[1]

Thorogood CJ, Ghazalli MN, Siti-Munirah MY, Nikong D, Kusuma YWC, et al. 2022. The king of fruits. Plants, People, Planet 4:538−547

doi: 10.1002/ppp3.10288
[2]

Shearman JR, Sonthirod C, Naktang C, Sangsrakru D, Yoocha T, et al. 2020. Assembly of the durian chloroplast genome using long PacBio reads. Scientific Reports 10(1):15980

doi: 10.1038/s41598-020-73549-4
[3]

Teh BT, Lim K, Yong CH, Ng CCY, Rao, SR, et al. 2017. The draft genome of tropical fruit durian (Durio zibethinus). Nature Genetics 49(11):1633−1641

doi: 10.1038/ng.3972
[4]

Nawae W, Naktang C, Charoensri S, U-thoomporn S, Narong N, et al. 2023. Resequencing of durian genomes reveals large genetic variations among different cultivars. Frontiers in Plant Science 14:1137077

doi: 10.3389/fpls.2023.1137077
[5]

Li W, Chen X, Yu J, Zhu Y. 2024. Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance. Science China Life Sciences 67(6):1266−1279

doi: 10.1007/s11427-024-2580-3
[6]

Ji X, Zhong Y, Zheng D, Xie S, Shi M et al. 2025. Chromosome-scale haploid genome assembly of Durio zibethinus KanYao. Scientific Data 12(1):384

doi: 10.1038/s41597-025-04656-y
[7]

Peska V, Garcia S. 2020. Origin, diversity, and evolution of telomere sequences in plants. Frontiers in Plant Science 11:117

doi: 10.3389/fpls.2020.00117
[8]

Shay JW, Wright WE. 2019. Telomeres and telomerase: three decades of progress. Nature Reviews Genetics 20(5):299−309

doi: 10.1038/s41576-019-0099-1
[9]

Zakian VA. 2012. Telomeres: the beginnings and ends of eukaryotic chromosomes. Experimental Cell Research 318(12):1456−1460

doi: 10.1016/j.yexcr.2012.02.015
[10]

Lan L, Hu H, Jia Y, Zhang X, Jia M, et al. 2025. Tips for improving genome annotation quality. Genomics Communications 2:e005

doi: 10.48130/gcomm-0025-0006
[11]

Zhou Y, Zhang J, Xiong X, Cheng Z, Chen F. 2022. De novo assembly of plant complete genomes. Tropical Plants 1:7

doi: 10.48130/tp-2022-0007
[12]

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
[13]

Dellaporta SL, Wood J, Hicks JB. 1983. A plant DNA minipreparation: version II. Plant Molecular Biology Reporter 1:19−21

doi: 10.1007/BF02712670
[14]

Marçais G, Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764−770

doi: 10.1093/bioinformatics/btr011
[15]

Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, et al. 2017. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33(14):2202−2204

doi: 10.1093/bioinformatics/btx153
[16]

Feng X, Cheng H, Portik D, Li H. 2022. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods 19(6):671−674

doi: 10.1038/s41592-022-01478-3
[17]

Guan D, McCarthy SA, Wood J, Howe K, Wang Y, et al. 2020. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36(9):2896−2898.

doi: 10.1093/bioinformatics/btaa025
[18]

Hu J, Fan J, Sun Z, Liu S. 2020. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36:2253−2255

doi: 10.1093/bioinformatics/btz891
[19]

Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, et al. 2016. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems 3:95−98

doi: 10.1016/j.cels.2016.07.002
[20]

Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, et al. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356(6333):92−95

doi: 10.1126/science.aal3327
[21]

Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, et al. 2018. Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Systems 6(2):256−258.e1

doi: 10.1016/j.cels.2018.01.001
[22]

Xu M, Guo L, Gu S, Wang O, Zhang R, et al. 2020. TGS-GapCloser: a fast and accurate gap closer for large genomes with low coverage of error-prone long reads. GigaScience 9(9):giaa094

doi: 10.1093/gigascience/giaa094
[23]

Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094−3100

doi: 10.1093/bioinformatics/bty191
[24]

Manni M, Berkeley MR, Seppey M, Zdobnov EM. 2021. BUSCO: assessing genomic data quality and beyond. Current Protocols 1:e323

doi: 10.1002/cpz1.323
[25]

Rhie A, Walenz BP, Koren S, Phillippy AM. 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology 21(1):245

doi: 10.1186/s13059-020-02134-9
[26]

Nevers Y, Warwick Vesztrocy A, Rossier V, Train CM, Altenhoff A, et al. 2025. Quality assessment of gene repertoire annotations with OMArk. Nature Biotechnology 43(1):124−133

doi: 10.1038/s41587-024-02147-w
[27]

Lin Y, Ye C, Li X, Chen Q, Wu Y, et al. 2023. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Horticulture Research 10(8):uhad127

doi: 10.1093/hr/uhad127
[28]

Lan MF, Wang XY, Zhang XC. 2026. CentriVision: an integrated platform for multiscale centromere analysis in plants. Plant Communications 7(2):101689

doi: 10.1016/j.xplc.2025.101689
[29]

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, et al. 2020. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117:9451−9457

doi: 10.1073/pnas.1921046117
[30]

Tarailo-Graovac M, Chen N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics 4:4.10. 1−4.10. 14

doi: 10.1002/0471250953.bi0410s25
[31]

Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357−360

doi: 10.1038/nmeth.3317
[32]

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078−2079

doi: 10.1093/bioinformatics/btp352
[33]

Gabriel L, Brůna T, Hoff KJ, Ebel M, Lomsadze A, et al. 2024. BRAKER3: fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA. Genome Research 34(5):769−777

doi: 10.1101/gr.278090.123
[34]

Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, et al. 2017. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Molecular Biology and Evolution 34:2115−2122

doi: 10.1093/molbev/msx148
[35]

Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, et al. 2025. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Research 53(D1):D444−D456

doi: 10.1093/nar/gkae1082
[36]

Sayers EW, Beck J, Bolton EE, Brister JR, Chan J, et al. 2025. Database resources of the national center for biotechnology information in 2025. Nucleic Acids Research 53(D1):D20−D29

doi: 10.1093/nar/gkae979
[37]

The UniProt Consortium. 2017. UniProt: the universal protein knowledgebase. Nucleic Acids Research 45(D1):D158−D169

doi: 10.1093/nar/gkw1099
[38]

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, et al. 2021. Pfam: the protein families database in 2021. Nucleic Acids Research 49:D412−D419

doi: 10.1093/nar/gkaa913
[39]

Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29(22):2933−2935

doi: 10.1093/bioinformatics/btt509
[40]

Ontiveros-Palacios N, Cooke E, Nawrocki EP, Triebel S, Marz M, et al. 2025. Rfam 15: RNA families database in 2025. Nucleic Acids Research 53(D1):D258−D267

doi: 10.1093/nar/gkae1023
[41]

Chan PP, Lin BY, Mak AJ, Lowe TM. 2021. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Research 49(16):9077−9096

doi: 10.1093/nar/gkab688
[42]

Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238

doi: 10.1186/s13059-019-1832-y
[43]

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−274

doi: 10.1093/molbev/msu300
[44]

Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19(2):301−302

doi: 10.1093/bioinformatics/19.2.301
[45]

Kumar S, Stecher G, Suleski M, Hedges SB. 2017. TimeTree: a resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution 7:1812−1819

doi: 10.1093/molbev/msx116
[46]

Mendes FK, Vanderpool D, Fulton B, Hahn MW. 2020. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36:5516−5518

doi: 10.1093/bioinformatics/btaa1022
[47]

Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. 2014. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 15:293

doi: 10.1186/1471-2105-15-293
[48]

Finn RD, Clements J, Eddy SR. 2011. HMMER web server: interactive sequence similarity searching. Nucleic Acids Research 39:W29−W37

doi: 10.1093/nar/gkr367
[49]

Edgar RC. 2022. Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nature Communications 13(1):6968

doi: 10.1038/s41467-022-34630-w
[50]

Kumar S, Stecher G, Suleski M, Sanderford M, Sharma S, et al. 2024. MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing. Molecular Biology And Evolution 41(12):msae263

doi: 10.1093/molbev/msae263
[51]

Bailey TL, Johnson J, Grant CE, Noble WS. 2015. The MEME suite. Nucleic Acids Research 43:W39−W49

doi: 10.1093/nar/gkv416
[52]

Li H, Durbin R. 2024. Genome assembly in the telomere-to-telomere era. Nature Reviews Genetics 25(9):658−670

doi: 10.1038/s41576-024-00718-w
[53]

Thuronyi BW, Koblan LW, Levy JM, Yeh WH, Zheng C, et al. 2019. Continuous evolution of base editors with expanded target compatibility and improved activity. Nature Biotechnology 37:1070−1079

doi: 10.1038/s41587-019-0193-0
[54]

Yang Y, Du W, Li Y, Lei J, Pan W. 2025. Recent advances and challenges in de novo genome assembly. Genomics Communications 2:e014

doi: 10.48130/gcomm-0025-0015
[55]

Husin NA, Rahman S, Karunakaran R, Bhore SJ. 2018. A review on the nutritional, medicinal, molecular and genome attributes of Durian (Durio zibethinus L.), the King of fruits in Malaysia. Bioinformation 14(6):265−270

doi: 10.6026/97320630014265
[56]

Wang P, Wang F. 2023. A proposed metric set for evaluation of genome assembly quality. Trends in Genetics 39(3):175−186

doi: 10.1016/j.tig.2022.10.005
[57]

Prihatini R, Anggraeni L, Hadiati S, Pramanik D, Nugroho K, et al. 2025. Genomic research on the king of fruit (Durio spp.): a systematic literature review. Genetic Resources and Crop Evolution 72:7619−7638

doi: 10.1007/s10722-025-02430-y
[58]

Wang T, Duan S, Xu C, Wang Y, Zhang X, et al. 2023. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nature Communications 14(1):7377

doi: 10.1038/s41467-023-43270-7
[59]

Cao S, Sawettalake N, Shen L. 2025. Lactuca super-pangenome provides insights into lettuce genome evolution and domestication. Nature Communications 16(1):7257

doi: 10.1038/s41467-025-62641-w
[60]

Fajkus P, Peška V, Fajkus J, Sýkorová E. 2021. Origin and fates of TERT gene copies in polyploid plants. International Journal of Molecular Sciences 22(4):1783

doi: 10.3390/ijms22041783