{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T23:59:53Z","timestamp":1790294393403,"version":"4.1.0"},"reference-count":113,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hort Innovation, \u2018Building an Advanced Genomics Platform for Australian Horticulture","award":["AS21006"],"award-info":[{"award-number":["AS21006"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Collapsed (haploid) genome assemblies omit large portions of genetic information, especially in heterozygous, clonally propagated crops such as pineapple. Here, we assembled a telomere-to-telomere, haplotype-resolved genome for a key pre-Colombian cultivar of pineapple (Ananas comosus) \u2018Smooth Cayenne\u2019 (F180) using PacBio HiFi and Hi-C data. The two 25-chromosome haplotypes span 858\u00a0Mb (N50\u2009\u2248\u200916.8\u00a0Mb) and are &amp;gt;99% complete, each resolving all centromeres and 22 of 25 telomeres. Comparison of the phased chromosomes reveals 1.5 million single nucleotide polymorphisms and 1953 large structural variants (74 inversions, 750 translocations, and 1129 segmental duplications). This assembly reveals that inversions have profoundly impacted the \u2018Smooth Cayenne\u2019 genome, reshaping ~3%\u20134% of the total sequence. Structural context dictates the genetic impact of these large inversions, as shown in recombination landscape analysis of 374 F1 seedlings, wherein a 1.3-Mb paracentric inversion on chromosome 20 forms a strict recombination coldspot, whereas a 6-Mb pericentric inversion on chromosome 24 still permits gene flow likely via short double crossovers, albeit at lower rates than the rest of the chromosome. Re-anchoring the 11\u2009879 DArTseq markers from the F1 seedlings to the phased reference assembly removes the dense network of spurious interchromosomal linkage seen in the collapsed F153 \u2018Smooth Cayenne\u2019 genome, likely providing markedly cleaner baselines for genome-wide association studies and genomic prediction. These results establish the new F180 assembly as a very high-quality reference, illustrate how undetected inversions can silently constrain genetic gain, and demonstrate the broader value of phased genomes for dissecting heterozygosity, structural variation, and meiotic behaviour in perennial crops.<\/jats:p>","DOI":"10.1093\/hr\/uhag189","type":"journal-article","created":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T14:28:16Z","timestamp":1778250496000},"source":"Crossref","is-referenced-by-count":0,"title":["The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes"],"prefix":"10.1093","volume":"13","author":[{"given":"Jingping","family":"Fang","sequence":"first","affiliation":[{"name":"College of Life Science, Fujian Normal University , Fuzhou 350117 ,","place":["China"]},{"name":"Queensland Alliance of Agriculture and Food Innovation, The University of Queensland , St Lucia, Queensland 4072 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick J","family":"Mason","sequence":"additional","affiliation":[{"name":"Queensland Alliance of Agriculture and Food Innovation, The University of Queensland , St Lucia, Queensland 4072 ,","place":["Australia"]},{"name":"ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland , St Lucia, Queensland 4072 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garth","family":"Sanewski","sequence":"additional","affiliation":[{"name":"Queensland Department of Primary Industries , EcoSciences Precinct, Dutton Park, Queensland 4102 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Webb","sequence":"additional","affiliation":[{"name":"Queensland Department of Primary Industries , EcoSciences Precinct, Dutton Park, Queensland 4102 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linwei","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Life Science, Fujian Normal University , Fuzhou 350117 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinbin","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Science, Fujian Normal University , Fuzhou 350117 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rhys G R","family":"Copeland","sequence":"additional","affiliation":[{"name":"WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University , Murdoch, WA 6150 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Zhuang","sequence":"additional","affiliation":[{"name":"College of Life Science, Fujian Normal University , Fuzhou 350117 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annapurna","family":"Chitikineni","sequence":"additional","affiliation":[{"name":"WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University , Murdoch, WA 6150 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanika","family":"Garg","sequence":"additional","affiliation":[{"name":"WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University , Murdoch, WA 6150 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Dillon","sequence":"additional","affiliation":[{"name":"Queensland Department of Primary Industries , EcoSciences Precinct, Dutton Park, Queensland 4102 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Parwinder","family":"Kaur","sequence":"additional","affiliation":[{"name":"School of Agriculture and Environment, University of Western Australia , 35 Stirling Way, Crawley, Western Australia 6009 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4562-9131","authenticated-orcid":false,"given":"Rajeev K","family":"Varshney","sequence":"additional","affiliation":[{"name":"WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University , Murdoch, WA 6150 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4060-0292","authenticated-orcid":false,"given":"Robert J","family":"Henry","sequence":"additional","affiliation":[{"name":"Queensland Alliance of Agriculture and Food Innovation, The University of Queensland , St Lucia, Queensland 4072 ,","place":["Australia"]},{"name":"ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland , St Lucia, Queensland 4072 ,","place":["Australia"]},{"name":"VinUni Big Data Research Institute, VinUniversity , Hanoi ,","place":["Vietnam"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,8]]},"reference":[{"key":"2026092419170414000_ref1","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1186\/s12859-021-04118-3","article-title":"Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms","volume":"22","author":"Guiglielmoni","year":"2021","journal-title":"BMC Bioinform"},{"key":"2026092419170414000_ref2","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/nature11413","article-title":"The oyster genome reveals stress adaptation and complexity of shell formation","volume":"490","author":"Zhang","year":"2012","journal-title":"Nature"},{"key":"2026092419170414000_ref3","doi-asserted-by":"crossref","first-page":"giab020","DOI":"10.1093\/gigascience\/giab020","article-title":"A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas","volume":"10","author":"Penaloza","year":"2021","journal-title":"GigaScience"},{"key":"2026092419170414000_ref4","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.ymeth.2012.05.001","article-title":"Hi-C: a comprehensive technique to capture the conformation of genomes","volume":"58","author":"Belton","year":"2012","journal-title":"Methods"},{"key":"2026092419170414000_ref5","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"Cheng","year":"2021","journal-title":"Nat Methods"},{"key":"2026092419170414000_ref6","doi-asserted-by":"crossref","first-page":"giz068","DOI":"10.1093\/gigascience\/giz068","article-title":"How can a high-quality genome assembly help plant breeders?","volume":"8","author":"Benevenuto","year":"2019","journal-title":"GigaScience"},{"key":"2026092419170414000_ref7","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.cell.2020.05.023","article-title":"Pan-genome of wild and cultivated soybeans","volume":"182","author":"Liu","year":"2020","journal-title":"Cell"},{"key":"2026092419170414000_ref8","doi-asserted-by":"crossref","first-page":"2535","DOI":"10.1111\/mec.15428","article-title":"Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype","volume":"29","author":"Huang","year":"2020","journal-title":"Mol Ecol"},{"key":"2026092419170414000_ref9","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1111\/pbi.13917","article-title":"Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley","volume":"21","author":"Zhang","year":"2023","journal-title":"Plant Biotechnol J"},{"key":"2026092419170414000_ref10","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1111\/nph.18004","article-title":"Epigenomic and structural events preclude recombination in Brassica napus","volume":"234","author":"Boideau","year":"2022","journal-title":"New Phytol"},{"key":"2026092419170414000_ref11","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1111\/nph.20252","article-title":"Centromeres are hotspots for chromosomal inversions and breeding traits in mango","volume":"245","author":"Wilkinson","year":"2025","journal-title":"New Phytol"},{"key":"2026092419170414000_ref12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1000501","article-title":"How and why chromosome inversions evolve","volume":"8","author":"Kirkpatrick","year":"2010","journal-title":"PLoS Biol"},{"key":"2026092419170414000_ref13","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1093\/genetics\/146.2.695","article-title":"Recombination and gene flux caused by gene conversion and crossing over in inversion heterokaryotypes","volume":"146","author":"Navarro","year":"1997","journal-title":"Genetics"},{"key":"2026092419170414000_ref14","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3003043","article-title":"Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly colour pattern supergene","volume":"23","author":"De-Kayne","year":"2025","journal-title":"PLoS Biol"},{"key":"2026092419170414000_ref15","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1038\/s41477-020-00817-6","article-title":"CRISPR-Cas9-mediated 75.5-Mb inversion in maize","volume":"6","author":"Schwartz","year":"2020","journal-title":"Nat Plants"},{"key":"2026092419170414000_ref16","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.tree.2018.04.002","article-title":"Eco-evolutionary genomics of chromosomal inversions","volume":"33","author":"Wellenreuther","year":"2018","journal-title":"Trends Ecol Evol"},{"key":"2026092419170414000_ref17","doi-asserted-by":"crossref","first-page":"msac101","DOI":"10.1093\/molbev\/msac101","article-title":"Mutation load in sunflower inversions is negatively correlated with inversion heterozygosity","volume":"39","author":"Huang","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2026092419170414000_ref18","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/978-3-319-63170-7_8","volume-title":"Genomic Selection for Crop Improvement: New Molecular Breeding Strategies for Crop Improvement","author":"Gemenet","year":"2017"},{"key":"2026092419170414000_ref19","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1590\/S1984-70332011000500006","article-title":"Breeding vegetatively propagated horticultural crops","volume":"11","author":"Bisognin","year":"2011","journal-title":"Crop Breed Appl Biotechnol"},{"key":"2026092419170414000_ref20","doi-asserted-by":"crossref","first-page":"769","DOI":"10.22271\/chemi.2021.v9.i1k.11317","article-title":"Wide hybridization for fruit crop improvement: a review","volume":"9","author":"Anushma","year":"2021","journal-title":"Int J Chem Stud"},{"key":"2026092419170414000_ref21","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1038\/s42003-021-02782-y","article-title":"Features and applications of haplotypes in crop breeding","volume":"4","author":"Bhat","year":"2021","journal-title":"Commun Biol"},{"key":"2026092419170414000_ref22","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1038\/s41588-019-0506-8","article-title":"The bracteatus pineapple genome and domestication of clonally propagated crops","volume":"51","author":"Chen","year":"2019","journal-title":"Nat Genet"},{"key":"2026092419170414000_ref23","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1038\/ng.3435","article-title":"The pineapple genome and the evolution of CAM photosynthesis","volume":"47","author":"Ming","year":"2015","journal-title":"Nat Genet"},{"key":"2026092419170414000_ref24","doi-asserted-by":"crossref","first-page":"0","DOI":"10.48130\/TP-2023-0018","article-title":"Overcoming key technical challenges in the genetic transformation of pineapple","volume":"2","author":"He","year":"2023","journal-title":"Trop Plant"},{"key":"2026092419170414000_ref25","doi-asserted-by":"crossref","first-page":"885","DOI":"10.4236\/ajps.2019.106063","article-title":"The cause for water-heart fruit of pineapple and protective measurements","volume":"10","author":"Shu","year":"2019","journal-title":"Am J Plant Sci"},{"key":"2026092419170414000_ref26","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/978-3-031-59268-3_7","volume-title":"Advances in Tropical Crop Protection","author":"Sapak","year":"2024"},{"key":"2026092419170414000_ref27","doi-asserted-by":"crossref","first-page":"2208","DOI":"10.1111\/jipb.13748","article-title":"The pineapple reference genome: telomere-to-telomere assembly, manually curated annotation, and comparative analysis","volume":"66","author":"Feng","year":"2024","journal-title":"J Integr Plant Biol"},{"key":"2026092419170414000_ref28","article-title":"Assessing genome assembly quality using the LTR Assembly Index (LAI)","volume":"46","author":"Ou","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026092419170414000_ref29","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.1038\/s41596-024-00968-2","article-title":"Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX","volume":"19","author":"Wang","year":"2024","journal-title":"Nat Protoc"},{"key":"2026092419170414000_ref30","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1101\/gad.1767209","article-title":"SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay","volume":"23","author":"Yamashita","year":"2009","journal-title":"Genes Dev"},{"key":"2026092419170414000_ref31","doi-asserted-by":"crossref","first-page":"15","DOI":"10.3389\/fgene.2021.730821","article-title":"Genome-wide investigation of SBT family genes in pineapple and functional analysis of AcoSBT1.12 in floral transition","volume":"12","author":"Jin","year":"2021","journal-title":"Front Genet"},{"key":"2026092419170414000_ref32","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1093\/pcp\/pcm176","article-title":"The FLX gene of Arabidopsis is required for FRI-dependent activation of FLC expression","volume":"49","author":"Andersson","year":"2008","journal-title":"Plant Cell Physiol"},{"key":"2026092419170414000_ref33","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1093\/hr\/uhae306","article-title":"Phased T2T genome assemblies facilitate the mining of disease-resistance genes in Vitis davidii","volume":"12","author":"Luo","year":"2025","journal-title":"Hortic Res"},{"key":"2026092419170414000_ref34","first-page":"8","article-title":"A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean","volume":"12","author":"Wang","year":"2021","journal-title":"Nat Commun"},{"key":"2026092419170414000_ref35","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.21273\/HORTSCI.42.5.1188","article-title":"Delaying natural flowering in pineapple through foliar application of aviglycine, an inhibitor of ethylene biosynthesis","volume":"42","author":"Wang","year":"2007","journal-title":"HortScience"},{"key":"2026092419170414000_ref36","doi-asserted-by":"crossref","first-page":"123","DOI":"10.21273\/HORTSCI.40.1.123","article-title":"Foliar application of aviglycine reduces natural flowering in pineapple","volume":"40","author":"Kuan","year":"2005","journal-title":"HortScience"},{"key":"2026092419170414000_ref37","doi-asserted-by":"crossref","first-page":"281","DOI":"10.17660\/ActaHortic.2016.1111.40","article-title":"Genetic resistance to the root rot pathogen Phytophthora cinnamomi in Ananas","volume":"1111","author":"Sanewski","year":"2016","journal-title":"Acta Hortic"},{"key":"2026092419170414000_ref38","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1146\/annurev-arplant-093020-035446","article-title":"Long noncoding RNAs in fruit crops","volume":"72","author":"Kumar","year":"2021","journal-title":"Annu Rev Plant Biol"},{"key":"2026092419170414000_ref39","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2021.100180","article-title":"Role of non-coding RNAs in plant immunity","volume":"2","author":"Song","year":"2021","journal-title":"Plant Commun"},{"key":"2026092419170414000_ref40","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1007\/s13313-022-00880-x","article-title":"Heart rot of Australian pineapples caused by Dickeya zeae","volume":"51","author":"Young","year":"2022","journal-title":"Australas Plant Pathol"},{"key":"2026092419170414000_ref41","doi-asserted-by":"crossref","first-page":"1514235","DOI":"10.3389\/fmicb.2024.1514235","article-title":"Comprehensive analysis of causal pathogens and determinants influencing black rot disease development in MD2 pineapples","volume":"15","author":"Kuruppu","year":"2025","journal-title":"Front Microbiol"},{"key":"2026092419170414000_ref42","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.tplants.2019.12.017","article-title":"Counting on crossovers: controlled recombination for plant breeding","volume":"25","author":"Taagen","year":"2020","journal-title":"Trends Plant Sci"},{"key":"2026092419170414000_ref43","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.tig.2024.09.009","article-title":"Crossover recombination between homologous chromosomes in meiosis: recent progress and remaining mysteries","volume":"41","author":"Payero","year":"2025","journal-title":"Trends Genet"},{"key":"2026092419170414000_ref44","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1111\/mec.14921","article-title":"Pervasive gene conversion in chromosomal inversion heterozygotes","volume":"28","author":"Korunes","year":"2019","journal-title":"Mol Ecol"},{"key":"2026092419170414000_ref45","doi-asserted-by":"crossref","first-page":"1761","DOI":"10.1111\/jeb.14242","article-title":"How chromosomal inversions reorient the evolutionary process","volume":"36","author":"Berdan","year":"2023","journal-title":"J Evol Biol"},{"key":"2026092419170414000_ref46","doi-asserted-by":"crossref","first-page":"10051","DOI":"10.1073\/pnas.0801848105","article-title":"Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence","volume":"105","author":"Kulathinal","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026092419170414000_ref47","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1093\/gbe\/evr081","article-title":"Effects of inversions on within-and between-species recombination and divergence","volume":"3","author":"Stevison","year":"2011","journal-title":"Genome Biol Evol"},{"key":"2026092419170414000_ref48","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1111\/tpj.14505","article-title":"Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis","volume":"100","author":"Termolino","year":"2019","journal-title":"Plant J"},{"key":"2026092419170414000_ref49","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2026092419170414000_ref50","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/nature22971","article-title":"Improved maize reference genome with single-molecule technologies","volume":"546","author":"Jiao","year":"2017","journal-title":"Nature"},{"key":"2026092419170414000_ref51","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.aac.2024.01.005","article-title":"Abiotic stress-induced gene expression in pineapple as a potential genetic marker","volume":"3","author":"Sinaga","year":"2024","journal-title":"Adv Agrochem"},{"key":"2026092419170414000_ref52","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/s43141-021-00231-1","article-title":"Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes","volume":"19","author":"Hasan","year":"2021","journal-title":"J Genet Eng Biotechnol"},{"key":"2026092419170414000_ref53","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1111\/jipb.12804","article-title":"Exploring the molecular basis of heterosis for plant breeding","volume":"62","author":"Liu","year":"2020","journal-title":"J Integr Plant Biol"},{"key":"2026092419170414000_ref54","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1038\/s41588-020-00723-9","article-title":"Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication","volume":"52","author":"Sun","year":"2020","journal-title":"Nat Genet"},{"key":"2026092419170414000_ref55","doi-asserted-by":"crossref","first-page":"101000","DOI":"10.1016\/j.xplc.2024.101000","article-title":"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","volume":"5","author":"Li","year":"2024","journal-title":"Plant Commun"},{"key":"2026092419170414000_ref56","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s13059-025-03535-4","article-title":"The haplotype-resolved genome assembly of an ancient citrus variety provides insights into the domestication history and fruit trait formation of loose-skin mandarins","volume":"26","author":"Yin","year":"2025","journal-title":"Genome Biol"},{"key":"2026092419170414000_ref57","doi-asserted-by":"crossref","first-page":"5653","DOI":"10.1073\/pnas.1820513116","article-title":"Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis","volume":"116","author":"Shao","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026092419170414000_ref58","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1038\/s41588-021-00895-y","article-title":"Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis","volume":"53","author":"Zhang","year":"2021","journal-title":"Nat Genet"},{"key":"2026092419170414000_ref59","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/tpj.70012","article-title":"Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit","volume":"121","author":"Usai","year":"2025","journal-title":"Plant J"},{"key":"2026092419170414000_ref60","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s12864-024-10395-y","article-title":"Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize","volume":"25","author":"Zhan","year":"2024","journal-title":"BMC Genomics"},{"key":"2026092419170414000_ref61","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/s41467-024-52376-5","article-title":"Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations","volume":"15","author":"Hou","year":"2024","journal-title":"Nat Commun"},{"key":"2026092419170414000_ref62","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/s41467-019-11385-5","article-title":"Transposition favors the generation of large effect mutations that may facilitate rapid adaption","volume":"10","author":"Quadrana","year":"2019","journal-title":"Nat Commun"},{"key":"2026092419170414000_ref63","doi-asserted-by":"crossref","first-page":"115032","DOI":"10.1016\/j.celrep.2024.115032","article-title":"The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil camellia plants","volume":"43","author":"Zhang","year":"2024","journal-title":"Cell Rep"},{"key":"2026092419170414000_ref64","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1093\/hr\/uhad244","article-title":"The haplotype-resolved telomere-to-telomere carnation (Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression","volume":"11","author":"Lan","year":"2024","journal-title":"Hortic Res"},{"key":"2026092419170414000_ref65","first-page":"13","article-title":"A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour","volume":"10","author":"Zhang","year":"2019","journal-title":"Nat Commun"},{"key":"2026092419170414000_ref66","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1038\/s41477-022-01260-5","article-title":"Concerted expansion and contraction of immune receptor gene repertoires in plant genomes","volume":"8","author":"Ngou","year":"2022","journal-title":"Nat Plants"},{"key":"2026092419170414000_ref67","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1126\/science.aaf6395","article-title":"Intracellular innate immune surveillance devices in plants and animals","volume":"354","author":"Jones","year":"2016","journal-title":"Science"},{"key":"2026092419170414000_ref68","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.pbi.2019.04.007","article-title":"NLR singletons, pairs, and networks: evolution, assembly, and regulation of the intracellular immunoreceptor circuitry of plants","volume":"50","author":"Adachi","year":"2019","journal-title":"Curr Opin Plant Biol"},{"key":"2026092419170414000_ref69","first-page":"18","article-title":"A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes","volume":"12","author":"Chen","year":"2023","journal-title":"GigaScience"},{"key":"2026092419170414000_ref70","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/nature01588","article-title":"Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana","volume":"423","author":"Tian","year":"2003","journal-title":"Nature"},{"key":"2026092419170414000_ref71","first-page":"1","volume-title":"Cereal Genomics: Methods and Protocols","author":"Furtado","year":"2014"},{"key":"2026092419170414000_ref72","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"2026092419170414000_ref73","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref74","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes","volume":"11","author":"Ranallo-Benavidez","year":"2020","journal-title":"Nat Commun"},{"key":"2026092419170414000_ref75","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/s41477-024-01755-3","article-title":"Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes","volume":"10","author":"Zeng","year":"2024","journal-title":"Nat Plants"},{"key":"2026092419170414000_ref76","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"key":"2026092419170414000_ref77","doi-asserted-by":"crossref","first-page":"uhad127","DOI":"10.1093\/hr\/uhad127","article-title":"quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification","volume":"10","author":"Lin","year":"2023","journal-title":"Hortic Res"},{"key":"2026092419170414000_ref78","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2026092419170414000_ref79","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref80","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref81","doi-asserted-by":"crossref","first-page":"D516","DOI":"10.1093\/nar\/gkae987","article-title":"OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes","volume":"53","author":"Tegenfeldt","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026092419170414000_ref82","doi-asserted-by":"crossref","first-page":"btad014","DOI":"10.1093\/bioinformatics\/btad014","article-title":"Protein-to-genome alignment with miniprot","volume":"39","author":"Li","year":"2023","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref83","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s40168-020-00808-x","article-title":"MetaEuk\u2014sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics","volume":"8","author":"Levy Karin","year":"2020","journal-title":"Microbiome"},{"key":"2026092419170414000_ref84","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies","volume":"21","author":"Rhie","year":"2020","journal-title":"Genome Biol"},{"key":"2026092419170414000_ref85","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref86","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026092419170414000_ref87","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref88","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026092419170414000_ref89","doi-asserted-by":"crossref","first-page":"4.10.1","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"25","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr Protoc Bioinformatics"},{"key":"2026092419170414000_ref90","doi-asserted-by":"crossref","first-page":"uhad058","DOI":"10.1093\/hr\/uhad058","article-title":"Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes","volume":"10","author":"Nakandala","year":"2023","journal-title":"Hortic Res"},{"key":"2026092419170414000_ref91","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1101\/gr.278090.123","article-title":"BRAKER3: fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA","volume":"34","author":"Gabriel","year":"2024","journal-title":"Genome Res"},{"key":"2026092419170414000_ref92","doi-asserted-by":"crossref","first-page":"9077","DOI":"10.1093\/nar\/gkab688","article-title":"tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes","volume":"49","author":"Chan","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026092419170414000_ref93","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1186\/s13059-019-1911-0","article-title":"SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies","volume":"20","author":"Goel","year":"2019","journal-title":"Genome Biol"},{"key":"2026092419170414000_ref94","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat Genet"},{"key":"2026092419170414000_ref95","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"2026092419170414000_ref96","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1093\/bioinformatics\/btw369","article-title":"Assemblytics: a web analytics tool for the detection of variants from an assembly","volume":"32","author":"Nattestad","year":"2016","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref97","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2026092419170414000_ref98","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS One"},{"key":"2026092419170414000_ref99","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/s13059-024-03359-8","article-title":"SynGAP: a synteny-based toolkit for gene structure annotation polishing","volume":"25","author":"Wu","year":"2024","journal-title":"Genome Biol"},{"key":"2026092419170414000_ref100","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: an integrative toolkit developed for interactive analyses of big biological data","volume":"13","author":"Chen","year":"2020","journal-title":"Mol Plant"},{"key":"2026092419170414000_ref101","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"2026092419170414000_ref102","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s13059-019-1905-y","article-title":"Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline","volume":"20","author":"Ou","year":"2019","journal-title":"Genome Biol"},{"key":"2026092419170414000_ref103","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/978-1-61779-870-2_5","article-title":"Diversity arrays technology: a generic genome profiling technology on open platforms","volume":"888","author":"Kilian","year":"2012","journal-title":"Methods Mol Biol"},{"key":"2026092419170414000_ref104","doi-asserted-by":"crossref","first-page":"181","DOI":"10.17660\/ActaHortic.2016.1111.27","article-title":"The application of DArTseq technology to pineapple","volume":"1111","author":"Kilian","year":"2016","journal-title":"Acta Hortic"},{"key":"2026092419170414000_ref105","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1093\/bioinformatics\/btm308","article-title":"TASSEL: software for association mapping of complex traits in diverse samples","volume":"23","author":"Bradbury","year":"2007","journal-title":"Bioinformatics"},{"key":"2026092419170414000_ref106","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1534\/g3.115.021667","article-title":"LinkImpute: fast and accurate genotype imputation for nonmodel organisms","volume":"5","author":"Money","year":"2015","journal-title":"G3 (Bethesda)"},{"key":"2026092419170414000_ref107","doi-asserted-by":"crossref","first-page":"jkad154","DOI":"10.1093\/g3journal\/jkad154","article-title":"GWLD: an R package for genome-wide linkage disequilibrium analysis","volume":"13","author":"Zhang","year":"2023","journal-title":"G3 (Bethesda)"},{"key":"2026092419170414000_ref108","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1534\/genetics.118.301595","article-title":"R\/qtl2: software for mapping quantitative trait loci with high-dimensional data and multiparent populations","volume":"211","author":"Broman","year":"2019","journal-title":"Genetics"},{"key":"2026092419170414000_ref109","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1186\/s12864-016-3197-x","article-title":"RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants","volume":"17","author":"Li","year":"2016","journal-title":"BMC Genomics"},{"key":"2026092419170414000_ref110","doi-asserted-by":"crossref","DOI":"10.7717\/peerj-cs.251","article-title":"RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms","volume":"6","author":"Hao","year":"2020","journal-title":"PeerJ Comput Sci"},{"key":"2026092419170414000_ref111","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2026092419170414000_ref112","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2026092419170414000_ref113","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Horticulture Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/hr\/advance-article-pdf\/doi\/10.1093\/hr\/uhag189\/68250389\/uhag189.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/13\/10\/uhag189\/68250389\/uhag189.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/13\/10\/uhag189\/68250389\/uhag189.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T23:17:24Z","timestamp":1790291844000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hr\/article\/doi\/10.1093\/hr\/uhag189\/8673000"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,8]]},"references-count":113,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/hr\/uhag189","relation":{},"ISSN":["2052-7276"],"issn-type":[{"value":"2052-7276","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,5,8]]},"article-number":"uhag189"}}