclature, horticulture and utilization. London: Academic Press |
[7] |
Bompard JM. 2009. Taxonomy and systematics. The mango: Botany, production and uses. Wallingford: CAB International. pp. 19-41. doi: 10.1079/9781845934897.0019 |
[8] |
Mango Genome Consortium, Bally IS, Bombarely A, Chambers AH, Cohen Y, et al. 2021. The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality. BMC Plant Biology 21:1−18 doi: 10.1186/s12870-021-02858-1 |
[9] |
Mukherjee S, Litz RE. 2009. Introduction: botany and importance. In The mango: Botany, production and uses. Wallingford, UK: CABI. pp. 1−18. doi: 10.1079/9781845934897.0001 |
[10] |
Eiadthong W, Yonemori K, Sugiura A, Utsunomiya N, Subhadrabandhu S. 1999. Analysis of phylogenetic relationships in Mangifera by restriction site analysis of an amplified region of cpDNA. Scientia horticulturae 80:145−55 doi: 10.1016/S0304-4238(98)00222-2 |
[11] |
Bompard JM. 1993. The genus Mangifera re-discovered: the potential contribution of wild species to mango cultivation. Acta Horticulturae 341:69−77 doi: 10.17660/actahortic.1993.341.5 |
[12] |
Iyer CPA. 1991. Recent advances in varietal improvement in mango. Acta Horticulturae 291:109−32 doi: 10.17660/actahortic.1991.291.14 |
[13] |
Fitmawati F, Harahap SP, Sofiyanti N. 2017. Phylogenetic analysis of mango ( Mangifera) in Northern Sumatra based on gene sequences of cpDNA trnL-F intergenic spacer. Biodiversitas Journal of Biological Diversity 18:715−19 doi: 10.13057/biodiv/d180238 |
[14] |
Fitmawati, Hartana A. 2010. Phylogenetic study of Mangifera laurina and its related species using cpDNA trnL-F spacer markers. HAYATI Journal of Biosciences 17:9−14 doi: 10.4308/hjb.17.1.9 |
[15] |
Hidayat T, Pancoro A, Kusumawaty D. 2011. Utility of K gene to assess evolutionary relationship of genus (Anacardiaceae) in Indonesia and Thailand. Biotropia: The Southeast Asian Journal of Tropical Biology 18(2):74−80 |
[16] |
Fitmawati F, Hayati I, Sofiyanti N. 2016. Using ITS as a molecular marker for Mangifera species identification in Central Sumatra. Biodiversitas Journal of Biological Diversity 17(2):635−56 doi: 10.13057/biodiv/d170238 |
[17] |
Schnell RJ, Knight RJ Jr. 1993. Genetic relationships among Mangifera spp. based on RAPD markers. Acta Horticulturae 341:86−92 doi: 10.17660/actahortic.1993.341.7 |
[18] |
Yonemori K, Honsho C, Kanzaki S, Eiadthong W, Sugiura A. 2002. Phylogenetic relationships of Mangifera species revealed by ITS sequences of nuclear ribosomal DNA and a possibility of their hybrid origin. Plant Systematics and Evolution 231:59−75 doi: 10.1007/s006060200011 |
[19] |
Niu Y, Gao C, Liu J. 2021. Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes. PeerJ 9:e10774 doi: 10.7717/peerj.10774 |
[20] |
Niu Y, Gao C, Liu J. 2022. Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes. BMC Genomics 23:147 doi: 10.1186/s12864-022-08383-1 |
[21] |
Corriveau JL, Coleman AW. 1988. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. American Journal of Botany 75:1443−58 doi: 10.2307/2444695 |
[22] |
Mukherjee. S. 1949. A monograph on the genus Mangifera. Lloydia 22:73−136 |
[23] |
Teo LL, Kiew R, Set O, Lee SK, Gan YY. 2002. Hybrid status of kuwini, Mangifera odorata Griff. (Anacardiaceae) verified by amplified fragment length polymorphism. Molecular Ecology 11:1465−69 doi: 10.1046/j.1365-294x.2002.01550.x |
[24] |
Matra DD, Fathoni MAN, Majiidu M, Wicaksono H, Sriyono A, et al. 2021. The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm. Scientific Reports 11:19766 doi: 10.1038/s41598-021-99381-y |
[25] |
Warschefsky E. 2018. The evolution and domestication genetics of the mango genus, mangifera (Anacardiaceae). Thesis. Florida International University, Miami, Florida. doi: 10.25148/etd.FIDC006564 |
[26] |
Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, et al. 2010. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 10:61 doi: 10.1186/1471-2148-10-61 |
[27] |
Singh N, Mahato A, Sharma N, Gaikwad K, Srivastava M, et al. A draft genome of the king of fruit, mango (Mangifera indica L.). Proc. Plant and Animal Genome XXII Conference, San Diego, USA, 2014. |
[28] |
Singh NK, Mahato AK, Jayaswal PK, Singh S, Singh N, et al. 2018. A Reference genome assembly of the mango variety Amrapali (Mangifera indica L.). Proc. Plant and Animal Genome XXVI Conference, San Diego, USA, January 13−17, 2018. https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/30811 |
[29] |
Wang P, Luo Y, Huang J, Gao S, Zhu G, et al. 2020. The genome evolution and domestication of tropical fruit mango. Genome Biology 21:60 doi: 10.1186/s13059-020-01959-8 |
[30] |
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 |
[31] |
Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in ecology & evolution 24:332−40 doi: 10.1016/j.tree.2009.01.009 |
[32] |
Jo S, Kim HW, Kim YK, Sohn JY, Cheon SH, et al. 2017. The complete plastome sequences of Mangifera indica L. (Anacardiaceae). Mitochondrial DNA Part B 2:698−700 doi: 10.1080/23802359.2017.1390407 |
[33] |
Nock CJ, Waters DLE, Edwards MA, Bowen SG, Rice N, et al. 2011. Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnology Journal 9:328−33 doi: 10.1111/j.1467-7652.2010.00558.x |
[34] |
Furtado A. 2014. DNA extraction from vegetative tissue for next-generation sequencing. In Cereal genomics. Methods in Molecular Biology, ed. Henry R, Furtado A. Vol 1099. Totowa, NJ: Humana Press. pp. 1-5. doi: 10.1007/978-1-62703-715-0_1 |
[35] |
Moner AM, Furtado A, Henry RJ. 2018. Chloroplast phylogeography of AA genome rice species. Molecular Phylogenetics and Evolution 127:475−87 doi: 10.1016/j.ympev.2018.05.002 |
[36] |
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 |
[37] |
Rabah SO, Lee C, Hajrah NH, Makki RM, Alharby HF, et al. 2017. Plastome sequencing of ten nonmodel crop species uncovers a large insertion of mitochondrial DNA in cashew. The Plant Genome 10:plantgenome2017.03.0020 doi: 10.3835/plantgenome2017.03.0020 |
[38] |
Wicke S, Naumann J. 2018. Molecular evolution of plastid genomes in parasitic flowering plants. In Advances in botanical research, ed. Chaw SM, Jansen RK. vol. 85. UK: Academic Press. pp. 315−47. doi: 10.1016/bs.abr.2017.11.014 |
[39] |
Li Z, De La Torre AR, Sterck L, Cánovas FM, Avila C, et al. 2017. Single-copy genes as molecular markers for phylogenomic studies in seed plants. Genome Biology and Evolution 9:1130−47 doi: 10.1093/gbe/evx070 |
[40] |
Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772 doi: 10.1038/nmeth.2109 |
[41] |
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 |
[42] |
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 |
[43] |
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 |
[44] |
Zhang C, Rabiee M, Sayyari E, Mirarab S. 2018. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC bioinformatics 19:153 doi: 10.1186/s12859-018-2129-y |
[45] |
Zhang N, Zeng L, Shan H, Ma H. 2012. Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms. New Phytologist 195:923−37 doi: 10.1111/j.1469-8137.2012.04212.x |
[46] |
Zhang Y, Ou KW, Huang GD, Lu YF, Yang GQ, et al. 2020. The complete chloroplast genome sequence of Mangifera sylvatica Roxb. (Anacardiaceae) and its phylogenetic analysis. Mitochondrial DNA Part B 5:738−39 doi: 10.1080/23802359.2020.1715286 |
[47] |
Liu S, Wang X, Xie L, Tan M, Li Z, et al. 2016. Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis. Molecular Ecology Resources 16:470−79 doi: 10.1111/1755-0998.12472 |
[48] |
Rieseberg LH, Soltis D. 1991. Phylogenetic consequences of cytoplasmic gene flow in plants. Evolutionary Trends in Plants 5(1):65−84 |
[49] |
Ananda G, Norton S, Blomstedt C, Furtado A, Møller B, et al. 2021. Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes. The Plant Genome 14:e20123 doi: 10.1002/tpg2.20123 |
[50] |
Moner AM, Furtado A, Henry RJ. 2020. Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production. BMC Plant Biology 20:472 doi: 10.1186/s12870-020-02689-6 |
[51] |
Guyeux C, Charr JC, Tran HT, Furtado A, Henry RJ, et al. 2019. Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species. PloS ONE 14:e0216347 doi: 10.1371/journal.pone.0216347 |
[52] |
Healey A, Lee DJ, Furtado A, Henry RJ. 2018. Evidence of inter-sectional chloroplast capture in Corymbia among sections Torellianae and Maculatae. Australian Journal of Botany 66:369−78 doi: 10.1071/BT18028 |
[53] |
Liu X, Wang Z, Shao W, Ye Z, Zhang J. 2017. Phylogenetic and taxonomic status analyses of the Abaso section from multiple nuclear genes and plastid fragments reveal new insights into the North America origin of Populus (Salicaceae). Frontiers in Plant Science 7:2022 doi: 10.3389/fpls.2016.02022 |
[54] |
Stegemann S, Keuthe M, Greiner S, Bock R. 2012. Horizontal transfer of chloroplast genomes between plant species. Proceedings of the National Academy of Sciences of the United States of America 109:2434−38 doi: 10.1073/pnas.1114076109 |
[55] |
Smith RL, Sytsma KJ. 1990. Evolution of Populus nigra (sect. Aigeiros): introgressive hybridization and the chloroplast contribution of Populus alba (sect. Populus). American Journal of Botany 77:1176−87 doi: 10.2307/2444628 |
[56] |
Tsitrone A, Kirkpatrick M, Levin DA. 2003. A model for chloroplast capture. Evolution 57:1776−82 doi: 10.1111/j.0014-3820.2003.tb00585.x |
[57] |
Bally ISE, Akem CN, Dillon NL, Grice C, Lakhesar D, et al. 2010. Screening and breeding for genetic resistance to anthracnose in mango. Acta Horticulturae 992:239−44 doi: 10.17660/actahortic.2013.992.31 |
[58] |
Warschefsky EJ, von Wettberg EJB. 2019. Population genomic analysis of mango ( Mangifera indica) suggests a complex history of domestication. New Phytologist 222:2023−37 doi: 10.1111/nph.15731 |
[59] |
Rhodes L, Maxted N. 2016. Mangifera casturi. The IUCN Red List of Threatened Species 2016. doi: 10.2305/IUCN.UK.2016-3.RLTS.T32059A61526819.en |
[60] |
Li D, Gan G, Li W, Li W, Jiang Y, et al. 2021. Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids. Mitochondrial DNA Part B 6:351−57 doi: 10.1080/23802359.2020.1866450 |
[61] |
Xin Y, Yu WB, Eiadthong W, Cao Z, Li Q, et al. 2023. Comparative analyses of 18 complete chloroplast genomes from eleven Mangifera species (Anacardiaceae): sequence characteristics and phylogenomics. Horticulturae 9:86 doi: 10.3390/horticulturae9010086 |