| [1] |
Thorogood CJ, Ghazalli MN, Siti-Munirah MY, Nikong D, Kusuma YWC, et al. 2022. The king of fruits. |
| [2] |
Shearman JR, Sonthirod C, Naktang C, Sangsrakru D, Yoocha T, et al. 2020. Assembly of the durian chloroplast genome using long PacBio reads. |
| [3] |
Teh BT, Lim K, Yong CH, Ng CCY, Rao, SR, et al. 2017. The draft genome of tropical fruit durian (Durio zibethinus). |
| [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. |
| [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. |
| [6] |
Ji X, Zhong Y, Zheng D, Xie S, Shi M et al. 2025. Chromosome-scale haploid genome assembly of Durio zibethinus KanYao. |
| [7] |
Peska V, Garcia S. 2020. Origin, diversity, and evolution of telomere sequences in plants. |
| [8] |
Shay JW, Wright WE. 2019. Telomeres and telomerase: three decades of progress. |
| [9] |
Zakian VA. 2012. Telomeres: the beginnings and ends of eukaryotic chromosomes. |
| [10] |
Lan L, Hu H, Jia Y, Zhang X, Jia M, et al. 2025. Tips for improving genome annotation quality. |
| [11] |
Zhou Y, Zhang J, Xiong X, Cheng Z, Chen F. 2022. De novo assembly of plant complete genomes. |
| [12] |
Porebski S, Bailey LG, Baum BR. 1997. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. |
| [13] |
Dellaporta SL, Wood J, Hicks JB. 1983. A plant DNA minipreparation: version II. |
| [14] |
Marçais G, Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. |
| [15] |
Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, et al. 2017. GenomeScope: fast reference-free genome profiling from short reads. |
| [16] |
Feng X, Cheng H, Portik D, Li H. 2022. Metagenome assembly of high-fidelity long reads with hifiasm-meta. |
| [17] |
Guan D, McCarthy SA, Wood J, Howe K, Wang Y, et al. 2020. Identifying and removing haplotypic duplication in primary genome assemblies. |
| [18] |
Hu J, Fan J, Sun Z, Liu S. 2020. NextPolish: a fast and efficient genome polishing tool for long-read assembly. |
| [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. |
| [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. |
| [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. |
| [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. |
| [23] |
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. |
| [24] |
Manni M, Berkeley MR, Seppey M, Zdobnov EM. 2021. BUSCO: assessing genomic data quality and beyond. |
| [25] |
Rhie A, Walenz BP, Koren S, Phillippy AM. 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. |
| [26] |
Nevers Y, Warwick Vesztrocy A, Rossier V, Train CM, Altenhoff A, et al. 2025. Quality assessment of gene repertoire annotations with OMArk. |
| [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. |
| [28] |
Lan MF, Wang XY, Zhang XC. 2026. CentriVision: an integrated platform for multiscale centromere analysis in plants. |
| [29] |
Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, et al. 2020. RepeatModeler2 for automated genomic discovery of transposable element families. |
| [30] |
Tarailo-Graovac M, Chen N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. |
| [31] |
Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. |
| [32] |
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The sequence alignment/map format and SAMtools. |
| [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. |
| [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. |
| [35] |
Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, et al. 2025. InterPro: the protein sequence classification resource in 2025. |
| [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. |
| [37] |
The UniProt Consortium. 2017. UniProt: the universal protein knowledgebase. |
| [38] |
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, et al. 2021. Pfam: the protein families database in 2021. |
| [39] |
Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. |
| [40] |
Ontiveros-Palacios N, Cooke E, Nawrocki EP, Triebel S, Marz M, et al. 2025. Rfam 15: RNA families database in 2025. |
| [41] |
Chan PP, Lin BY, Mak AJ, Lowe TM. 2021. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. |
| [42] |
Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. |
| [43] |
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. |
| [44] |
Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. |
| [45] |
Kumar S, Stecher G, Suleski M, Hedges SB. 2017. TimeTree: a resource for timelines, timetrees, and divergence times. |
| [46] |
Mendes FK, Vanderpool D, Fulton B, Hahn MW. 2020. CAFE 5 models variation in evolutionary rates among gene families. |
| [47] |
Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. 2014. jvenn: an interactive Venn diagram viewer. |
| [48] |
Finn RD, Clements J, Eddy SR. 2011. HMMER web server: interactive sequence similarity searching. |
| [49] |
Edgar RC. 2022. Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. |
| [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. |
| [51] |
Bailey TL, Johnson J, Grant CE, Noble WS. 2015. The MEME suite. |
| [52] |
Li H, Durbin R. 2024. Genome assembly in the telomere-to-telomere era. |
| [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. |
| [54] |
Yang Y, Du W, Li Y, Lei J, Pan W. 2025. Recent advances and challenges in de novo genome assembly. |
| [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. |
| [56] |
Wang P, Wang F. 2023. A proposed metric set for evaluation of genome assembly quality. |
| [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. |
| [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. |
| [59] |
Cao S, Sawettalake N, Shen L. 2025. Lactuca super-pangenome provides insights into lettuce genome evolution and domestication. |
| [60] |
Fajkus P, Peška V, Fajkus J, Sýkorová E. 2021. Origin and fates of TERT gene copies in polyploid plants. |