In higher plants as an example, one can see that the era of sequencing of their diploid genomes is coming
01.07.2025
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In higher plants as an example, one can see that the era of sequencing of their diploid genomes is coming
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17 – 41
The first complete genome of the plant Arabidopsis thaliana was sequenced a quarter of a century ago, but it took another decade and a half to get it reassembled as a diploid genome in the form of haplotypes. Since then by the end of 2024, functionalized diploid genomes with phased assembly have been sequenced for 258 samples representing 143 species of higher plants belonging to 95 genera from 50 families, and the results have been published in 198 articles. Diploid genomes have been sequenced for species of different ploidy, among which most species are diploids, but there are also triploids, tetraploids, hexaploids, several octaploids, and even nonaploids. Already 30 diploid genomes of different plant species have been assembled at the T2T gapless level. For 7 plant species, the diploid genomes are already supplemented by pangenomes, and for two genera, by a super-pangenome. A noticeable increase in the number of genomes with phased assembly of plant haplotypes occurred in the last couple of years, explained by the improvement of DNA sequencing technologies of new generations and by awareness of the need for such information. Interest in phased genome assembly can be attributed to the fact that currently sequenced genomes are essentially quasi-genomes in which fragments of maternal and paternal genomes are interspersed in a mosaic manner, which makes it difficult to identify genotype–phenotype relationships. In most articles describing the phased assembly of haplotyped genomes, it is emphasized that knowledge of nucleotide sequences of a complete set of chromosomes facilitates determination of biosynthesis pathways of various secondary metabolites and the understanding of mechanisms of heterosis manifestation, allows to improve resistance to various pathogens and adaptability to adverse environmental factors, and helps to determine sex in dioecious plants, to develop advanced breeding programs, and to identify processes that took place during domestication. It can be confidently stated that the genomics of higher organisms and plants in particular has entered the era of sequencing of diploid genomes, despite much greater difficulties with obtaining valid results. At the same time, more than 5,000 plant quasi-genomes are already known for approximately 2 thousand species; however, such quasi-genomes, devoid of phased assembly and consisting of mosaic fragments of parental chromosomes, serve only as a necessary stage of analysis in those species whose genomes have not yet been sequenced in order to subsequently assemble haplotypes in a phased manner by means of chromosomes at the T2T gapless level. The latter is a higher level of establishing the structure of genomes and of their annotation.
- Kuluev BR, Baymiev AnKh, Gerashchenkov GA et al. One hundred years of haploid genomes. Now time comes for diploid genomes. Biomics. 2020. V. 12(4). P. 411-434. DOI: 10.31301/2221-6197.bmcs.2020-33 (In Russian) 2. Winkler H. Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. 1920. Jena: Gustav Fischer Verlag. 250 s. 3. Chemeris A.V., Akhunov E.D., Vakhitov V.A. DNA sequencing. M., Nauka, 1999. 429 p. (In Russian) 4. Zubov V.V., Chemeris D.A., Vasilov R.G. et al. Brief history of high-throughput nucleic acid sequencing methods. Biomics. 2021. V.13(1). P. 27-46. DOI:10.31301/2221-6197.bmcs.2021-4 (In Russian) 5. Matniyazov R.T., Kuluev A.R., Baymiev An.Kh. et al. T2T genomes of higher plants. Biomics. 2025. V.17(1). P. 65-76. DOI:10.31301/2221-6197.bmcs.2025-5 6. Kuluev B.R., Chemeris D.A., Gerashchenkov G.A. et al. Pangenomics of plants. Biomics. 2025. V.17(1). P. 42-64. DOI:10.31301/2221-6197.bmcs.2025-4 7. Xie L, Gong X, Yang K et al. Technology-enabled great leap in deciphering plant genomes. Nat Plants. 2024. V.10(4). P.551-566. doi:10.1038/s41477-024-01655-6 8. Kong W, Wang Y, Zhang S, Yu J, Zhang X. Recent Advances in Assembly of Plant Complex Genomes. Genomics Proteomics Bioinformatics. 2023. S1672-0229(23)00070-0. doi:10.1016/j.gpb.2023.04.004 9. Chin CS, Peluso P, Sedlazeck FJ. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods. 2016. V.13(12). P.1050-1054. doi:10.1038/nmeth.4035 10. Yang J, Moeinzadeh MH, Kuhl H. et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nat Plants. 2017. V.3(9). P.696-703. doi:10.1038/s41477-017-0002-z 11. Hulse-Kemp AM, Maheshwari S, Stoffel K. et al. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Hortic Res. 2018. V.5. 4. doi:10.1038/s41438-017-0011-0 12. Reuscher S, Furuta T, Bessho-Uehara K, Cosi M, Jena KK, Toyoda A, Fujiyama A, Kurata N, Ashikari M. Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. Commun Biol. 2018. V.1. 162. doi:10.1038/s42003-018-0171-y 13. Zhang J, Zhang X, Tang H et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat Genet. 2018. V.50(11). P.1565-1573. doi:10.1038/s41588-018-0237-2. 14. Shirasawa K, Esumi T, Hirakawa H. et al. Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis). DNA Res. 2019. V.26(5). P.379-389. doi:10.1093/dnares/dsz016 15. Kuon JE, Qi W, Schläpfer P et al. Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. BMC Biol. 2019. V.17(1). 75. doi:10.1186/s12915-019-0697-6 16. Shi D, Wu J, Tang H et al. Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants. Genome Res. 2019. V.29(11). P.1889-1899. doi:10.1101/gr.251033.119 17. Minio A, Massonnet M, Figuerosa-Balderas R, Castro A, Cantu D. Diploid Genome Assembly of the Wine Grape Carmenere. G3 (Bethesda). 2019. V.9(5). P.1331-1337. doi:10.1534/g3.119.400030 18. Vondras AM, Minio A, Blanco-Ulate B. et al. The genomic diversification of grapevine clones. BMC Genomics. 2019. V.20(1). 972. doi:10.1186/s12864-019-6211-2 19. Colle M, Leisner C, Wai CM. et al. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Gigascience. 2019. V.8(3). giz012. doi:10.1093/gigascience/giz012 20. Montgomery JS, Giacomini D, Waithaka B et al. Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri. Genome Biol Evol. 2020. V.12(11). P.1988-1993. doi:10.1093/gbe/evaa177 21. Usai G, Mascagni F, Giordani T et al. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. Plant J. 2020. V.102(3). P.600-614. doi:10.1111/tpj.14635 22. Sun X, Jiao C, Schwaninger H. et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat Genet. 2020. V.52(12). P.1423-1432. doi:10.1038/s41588-020-00723-9 23. Chen H, Zeng Y, Yang Y et al. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nat Commun. 2020. V.11(1). 2494. doi:10.1038/s41467-020-16338-x 24. Campoy JA, Sun H, Goel M. et al. Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol. 2020. V.21(1). 306. doi:10.1186/s13059-020-02235-5 25. Wang J, Liu W, Zhu D, Hong P, Zhang S, Xiao S, Tan Y, Chen X, Xu L, Zong X, Zhang L, Wei H, Yuan X, Liu Q. Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. Hortic Res. 2020. V.7(1). 122. doi:10.1038/s41438-020-00343-8 26. Zhou Q, Tang D, Huang W. et al. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nat Genet. 2020. V.52(10). P.1018-1023. doi:10.1038/s41588-020-0699-x 27. Hasing T, Tang H, Brym M et al. A phased Vanilla planifolia genome enables genetic improvement of flavour and production. Nat Food. 2020. V.1(12). 811-819. doi:10.1038/s43016-020-00197-2 28. Holtgräwe D, Rosleff Soerensen T, Hausmann L et al. A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. Front Plant Sci. 2020. V.11. 156. doi:10.3389/fpls.2020.00156 29. Massonnet M, Cochetel N, Minio A. et al. The genetic basis of sex determination in grapes. Nat Commun. 2020. V.11(1). 2902. doi:10.1038/s41467-020-16700-z 30. Yow AG, Bostan H, Castanera R. et al. Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family. Genes (Basel). 2021. V.13(1). 52. doi:10.3390/genes13010052 31. Wang P, Yu J, Jin S. et al. Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome. Hortic Res. 2021. V.8(1). 107. doi:10.1038/s41438-021-00542-x 32. Zhang X, Chen S, Shi L et al. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nat Genet. 2021. V.53(8). P.1250-1259. doi:10.1038/s41588-021-00895-y 33. Zhang W, Luo C, Scossa F et al. A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants. Plant J. 2021. V.105(1). P.197-208. doi:10.1111/tpj.15051 34. Lovell JT, Bentley NB, Bhattarai G et al. Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nat Commun. 2021. V.12(1). 4125. doi:10.1038/s41467-021-24328-w 35. Shirasawa K, Itai A, Isobe S. Genome sequencing and analysis of two early-flowering cherry (Cerasus × kanzakura) varieties, 'Kawazu-zakura' and 'Atami-zakura'. DNA Res. 2021. V.28(6). dsab026. doi:10.1093/dnares/dsab026 36. Bodrug-Schepers A, Stralis-Pavese N, Buerstmayr H et al. Quinoa genome assembly employing genomic variation for guided scaffolding. Theor Appl Genet. 2021. V.134(11). P.3577-3594. doi:10.1007/s00122-021-03915-x 37. Hardigan MA, Feldmann MJ, Picot DDA. et al. Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry. bioRxiv. 2021. 2021.11.03.467115. doi:10.1101/2021.11.03.467115 38. Padgitt-Cobb LK, Kingan SB, Wells J. et al. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. Plant Genome. 2021. V.14(1). e20072. doi:10.1002/tpg2.20072 39. Nashima K, Shirasawa K, Ghelfi A. et al. Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype. DNA Res. 2021. V.28(1). dsaa026. doi:10.1093/dnares/dsaa026 40. Mango Genome Consortium. The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality. BMC Plant Biol. 2021. V.21(1). 108. doi:10.1186/s12870-021-02858-1 41. Mansfeld BN, Boyher A, Berry JC. et al. Large structural variations in the haplotype-resolved African cassava genome. Plant J. 2021. V.108(6). P.1830-1848. doi:10.1111/tpj.15543 42. Cochetel N, Minio A, Massonnet M. et al. Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. G3 (Bethesda). 2021. V.11(4). jkab033. doi:10.1093/g3journal/jkab033 43. Wu C, Deng C, Hilario E et al. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Mol Ecol Resour. 2021. V.22(1). P.345-360. doi:10.1111/1755-0998.13467 44. Cheng SP, Jia KH, Liu H et al. Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. Hortic Res. 2021. V.8(1). 188. doi:10.1038/s41438-021-00599-8 45. Li HL, Wu L, Dong Z et al. Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway. Hortic Res. 2021. V.8(1). 189. doi:10.1038/s41438-021-00627-7 46. Nashima K., Shirasawa K., Isobe S. et al. Gene prediction for leaf margin phenotype and fruit flesh color in pineapple (Ananas comosus) using haplotype-resolved genome sequencing. Plant J. 2022. V.110(3). P.720-734. doi:10.1111/tpj.15699 47. Liao B, Shen X, Xiang L et al. Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield. Mol Plant. 2022. V.15(8). P.1310-1328. doi:10.1016/j.molp.2022.05.013 48. Shirasawa K, Ueta S, Murakami K et al. Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species. DNA Res. 2022. V.29(1). dsac002. doi:10.1093/dnares/dsac002 49. Bellinger MR, Datlof EM, Selph KE, Gallaher TJ, Knope ML. A Genome for Bidens hawaiensis: A Member of a Hexaploid Hawaiian Plant Adaptive Radiation. J Hered. 2022. V.113(2). P.205-214. doi:10.1093/jhered/esab077 50. Jiang L, Lin M, Wang H et al. Haplotype-resolved genome assembly of Bletilla striata (Thunb.) Reichb. f. to elucidate medicinal value. Plant J. 2022. V.111(5). P.1340-1353. doi:10.1111/tpj.15892 51. Zhang Q, Li M, Chen X et al. Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis. Front Genet. 2022. V.13. 878431. doi:10.3389/fgene.2022.878431 52. Zhang B, Chen S, Liu J et al. A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth. Front Plant Sci. 2022. V.13. 890980. doi:10.3389/fpls.2022.890980 53. Zheng Y, Yang D, Rong J. et al. Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro). J Integr Plant Biol. 2022. V.64(3). P.649-670. doi:10.1111/jipb.13217 54. Fan Z, Tieman DM, Knapp SJ et al. A multi-omics framework reveals strawberry flavor genes and their regulatory elements. New Phytol. 2022. V.236(3). P.1089-1107. doi:10.1111/nph.18416 55. Hu G, Feng J, Xiang X et al. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nat Genet. 2022. V.54(1). P.73-83. doi:10.1038/s41588-021-00971-3 56. Khan A, Carey SB, Serrano A et al. A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica). GigaByte. 2022. gigabyte69. doi:10.46471/gigabyte.69 57. Qi W, Lim Y-W, Patrignani A. et al. The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. Gigascience. 2022. V.11. giac028. doi:10.1093/gigascience/giac028 58. Long R, Zhang F, Zhang Z. et al. Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits. Genomics Proteomics Bioinformatics. 2022. V.20(1). P.14-28. doi:10.1016/j.gpb.2022.01.002 59. Nath O, Fletcher SJ, Hayward A et al. A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes. Hortic Res. 2022. V.9. uhac157. doi:10.1093/hr/uhac157 60. Shen Y, Li W, Zeng Y. et al. Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli. Nat Commun. 2022. V.13(1). 3511. doi:10.1038/s41467-022-31121-w 61. An X, Gao K, Chen Z et al. High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia. Mol Ecol Resour. 2022. V.22(2). P.786-802. doi:10.1111/1755-0998.13507 62. Tong S, Wang Y, Chen N. et al. PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar. Genome Biol. 2022. V.23(1). 148. doi:10.1186/s13059-022-02718-7 63. Zhang Q, Qi Y, Pan H. et al. Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. Nat Genet. 2022. V.54(6). P.885-896. doi:10.1038/s41588-022-01084-1 64. Hoopes G, Meng X, Hamilton JP et al. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol Plant. 2022. V.15(3). P.520-536. doi:10.1016/j.molp.2022.01.003 65. Bao Z, Li C, Li G et al. Genome architecture and tetrasomic inheritance of autotetraploid potato. Mol Plant. 2022. V.15(7). P.1211-1226. doi:10.1016/j.molp.2022.06.009 66. Sun H, Jiao WB, Krause K. et al. Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nat Genet. 2022. V.54(3). P.342-348. doi:10.1038/s41588-022-01015-0 67. Yi L, Sa R, Zhao S. et al. Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca. Front Genet. 2022. V.13. 884081. doi:10.3389/fgene.2022.884081 68. Bickhart DM, Koch LM, Smith TPL et al. Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species. GigaByte. 2022. 2022. gigabyte42. doi:10.46471/gigabyte.42 69. Cui F, Ye X, Li X et al. Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. Plant Commun. 2022. V.3(4). 100307. doi:10.1016/j.xplc.2022.100307 70. Piet Q, Droc G, Marande W. et al. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly. Plant Commun. 2022. V.3(5). 100330. doi:10.1016/j.xplc.2022.100330 71. Shirasawa K., Hirakawa H., Azuma A. et al. De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'. DNA Res. 2022. V.29(6). dsac040. doi:10.1093/dnares/dsac040 72. Minio A, Cochetel N, Massonnet M. et al. HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt. Sci Data. 2022. V.9(1). 660. doi:10.1038/s41597-022-01753-0 73. Maestri S, Gambino G, Lopatriello G. et al. 'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.). BMC Genomics. 2022. V.23(1). 159. doi:10.1186/s12864-022-08389-9 74. Yue J, Chen Q, Wang Y et al. Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis. Hortic Res. 2023. V.10(2). uhac264. doi:10.1093/hr/uhac264 75. Han X, Zhang Y, Zhang Q et al. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Mol Plant. 2023. V.16(2). P.452-470. doi:10.1016/j.molp.2022.12.022 76. Wang Y, Dong M, Wu Y et al. Telomere-to-telomere and haplotype-resolved genome of the kiwifruit Actinidia eriantha. Mol Hortic. 2023. V.3(1). 4. doi:10.1186/s43897-023-00052-5 77. Zhu S, Zhang Y, Copsy L et al. The Snapdragon Genomes Reveal the Evolutionary Dynamics of the S-Locus Supergene. Mol Biol Evol. 2023. V.40(4). msad080. doi:10.1093/molbev/msad080 78. Delorean EE, Youngblood RC, Simpson SA. et al. Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning. Front Plant Sci. 2023. V.14. 184112. doi:10.3389/fpls.2023.1184112 79. He S, Weng D, Zhang Y et al. A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa. Hortic Res. 2023. V.10(10). uhad183. doi:10.1093/hr/uhad183 80. Nakandala U, Masouleh AK, Smith MW. et al. Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes. Hortic Res. 2023. V.10(5). uhad058. doi:10.1093/hr/uhad058 81. Bao Y, Zeng Z, Yao W et al. A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance. Hortic Res. 2023. V.10(4). uhad020. doi:10.1093/hr/uhad020 82. Wu B, Yu Q, Deng Z et al. A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance. Hortic Res. 2023. V.10(1). uhac247. doi:10.1093/hr/uhac247 83. Gao Y, Xu J, Li Z et al. Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. iScience. 2023. V.26(2). 106024. doi:10.1016/j.isci.2023.106024. 84. Zhao SW, Guo JF, Kong L et al. Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub. Sci Data. 2023. V.10(1). 259. doi:10.1038/s41597-023-02171-6 85. Li G, Tang L, He Y et al. The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon. Hortic Res. 2023. V.10(10). uhad182. doi:10.1093/hr/uhad182 86. Qu Y, Shang X, Fang S et al. Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes. Sci Data. 2023. V.10(1). 507. doi:10.1038/s41597-023-02402-w 87. Yu RM, Zhang N, Zhang BW et al. Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus. BMC Biol. 2023. V.21(1). 168. doi:10.1186/s12915-023-01668-1 88. Jiang H, Zhang X, Leng L et al. A chromosome-scale and haplotype-resolved genome assembly of carnation (Dianthus caryophyllus) based on high-fidelity sequencing. Front Plant Sci. 2023. V.14. 1230836. doi:10.3389/fpls.2023.1230836 89. Lan L, Leng L, Liu W, Ren Y, Reeve W, Fu X, Wu Z, Zhang X. The haplotype-resolved telomere-to-telomere carnation (Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression. Hortic Res. 2023. V.11(1). uhad244. doi:10.1093/hr/uhad244 90. Li H, Sun P, Wang Y. et al. Allele-aware chromosome-level genome assembly of the autohexaploid Diospyros kaki Thunb. Sci Data. 2023. V.10(1). 270. doi:10.1038/s41597-023-02175-2 91. Lötter A, Duong TA, Candotti J et al. Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids. Gigascience. 2023. V.12. giad064. doi:10.1093/gigascience/giad064 92. Tanaka H, Hori T, Yamamoto S et al. Haplotype-resolved chromosomal-level assembly of wasabi (Eutrema japonicum) genome. Sci Data. 2023. V.10(1). 441. doi:10.1038/s41597-023-02356-z 93. He Q, Ma D, Li W et al. High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility. J Integr Plant Biol. 2023. V.65(6). P.1423-1441. doi:10.1111/jipb.13459 94. Lin H, Yao Y, Sun P et al. Haplotype-resolved genomes of two buckwheat crops provide insights into their contrasted rutin concentrations and reproductive systems. BMC Biol. 2023. V.21(1). 87. doi:10.1186/s12915-023-01587-1 95. Jin X, Du H, Zhu C et al. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. Nat Plants. 2023. V.9(8). P.1252-1266. doi:10.1038/s41477-023-01473-2 96. Mao J, Wang Y, Wang B. et al. High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry. Hortic Res. 2023. V.10(1). uhad002. doi:10.1093/hr/uhad002 97. Padgitt-Cobb LK, Pitra NJ, Matthews PD et al. An improved assembly of the "Cascade" hop (Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. Hortic Res. 2023. 10(2). uhac281. doi:10.1093/hr/uhac281 98. Wu X, Simpson SA, Youngblood RC et aal. Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution. Hortic Res. 2023. V.10(12). uhad217. doi:10.1093/hr/uhad217 99. Xu M, Gao Q, Jiang M et al. A novel genome sequence of Jasminum sambac helps uncover the molecular mechanism underlying the accumulation of jasmonates. J Exp Bot. 2023. V.74(4). P.1275-1290. doi:10.1093/jxb/erac464 100. Mansfeld BN, Ou S, Burchard E et al. Genome of the North American wild apple species Malus angustifolia. bioRxiv. 2023. doi:10.1101/2023.11.16.567428 101. Švara A, Sun H, Fei Z, Khan A. Chromosome-level phased genome assembly of 'Antonovka' identified candidate apple scab resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1. G3 (Bethesda). 2023. V.4. jkad253. doi:10.1093/g3journal/jkad253 102. Mansfeld BN, Yocca A, Ou S et al. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. Plant J. 2023. V.116(4). P.989-1002. doi:10.1111/tpj.16433 103. Landi M, Shah T, Falquet L et al. Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta). Sci Data. 2023. V.10(1). 887. doi:10.1038/s41597-023-02800-0 104. Xu XD, Zhao RP, Xiao L et al. Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression. Hortic Res. 2023. V.10(11). uhad200. doi:10.1093/hr/uhad200 105. Chen SH, Martino AM, Luo Z et al. A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes. Gigascience. 2023. V.12. giad102. doi:10.1093/gigascience/giad102 106. Liu D, Tian X, Shao S et al. Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata). Sci Data. 2023. V.10(1). 901. doi:10.1038/s41597-023-02821-9 107. Huang HR, Liu X, Arshad R et al. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. Hortic Res. 2023. V.10(9). uhad153. doi:10.1093/hr/uhad153 108. Liu X, Arshad R, Wang X. et al. The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars. Sci Data. 2023. V.10(1). 631. doi:10.1038/s41597-023-02546-9 109. Xie WZ, Zheng YY, He W. et al. Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control. Plant Commun. 2023. 100766. doi:10.1016/j.xplc.2023.100766 110. Yang J, Xue H, Li Z et al. Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica. New Phytol. 2023. V.240(5). P.2058-2071. doi:10.1111/nph.19264 111. Wang Z, Huang S, Yang Z et al. A high-quality, phased genome assembly of broomcorn millet reveals the features of its subgenome evolution and 3D chromatin organization. Plant Commun. 2023. V.4(3). 100557. doi:10.1016/j.xplc.2023.100557 112. Zhou R, Jenkins JW, Zeng Y et al. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. Plant J. 2023. V.116(4). P.1003-1017. doi:10.1111/tpj.16454 113. Luo CS, Li TT, Jiang XL. et al. High-quality haplotype-resolved genome assembly for ring-cup oak (Quercus glauca) provides insight into oaks demographic dynamics. Mol Ecol Resour. 2023. e13914. doi:10.1111/1755-0998.13914 114. Kapoor B, Jenkins J, Schmutz J et al. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3 (Bethesda). 2023. V.13(11). jkad209. doi:10.1093/g3journal/jkad209 115. Wang L, Li LL, Chen L. et al. Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis). Front Plant Sci. 2023. V.14. 1290913. doi:10.3389/fpls.2023.1290913 116. Zhang H, He Q, Xing L. et al. The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones. Plant Commun. 2023. V.26. 100677. doi:10.1016/j.xplc.2023.100677 117. Shen J-S, Lan L, Kan S-L et al. A haplotype-resolved genome for Rhododendron × pulchrum and the expression analysis of heat shock genes. Journal of Systematics and Evolution. 2023. V.62(3). P.489-504. doi:10.1111/jse.13007 118. Chang Y, Zhang R, Ma Y, Sun W. A haplotype-resolved genome assembly of Rhododendron vialii based on PacBio HiFi reads and Hi-C data. Sci Data. 2023. V.10(1). 451. doi:10.1038/s41597-023-02362-1 119. Hyden B, Zou J, Wilkerson DG et al. Structural variation of a sex-linked region confers monoecy and implicates GATA15 as a master regulator of sex in Salix purpurea. New Phytol. 2023. V.238(6). P.2512-2523. doi:10.1111/nph.18853 120. Cheng Y, Sun J, Jiang M et al. Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes. Hortic Res. 2023. V.10(9). uhad161. doi:10.1093/hr/uhad161 121. Wei X, Chen M, Zhang X et al. The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple (Syzygium samarangense (Blume) Merr. and Perry). Hortic Res. 2023. V.10(12). uhad214. doi:10.1093/hr/uhad214 122. Santangelo JS, Battlay P, Hendrickson BT et al. Haplotype-Resolved, Chromosome-Level Assembly of White Clover (Trifolium repens L., Fabaceae). Genome Biol Evol. 2023. V.15(8). evad146. doi:10.1093/gbe/evad146 123. Mengist MF, Bostan H, De Paola D. et al. Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum). New Phytol. 2023. V.237(3). P.1024-1039. doi:10.1111/nph.18428 124. Cochetel N, Minio A, Guarracino A et al. A super-pangenome of the North American wild grape species. Genome Biol. 2023. V.24(1). 290. doi:10.1186/s13059-023-03133-2 125. Zou C, Sapkota S, Figueroa-Balderas R et al. A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus. Plant Physiol. 2023. V.193(4). P.2321-2336. doi:10.1093/plphys/kiad494 126. Frommer B, Müllner S, Holtgräwe D. et al. Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola. Front Plant Sci. 2023. V.14. 1180982. doi:10.3389/fpls.2023.1180982 127. Zhang K, Du M, Zhang H et al. The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes. Hortic Res. 2023. V.10(11). uhad205. doi:10.1093/hr/uhad205 128. Sichel V, Sarah G, Girollet N et al. Chimeras in Merlot grapevine revealed by phased assembly. BMC Genomics. 2023. V.24(1). 396. doi:10.1186/s12864-023-09453-8 129. Wang X, Tu M, Wang Y et al. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. Hortic Res. 2023. V.11. uhad260. doi:10.1093/hr/uhad260 130. Zhang F, Wang Y, Lin Y et al. Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid. Mol Hortic. 2024. V.4(1). 4. doi:10.1186/s43897-024-00083-6 131. Wang Y, Li P, Zhu Y, Zhang F et al. Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening. Adv Sci (Weinh). 2024. V.11(28). e2400322. doi:10.1002/advs.202400322 132. Carey SB, Aközbek L, Lovell JT et al. ZW sex chromosome structure in Amborella trichopoda. Nat Plants. 2024. V.10(12). P.1944-1954. doi:10.1038/s41477-024-01858-x 133. Feng J, Zhang W, Chen C et al. The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis. J Integr Plant Biol. 2024. V.66(10). P.2208-2225. doi:10.1111/jipb.13748 134. Miao K, Wang Y, Hou L et al. Haplotype-resolved genome assembly of the upas tree (Antiaris toxicaria). Sci Data. 2024. V.11(1). 1011. doi:10.1038/s41597-024-03860-6 135. Wang YJ, Guo C, Zhao L et al. Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboos. Hortic Res. 2024. V.11(12). uhae250. doi:10.1093/hr/uhae250 136. Wang H, Xu D, Jiang F et al. The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis. Gigascience. 2024. V.13. giae032. doi:10.1093/gigascience/giae032 137. Zhang L, Shi Y, Gong W et al. The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants. Cell Rep. 2024. V.43(11). 114902. doi:10.1016/j.celrep.2024.114902 138. Bianco L, Fontana P, Marchesini A et al. The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio. BMC Genom Data. 2024. V.25(1). 64. doi:10.1186/s12863-024-01245-7 139. Wang J, Xu D, Sang YL et al. A telomere-to-telomere gap-free reference genome of Chionanthus retusus provides insights into the molecular mechanism underlying petal shape changes. Hortic Res. 2024. V.11(12). uhae249. doi:10.1093/hr/uhae249 140. Hou Z, Yang S, He W et al. The haplotype-resolved genome of diploid Chrysanthemum indicum unveils new acacetin synthases genes and their evolutionary history. Plant J. 2024. V.119(3). P.1336-1352. doi:10.1111/tpj.16854 141. Nakandala, U., Furtado, A., Masouleh, A.K. et al. The genome of Citrus australasica reveals disease resistance and other species specific genes. BMC Plant Biol. 2024. V.24. 260. doi:10.1186/s12870-024-04988-8 142. Singh K, Huff M, Liu J et al. Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes: Citrus australasica, C. inodora, and C. glauca. Plants (Basel). 2024. V.13(11). 1460. doi:10.3390/plants13111460 143. Miao C, Wu Y, Wang L et al. Haplotype-resolved chromosome-level genome assembly of Huyou (Citrus changshanensis). Sci Data. 2024. V.11(1). 605. doi:10.1038/s41597-024-03437-3 144. Wang N, Chen P, Xu Y et al. Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange. Hortic Res. 2023. V.11(2). uhad268. doi:10.1093/hr/uhad268 145. Wang Y, Liu Y, Miao K et al. A haplotype-resolved genome assembly of Coptis teeta, an endangered plant of significant medicinal value. Sci Data. 2024. V.11(1). 1012. doi:10.1038/s41597-024-03861-5 146. Talbot SC, Vining KJ, Snelling JW et al. A haplotype-resolved chromosome-level assembly and annotation of European hazelnut (C. avellana cv. Jefferson) provides insight into mechanisms of eastern filbert blight resistance. G3 (Bethesda). 2024. V.14(6). jkae021. doi:10.1093/g3journal/jkae021 147. Xu D, Ye Z, Huang Y et al. Haplotype-resolved genome assembly of Corydalis yanhusuo, a traditional Chinese medicine with unusual telomere motif. Hortic Res. 2024. V.11(2). uhad296. doi:10.1093/hr/uhad296 148. Chen BZ, Li DW, Wang WJ et al. Chromosome-level and haplotype-resolved genome assembly of Dracaena cambodiana (Asparagaceae). Sci Data. 2024. 11(1). 873. doi:10.1038/s41597-024-03670-w 149. Ferguson S, Bar-Ness YD, Borevitz J, Jones A. A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world's tallest trees. BMC Genomics. 2024. V.25(1). 913. doi:10.1186/s12864-024-10810-4 150. Cheng S, Zhang Q, Geng X et al. Haplotype-resolved chromosome-level genome assembly of Ehretia macrophylla. Sci Data. 2024. V.11(1). 589. doi:10.1038/s41597-024-03431-9. 151. Wang B, Zhang R, Sun W, Yang J. A nearly telomere-to-telomere diploid genome assembly of Firmiana kwangsiensis, a threatened species in China. Sci Data. 2024. V.11(1). 1394. doi:10.1038/s41597-024-04250-8 152. Chen BZ, Yang ZJ, Wang WB et al. Chromosome-level genome assembly and annotation of Flueggea virosa (Phyllanthaceae). Sci Data. 2024. V.11(1). 875. doi:10.1038/s41597-024-03681-7 153. Song Y, Peng Y, Liu L et al. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. Hortic Res. 2023. V.11(1). uhad252. doi:10.1093/hr/uhad252 154. Hu S, Zeng X, Liu Y et al. Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries. Genome Res. 2024. V.34(10). P.1582-1594. doi:10.1101/gr.279378.124 155. Qiao Q, Cao Q, Zhang R et al. Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis). Plant Biotechnol J. 2024. V.22(6). P.1552-1565. doi:10.1111/pbi.14286 156. Wang S, Wang A, Chen R. et al. Haplotype-resolved chromosome-level genome of hexaploid Jerusalem artichoke provides insights into its origin, evolution, and inulin metabolism. Plant Commun. 2024. V.5(3). 100767. doi:10.1016/j.xplc.2023.100767 157. Kim T, Lee JH, Seo HH et al. Genome assembly of Hibiscus sabdariffa L. provides insights into metabolisms of medicinal natural products. G3 (Bethesda). 2024. V.14(8). jkae134. doi:10.1093/g3journal/jkae134 158. Han L, Luo X, Zhao Y et al. A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.). Sci Data. 2024. V.11(1). 278. doi:10.1038/s41597-024-03096-4 159. Nie B, Chen X, Hou Z et al. Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong. Sci Adv. 2024. V.10(6). eadj6547. doi:10.1126/sciadv.adj6547 160. Švara A, Sun H, Fei Z, Khan A. Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples. DNA Res. 2024. V.31(5). dsae026. doi:10.1093/dnares/dsae026 161. Peng H, Yi Y, Li J et al. A haplotype-resolved genome assembly of Malus domestica 'Red Fuji'. Sci Data. 2024. V.11(1). 592. doi:10.1038/s41597-024-03401-1 162. Li W, Chu C, Li H et al. Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing. Nat Genet. 2024. V.56(3). P.505-516. doi:10.1038/s41588-024-01657-2 163. Su Y, Yang X, Wang Y et al. Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication. Plant Physiol. 2024. V.195(4). P.2799-2814. doi:10.1093/plphys/kiae258 164. Zhang H, Ko I, Eaker A et al. A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'. G3 (Bethesda). 2024. V.14(12). jkae222. doi:10.1093/g3journal/jkae222 165. Li J, Cai H, Peng H et al. The chromosome-level genome assembly of the dwarfing apple interstock Malus hybrid 'SH6'. Sci Data. 2024. V.11(1). 552. doi:10.1038/s41597-024-03405-x 166. Li H, Zhai X, Peng H et al. Chromosomal level genome assemblies of two Malus crabapple cultivars Flame and Royalty. Sci Data. 2024. V.11(1). 201. doi:10.1038/s41597-024-03049-x 167. Wijesundara UK, Masouleh AK, Furtado A et al. A chromosome-level genome of mango exclusively from long-read sequence data. Plant Genome. 2024. V.17(2). e20441. doi:10.1002/tpg2.20441 168. Li W, Li X, Li W et al. A haplotype-resolved genome assembly of tetraploid Medicago sativa ssp. falcata. Sci China Life Sci. 2025. V.68(4). P.1186-1189. doi:10.1007/s11427-024-2753-2 169. Yang H, Wang C, Zhou G et al. A haplotype-resolved gap-free genome assembly provides novel insight into monoterpenoid diversification in Mentha suaveolens 'Variegata'. Hortic Res. 2024. V.11(3). uhae022. doi:10.1093/hr/uhae022 170. Jiang S, Zou M, Zhang C et al. A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics. Mol Hortic. 2024. V.4(1). 23. doi:10.1186/s43897-024-00098-z 171. Jia H, Lin J, Lin Z et al. Haplotype-resolved genome of Mimosa bimucronata revealed insights into leaf movement and nitrogen fixation. BMC Genomics. 2024. V.25(1). 334. doi:10.1186/s12864-024-10264-8 172. Xia Z, Fan W, Liu D et al. Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content. Hortic Res. 2024. V.11(6). uhae120. doi:10.1093/hr/uhae120 173. Zhao L, Li Z, Jiang S et al. The Telomere-to-Telomere Genome of Jaboticaba Reveals the Genetic Basis of Fruit Color and Citric Acid Content. Int J Mol Sci. 2024. V.25(22). 11951. doi:10.3390/ijms252211951 174. Cai Y, Anderson E, Xue W et al. Assembly and analysis of the genome of Notholithocarpus densiflorus. G3 (Bethesda). 2024. V.14(5). jkae043. doi:10.1093/g3journal/jkae043 175. Lian X, Zhong L, Bai Y et al. Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata. Plant Biotechnol J. 2024. V.22(6). P.1652-1668. doi:10.1111/pbi.14294 176. Huang J, Zhang Y, Li Y et al. Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice. Nat Commun. 2024. V.15(1). 4573. doi:10.1038/s41467-024-48845-6 177. Lu Y, Chen X, Yu H et al. Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution. Plant J. 2024. V.118(2). P.488-505. doi:10.1111/tpj.16620 178. Li F, Hou Z, Xu S et al. Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation. Plant J. 2024. V.119(1). P.348-363. doi:10.1111/tpj.16767 179. Hou Y, Gan J, Fan Z et al. Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations. Nat Commun. 2024. V.15(1). 8085. doi:10.1038/s41467-024-52376-5 180. Jang MJ, Cho HJ, Park YS et al. Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora. Nat Genet. 2024. V.56(11). P.2551-2561. doi:10.1038/s41588-024-01944-y 181. Shi TL, Jia KH, Bao YT et al. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar. Plant Physiol. 2024. V.195(1). P.652-670. doi:10.1093/plphys/kiae078 182. Luo J, Wang Y, Li Z et al. Haplotype-resolved genome assembly of poplar line NL895 provides a valuable tree genomic resource. For Res (Fayettev). 2024. V.4. e015. doi:10.48130/forres-0024-0013 183. Li J, Chen T, Gao K et al. Unravelling the novel sex determination genotype with 'ZY' and a distinctive 2.15-2.95 Mb inversion among poplar species through haplotype-resolved genome assembly and comparative genomics analysis. Mol Ecol Resour. 2024. V.24(7). e14002. doi:10.1111/1755-0998.14002 184. Wang JX, Li Y, Wang XW et al. Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis. J Integr Plant Biol. 2024. V.66(12). P.2716-2735. doi:10.1111/jipb.13782 185. Castanera R, de Tomás C, Ruggieri V et al. A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants. Hortic Res. 2024. V.11(6). uhae106. doi:10.1093/hr/uhae106 186. Jiu S, Lv Z, Liu M et al. Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness. Hortic Res. 2024. V.11(7). uhae142. doi:10.1093/hr/uhae142 187. Yang X, Su Y, Huang S et al. Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex. Hortic Res. 2024. V.11(6). uhae109. doi:10.1093/hr/uhae109 188. Tan W, Zhou P, Huang X et al. Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot. Hortic Res. 2024. V.11(4). uhae103. doi:10.1093/hr/uhae103 189. Yocca A, Akinyuwa M, Bailey N et al. A chromosome-scale assembly for 'd'Anjou' pear. G3 (Bethesda). 2024. V.14(3). jkae003. doi:10.1093/g3journal/jkae003 190. Li Q, Qiao X, Li L et al. Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits. Plant Commun. 2024. V.5(10). 101000. doi:10.1016/j.xplc.2024.101000 191. Lyu ZY, Zhou XL, Wang SQ et al. The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation. Gigascience. 2024. V.13. giae052. doi:10.1093/gigascience/giae052 192. Zhang X, Wu Q, Lan L et al. Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits. Mol Hortic. 2024. V.4(1). 14. doi:10.1186/s43897-024-00088-1 193. Zhang Z, Yang T, Liu Y et al. Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose. Nat Plants. 2024. V.10(11). P.1659-1671. doi:10.1038/s41477-024-01820-x 194. Bao Y, Zhang Q, Huang J et al. A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution. Nat Commun. 2024. V.15(1). 3041. doi:10.1038/s41467-024-47390-6 195. He L, Wang Y, Wang Y et al. Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes. Nat Commun. 2024. V.15(1). 6893. doi:10.1038/s41467-024-51158-3 196. Dong J, Li J, Zuo Y et al. Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii. Hortic Res. 2024. V.11(9). uhae181. doi:10.1093/hr/uhae181 197. Feng Y, Zhou J, Li D et al. The haplotype-resolved T2T genome assembly of the wild potato species Solanum commersonii provides molecular insights into its freezing tolerance. Plant Commun. 2024. V.5(10). 100980. doi:10.1016/j.xplc.2024.100980 198. Achakkagari SR, Bozan I, Camargo-Tavares JC et al. The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids. Sci Data. 2024. V.11(1). 454. doi:10.1038/s41597-024-03300-5 199. Serra Mari R, Schrinner S, Finkers R et al. Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data. Genome Biol. 2024. V.25(1). 26. doi:10.1186/s13059-023-03160-z 200. Masand M, Sharma S, Kumari S et al. High-quality haplotype-resolved chromosome assembly provides evolutionary insights and targeted steviol glycosides (SGs) biosynthesis in Stevia rebaudiana Bertoni. Plant Biotechnol J. 2024. V.22(12). P.3262-3277. doi:10.1111/pbi.14446 201. Kuo WH, Wright SJ, Small LL, Olsen KM. De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation. BMC Biol. 2024. V.22(1). 165. doi:10.1186/s12915-024-01962-6 202. Luo Y, Liu Z, Jin Z et al. Phased T2T genome assemblies facilitate the mining of disease-resistance genes in Vitis davidii. Hortic Res. 2024. V.12(2). uhae306. doi:10.1093/hr/uhae306 203. Djari A, Madignier G, Di Valentin O et al. Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine. Proc Natl Acad Sci USA. 2024. V.121(23). e2403750121. doi:10.1073/pnas.2403750121 204. Chen Z, Zhang L, Lv Y et al. A genome assembly of ginger (Zingiber officinale Roscoe) provides insights into genome evolution and 6-gingerol biosynthesis. Plant J. 2024. V.118(3). P.682-695. doi:10.1111/tpj.16625 205. Li K, Chen R, Abudoukayoumu A et al. Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube. Hortic Res. 2024. V.11(5). uhae071. doi:10.1093/hr/uhae071 206. Guo M, Bi G, Wang H et al. Genomes of autotetraploid wild and cultivated Ziziphus mauritiana reveal polyploid evolution and crop domestication. Plant Physiol. 2024. V.196(4). P.2701-2720. doi:10.1093/plphys/kiae512