{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T08:52:37Z","timestamp":1775638357888,"version":"3.50.1"},"reference-count":93,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,3,25]],"date-time":"2022-03-25T00:00:00Z","timestamp":1648166400000},"content-version":"vor","delay-in-days":83,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-008213"],"award-info":[{"award-number":["INV-008213"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Findings<\/jats:title>\n                  <jats:p>Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy &amp;gt;QV46, contig N50 &amp;gt;18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20\u201330% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in &amp;lt;2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/gigascience\/giac028","type":"journal-article","created":{"date-parts":[[2022,3,25]],"date-time":"2022-03-25T19:40:56Z","timestamp":1648237256000},"source":"Crossref","is-referenced-by-count":56,"title":["The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8581-908X","authenticated-orcid":false,"given":"Weihong","family":"Qi","sequence":"first","affiliation":[{"name":"Functional Genomics Center Zurich, ETH Zurich and University of Zurich , Winterthurerstrasse 190, 8057, Zurich,","place":["Switzerland"]},{"name":"Department of Biology, Institute of Molecular Plant Biology , ETH Zurich, Universit\u00e4tstrasse 2, 8092, Zurich,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , 1202, Geneva,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2213-5777","authenticated-orcid":false,"given":"Yi-Wen","family":"Lim","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Molecular Plant Biology , ETH Zurich, Universit\u00e4tstrasse 2, 8092, Zurich,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8019-3911","authenticated-orcid":false,"given":"Andrea","family":"Patrignani","sequence":"additional","affiliation":[{"name":"Functional Genomics Center Zurich, ETH Zurich and University of Zurich , Winterthurerstrasse 190, 8057, Zurich,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0828-8681","authenticated-orcid":false,"given":"Pascal","family":"Schl\u00e4pfer","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Molecular Plant Biology , ETH Zurich, Universit\u00e4tstrasse 2, 8092, Zurich,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9254-9110","authenticated-orcid":false,"given":"Anna","family":"Bratus-Neuenschwander","sequence":"additional","affiliation":[{"name":"Functional Genomics Center Zurich, ETH Zurich and University of Zurich , Winterthurerstrasse 190, 8057, Zurich,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0124-8625","authenticated-orcid":false,"given":"Simon","family":"Gr\u00fcter","sequence":"additional","affiliation":[{"name":"Functional Genomics Center Zurich, ETH Zurich and University of Zurich , Winterthurerstrasse 190, 8057, Zurich,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3432-4375","authenticated-orcid":false,"given":"Christelle","family":"Chanez","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Molecular Plant Biology , ETH Zurich, Universit\u00e4tstrasse 2, 8092, Zurich,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3361-4730","authenticated-orcid":false,"given":"Nathalie","family":"Rodde","sequence":"additional","affiliation":[{"name":"INRAE, CNRGV French Plant Genomic Resource Center , F-31320, Castanet Tolosan,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5640-4264","authenticated-orcid":false,"given":"Elisa","family":"Prat","sequence":"additional","affiliation":[{"name":"INRAE, CNRGV French Plant Genomic Resource Center , F-31320, Castanet Tolosan,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4446-1426","authenticated-orcid":false,"given":"Sonia","family":"Vautrin","sequence":"additional","affiliation":[{"name":"INRAE, CNRGV French Plant Genomic Resource Center , F-31320, Castanet Tolosan,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1348-6164","authenticated-orcid":false,"given":"Margaux-Alison","family":"Fustier","sequence":"additional","affiliation":[{"name":"INRAE, CNRGV French Plant Genomic Resource Center , F-31320, Castanet Tolosan,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1176-552X","authenticated-orcid":false,"given":"Diogo","family":"Pratas","sequence":"additional","affiliation":[{"name":"Department of Electronics, Telecommunications and Informatics and Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro , Campus Universit\u00e1rio de Santiago, 3810-193 Aveiro,","place":["Portugal"]},{"name":"Department of Virology, University of Helsinki , Haartmaninkatu 3, 00014 Helsinki,","place":["Finland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7488-4262","authenticated-orcid":false,"given":"Ralph","family":"Schlapbach","sequence":"additional","affiliation":[{"name":"Functional Genomics Center Zurich, ETH Zurich and University of Zurich , Winterthurerstrasse 190, 8057, Zurich,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1872-2998","authenticated-orcid":false,"given":"Wilhelm","family":"Gruissem","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Molecular Plant Biology , ETH Zurich, Universit\u00e4tstrasse 2, 8092, Zurich,","place":["Switzerland"]},{"name":"Biotechnology Center, National Chung Hsing University , 145 Xingda Road, Taichung 40227,","place":["Taiwan"]}]}],"member":"286","published-online":{"date-parts":[[2022,3,24]]},"reference":[{"issue":"2","key":"2024111706375946100_bib1","doi-asserted-by":"crossref","first-page":"439","DOI":"10.3390\/biology1020439","article-title":"Why assembling plant genome sequences is so challenging","volume":"1","author":"Claros","year":"2012","journal-title":"Biology"},{"issue":"1","key":"2024111706375946100_bib2","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1093\/genetics\/144.1.427","article-title":"Heterozygosity, heteromorphy, and phylogenetic trees in asexual eukaryotes","volume":"144","author":"Birky","year":"1996","journal-title":"Genetics"},{"issue":"4","key":"2024111706375946100_bib3","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/genetics\/164.4.1635","article-title":"The population genetics of clonal and partially clonal diploids","volume":"164","author":"Balloux","year":"2003","journal-title":"Genetics"},{"issue":"6","key":"2024111706375946100_bib4","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1002\/ece3.571","article-title":"Effects of clonality on the genetic variability of rare, insular species: the case of Ruta microcarpa from the Canary Islands","volume":"3","author":"Meloni","year":"2013","journal-title":"Ecol Evol"},{"key":"2024111706375946100_bib5","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.pbi.2019.12.009","article-title":"Building near-complete plant genomes","volume":"54","author":"Michael","year":"2020","journal-title":"Curr Opin Plant Biol"},{"issue":"21","key":"2024111706375946100_bib6","doi-asserted-by":"crossref","first-page":"10994","DOI":"10.1093\/nar\/gkz841","article-title":"Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases","volume":"47","author":"T\u00f8rresen","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2024111706375946100_bib7","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nbt.3535","article-title":"Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity","volume":"34","author":"Bredeson","year":"2016","journal-title":"Nat Biotechnol"},{"issue":"1","key":"2024111706375946100_bib8","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s12915-019-0697-6","article-title":"Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars","volume":"17","author":"Kuon","year":"2019","journal-title":"BMC Biol"},{"issue":"6","key":"2024111706375946100_bib9","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1016\/j.molp.2021.04.009","article-title":"Allele-defined genome reveals biallelic differentiation during cassava evolution","volume":"14","author":"Hu","year":"2021","journal-title":"Mol Plant"},{"key":"2024111706375946100_bib10","doi-asserted-by":"crossref","first-page":"5110","DOI":"10.1038\/ncomms6110","article-title":"Cassava genome from a wild ancestor to cultivated varieties","volume":"5","author":"Wang","year":"2014","journal-title":"Nat Commun"},{"key":"2024111706375946100_bib11","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41438-019-0195-6","article-title":"Genome sequences of horticultural plants: past, present, and future","volume":"6","author":"Chen","year":"2019","journal-title":"Hortic Res"},{"issue":"1","key":"2024111706375946100_bib12","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1007\/s12042-011-9088-z","article-title":"The cassava genome: current progress, future directions","volume":"5","author":"Prochnik","year":"2012","journal-title":"Trop Plant Biol"},{"issue":"9","key":"2024111706375946100_bib13","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.tig.2018.05.008","article-title":"The third revolution in sequencing technology","volume":"34","author":"van\u00a0Dijk","year":"2018","journal-title":"Trends Genet"},{"key":"2024111706375946100_bib14","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1038\/nbt.4318","article-title":"A reference standard for genome biology","volume":"36","year":"2018","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2024111706375946100_bib15","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1101\/gr.263566.120","article-title":"HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads","volume":"30","author":"Nurk","year":"2020","journal-title":"Genome Res"},{"issue":"10","key":"2024111706375946100_bib16","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","article-title":"Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome","volume":"37","author":"Wenger","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"2","key":"2024111706375946100_bib17","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/ahg.12364","article-title":"Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads","volume":"84","author":"Vollger","year":"2020","journal-title":"Ann Hum Genet"},{"issue":"3","key":"2024111706375946100_bib18","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1038\/s41587-020-0719-5","article-title":"Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads","volume":"39","author":"Porubsky","year":"2021","journal-title":"Nat Biotechnol"},{"issue":"2","key":"2024111706375946100_bib19","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"},{"issue":"10","key":"2024111706375946100_bib20","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1038\/s41588-020-0699-x","article-title":"Haplotype-resolved genome analyses of a heterozygous diploid potato","volume":"52","author":"Zhou","year":"2020","journal-title":"Nat Genet"},{"issue":"3","key":"2024111706375946100_bib21","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/s41588-019-0356-4","article-title":"Origin and evolution of the octoploid strawberry genome","volume":"51","author":"Edger","year":"2019","journal-title":"Nat Genet"},{"key":"2024111706375946100_bib22","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.virusres.2013.12.028","article-title":"High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding","volume":"186","author":"Rabbi","year":"2014","journal-title":"Virus Res"},{"issue":"12","key":"2024111706375946100_bib23","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1038\/nmeth.4035","article-title":"Phased diploid genome assembly with single-molecule real-time sequencing","volume":"13","author":"Chin","year":"2016","journal-title":"Nat Methods"},{"issue":"2","key":"2024111706375946100_bib24","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"},{"issue":"7856","key":"2024111706375946100_bib25","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species","volume":"592","author":"Rhie","year":"2021","journal-title":"Nature"},{"issue":"9","key":"2024111706375946100_bib26","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1093\/bioinformatics\/btu023","article-title":"Exploring genome characteristics and sequence quality without a reference","volume":"30","author":"Simpson","year":"2014","journal-title":"Bioinformatics"},{"issue":"2","key":"2024111706375946100_bib27","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/ng.1028","article-title":"De novo assembly and genotyping of variants using colored de Bruijn graphs","volume":"44","author":"Iqbal","year":"2012","journal-title":"Nat Genet"},{"issue":"1","key":"2024111706375946100_bib28","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"},{"issue":"6","key":"2024111706375946100_bib29","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","author":"Chin","year":"2013","journal-title":"Nat Methods"},{"issue":"1","key":"2024111706375946100_bib30","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1534\/g3.114.015008","article-title":"High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations","volume":"5","author":"International Cassava Genetic Map Consortium (ICGMC)","year":"2014","journal-title":"G3 (Bethesda)"},{"key":"2024111706375946100_bib31","article-title":"Phytozome info: Manihot esculenta v8.1","author":"Phytozome"},{"issue":"4","key":"2024111706375946100_bib32","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1111\/nph.14443","article-title":"Gene expression atlas for the food security crop cassava","volume":"213","author":"Wilson","year":"2017","journal-title":"New Phytol"},{"issue":"8","key":"2024111706375946100_bib33","doi-asserted-by":"crossref","first-page":"2898","DOI":"10.1073\/pnas.1300127110","article-title":"Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants","volume":"110","author":"Smet","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"19","key":"2024111706375946100_bib34","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"},{"issue":"1","key":"2024111706375946100_bib35","doi-asserted-by":"crossref","first-page":"e1005944","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"},{"issue":"5","key":"2024111706375946100_bib36","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa048","article-title":"Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements","volume":"9","author":"Hosseini","year":"2020","journal-title":"Gigascience"},{"issue":"1","key":"2024111706375946100_bib37","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1186\/s13059-019-1755-7","article-title":"Benchmarking of alignment-free sequence comparison methods","volume":"20","author":"Zielezinski","year":"2019","journal-title":"Genome Biol"},{"issue":"1","key":"2024111706375946100_bib38","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/s41438-021-00599-8","article-title":"Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger","volume":"8","author":"Cheng","year":"2021","journal-title":"Hortic Res"},{"issue":"8","key":"2024111706375946100_bib39","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"},{"issue":"12","key":"2024111706375946100_bib40","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1038\/nbt.4277","article-title":"De novo assembly of haplotype-resolved genomes with trio binning","volume":"36","author":"Koren","year":"2018","journal-title":"Nat Biotechnol"},{"issue":"6","key":"2024111706375946100_bib41","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.2741\/4531","article-title":"Plant mitochondrial DNA","volume":"22","author":"Morley","year":"2017","journal-title":"Front Biosci (Landmark Ed)"},{"issue":"8","key":"2024111706375946100_bib42","doi-asserted-by":"crossref","first-page":"e1008373","DOI":"10.1371\/journal.pgen.1008373","article-title":"The alternative reality of plant mitochondrial DNA: one ring does not rule them all","volume":"15","author":"Kozik","year":"2019","journal-title":"PLoS Genet"},{"issue":"9","key":"2024111706375946100_bib43","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1038\/s41477-019-0507-8","article-title":"The population genetics of structural variants in grapevine domestication","volume":"5","author":"Zhou","year":"2019","journal-title":"Nat Plants"},{"issue":"12","key":"2024111706375946100_bib44","doi-asserted-by":"crossref","first-page":"3507","DOI":"10.1093\/molbev\/msaa185","article-title":"Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication","volume":"37","author":"Kou","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"8","key":"2024111706375946100_bib45","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1038\/s41477-020-0733-0","article-title":"Plant pan-genomes are the new reference","volume":"6","author":"Bayer","year":"2020","journal-title":"Nat Plants"},{"issue":"1","key":"2024111706375946100_bib46","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13059-020-02224-8","article-title":"How the pan-genome is changing crop genomics and improvement","volume":"22","author":"Della\u00a0Coletta","year":"2021","journal-title":"Genome Biol"},{"issue":"1","key":"2024111706375946100_bib47","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s13059-021-02351-w","article-title":"Cotton pan-genome retrieves the lost sequences and genes during domestication and selection","volume":"22","author":"Li","year":"2021","journal-title":"Genome Biol"},{"issue":"12","key":"2024111706375946100_bib48","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"},{"issue":"1","key":"2024111706375946100_bib49","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/s13059-020-02168-z","article-title":"The design and construction of reference pangenome graphs with minigraph","volume":"21","author":"Li","year":"2020","journal-title":"Genome Biol"},{"key":"2024111706375946100_bib50","first-page":"1","article-title":"Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide","volume":"5","author":"Peterson","year":"2000","journal-title":"J Agric Genomics"},{"key":"2024111706375946100_bib51","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1186\/1756-0500-3-225","article-title":"Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)","volume":"3","author":"Gonthier","year":"2010","journal-title":"BMC Res Notes"},{"issue":"3","key":"2024111706375946100_bib52","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1111\/j.1467-7652.2004.00065.x","article-title":"Efficient cloning of plant genomes into bacterial artificial chromosome (BAC) libraries with larger and more uniform insert size","volume":"2","author":"Chalhoub","year":"2004","journal-title":"Plant Biotechnol J"},{"key":"2024111706375946100_bib53","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.12688\/f1000research.7334.1","article-title":"HiCUP: pipeline for mapping and processing Hi-C data","volume":"4","author":"Wingett","year":"2015","journal-title":"F1000Res"},{"issue":"3","key":"2024111706375946100_bib54","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.126953.111","article-title":"Efficient de novo assembly of large genomes using compressed data structures","volume":"22","author":"Simpson","year":"2012","journal-title":"Genome Res"},{"key":"2024111706375946100_bib55","article-title":"IPA HiFi Genome Assembler","author":"Pacific Biosciences"},{"issue":"8","key":"2024111706375946100_bib56","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"},{"issue":"12","key":"2024111706375946100_bib57","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1101\/gr.126599.111","article-title":"Assemblathon 1: a competitive assessment of de novo short read assembly methods","volume":"21","author":"Earl","year":"2011","journal-title":"Genome Res"},{"key":"2024111706375946100_bib58","author":"Guan"},{"key":"2024111706375946100_bib59","first-page":"227","article-title":"Gene prediction: methods and protocols","volume-title":"Methods Mol. Biol","author":"Seppey","year":"1962"},{"issue":"D1","key":"2024111706375946100_bib60","doi-asserted-by":"crossref","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"2024111706375946100_bib61","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":"2024111706375946100_bib62","doi-asserted-by":"crossref","first-page":"100","DOI":"10.12688\/f1000research.10571.2","article-title":"Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis","volume":"6","author":"Weirather","year":"2017","journal-title":"F1000Res"},{"issue":"4","key":"2024111706375946100_bib63","first-page":"656","article-title":"BLAT\u2014The BLAST-Like Alignment Tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2024111706375946100_bib64","article-title":"Arima mapping pipeline","author":"Arima"},{"issue":"8","key":"2024111706375946100_bib65","doi-asserted-by":"crossref","first-page":"e1007273","DOI":"10.1371\/journal.pcbi.1007273","article-title":"Integrating Hi-C links with assembly graphs for chromosome-scale assembly","volume":"15","author":"Ghurye","year":"2019","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"2024111706375946100_bib66","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13059-014-0573-1","article-title":"ALLMAPS: robust scaffold ordering based on multiple maps","volume":"16","author":"Tang","year":"2015","journal-title":"Genome Biol"},{"issue":"2","key":"2024111706375946100_bib67","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2024111706375946100_bib68","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1101\/gr.88502","article-title":"Automated de novo identification of repeat sequence families in sequenced genomes","volume":"12","author":"Bao","year":"2002","journal-title":"Genome Res"},{"issue":"2","key":"2024111706375946100_bib69","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/0097-8485(93)85006-X","article-title":"Statistics of local complexity in amino acid sequences and sequence databases","volume":"17","author":"Wootton","year":"1993","journal-title":"Comput Chem"},{"key":"2024111706375946100_bib70","author":"Smit","year":"2013-2015"},{"issue":"3","key":"2024111706375946100_bib71","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1109\/TCBB.2013.68","article-title":"GenomeTools: a comprehensive software library for efficient processing of structured genome annotations","volume":"10","author":"Gremme","year":"2013","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"2","key":"2024111706375946100_bib72","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.1104\/pp.17.01310","article-title":"LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons","volume":"176","author":"Ou","year":"2018","journal-title":"Plant Physiol"},{"key":"2024111706375946100_bib73","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1007\/978-3-642-04241-6_31","article-title":"Large-scale neighbor-joining with NINJA","volume-title":"Algorithms in Bioinformatics","author":"Wheeler","year":"2009"},{"issue":"4","key":"2024111706375946100_bib74","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"23","key":"2024111706375946100_bib75","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"issue":"17","key":"2024111706375946100_bib76","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"},{"issue":"2","key":"2024111706375946100_bib77","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1104\/pp.113.230144","article-title":"MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations","volume":"164","author":"Campbell","year":"2014","journal-title":"Plant Physiol"},{"issue":"12","key":"2024111706375946100_bib78","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1093\/bioinformatics\/btaa1016","article-title":"Liftoff: an accurate gene annotation mapping tool","volume":"37","author":"Shumate","year":"2020","journal-title":"Bioinformatics"},{"issue":"7","key":"2024111706375946100_bib79","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2024111706375946100_bib80","volume-title":"SynVisio: A Multiscale Tool to Explore Genomic Conservation","author":"Bandi","year":"2020"},{"issue":"1","key":"2024111706375946100_bib81","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1002\/cpbi.57","article-title":"Predicting genes in single genomes with AUGUSTUS","volume":"65","author":"Hoff","year":"2019","journal-title":"Curr Protoc Bioinformatics"},{"issue":"5","key":"2024111706375946100_bib82","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat Biotechnol"},{"issue":"12","key":"2024111706375946100_bib83","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"issue":"18","key":"2024111706375946100_bib84","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"2024111706375946100_bib85","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-12683-3_28","article-title":"IDBA - a practical iterative de Bruijn graph de novo assembler","volume-title":"Research in Computational Molecular Biology. RECOMB 2010","author":"Peng","year":"2010"},{"key":"2024111706375946100_bib86","article-title":"PacificBiosciences\/pbsv","author":"Pacific Biosciences"},{"key":"2024111706375946100_bib87","doi-asserted-by":"crossref","first-page":"14061","DOI":"10.1038\/ncomms14061","article-title":"Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast","volume":"8","author":"Jeffares","year":"2017","journal-title":"Nat Commun"},{"key":"2024111706375946100_bib88","article-title":"lh3\/gfatools","author":"Li"},{"key":"2024111706375946100_bib89","article-title":"topGO: Enrichment Analysis for Gene Ontology","author":"Alexa","year":"2021"},{"key":"2024111706375946100_bib90","article-title":"topGO: Enrichment Analysis for Gene Ontology","author":"Alexa"},{"key":"2024111706375946100_bib91","doi-asserted-by":"crossref","unstructured":"Qi W, Lim Y, Patrignani A, et al. \u00a0The haplotype-resolved chromosome pairs and transcriptome data of a heterozygous diploid African cassava cultivar. GigaScience Database. 2022. 10.5524\/102193.","DOI":"10.1101\/2021.11.16.468774"},{"key":"2024111706375946100_bib92_1646847648352"},{"key":"2024111706375946100_bib93_1646847892167"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giac028\/60706904\/giac028.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giac028\/60706904\/giac028.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,17]],"date-time":"2024-11-17T06:38:55Z","timestamp":1731825535000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/giac028\/6554099"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"references-count":93,"URL":"https:\/\/doi.org\/10.1093\/gigascience\/giac028","relation":{},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022]]},"published":{"date-parts":[[2022]]},"article-number":"giac028"}}