{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T05:20:29Z","timestamp":1788931229265,"version":"build-2803163510"},"reference-count":87,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T00:00:00Z","timestamp":1745452800000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP200102214"],"award-info":[{"award-number":["DP200102214"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Haplotype-resolved (phased) genome assemblies are emerging as important assets for genomic studies of species with high heterozygosity, but remain lacking for key animal lineages. Here, we use PacBio HiFi and Omni-C technologies to assemble the first phased, annotated, chromosome-level genome for any annelid: the reef-building tubeworm Galeolaria caespitosa (Serpulidae). The assembly is 803.5 Mbp long (scaffold N50\u2005=\u200576.5 Mbp) for haplotype 1 and 789.3 Mbp long (scaffold N50\u2005=\u200575.4 Mbp) for haplotype 2, which are arranged into 11 pairs of chromosomes showing no sign of sex chromosomes. This compares with cytological analyses reporting 12 to 13 pairs in G. caespitosa\u2019s closest relatives, including species that are protandrous hermaphrodites. We combined long-read and short-read transcriptome sequencing to annotate both haplotypes, resulting in 30,495 predicted proteins for haplotype 1, 27,423 proteins for haplotype two, and 79.5% of proteins with at least one functional annotation. We also assembled a mitochondrial genome 23 kbp long, annotating all genes typically found in mitochondrial DNA apart from those coding the 16S ribosomal subunit (rrnL) and the protein atp8\u2014a short, fast-evolving mitochondrial gene missing in other metazoans. Comparing G. caespitosa\u2019s genome to those of three other annelids reveals limited collinearity despite 36.0% of shared orthologous gene clusters (4,238 of 11,763 clusters counted in G. caespitosa), suggesting extensive chromosomal rearrangements among lineages. New high-quality annelid genomes may help resolve the genetic and evolutionary basis of this diversity.<\/jats:p>","DOI":"10.1093\/jhered\/esaf025","type":"journal-article","created":{"date-parts":[[2025,4,15]],"date-time":"2025-04-15T07:17:48Z","timestamp":1744701468000},"page":"702-712","source":"Crossref","is-referenced-by-count":5,"title":["A phased chromosome-level genome of the annelid tubeworm <i>Galeolaria caespitosa<\/i>"],"prefix":"10.1093","volume":"116","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5719-1465","authenticated-orcid":false,"given":"Monique","family":"van Dorssen","sequence":"first","affiliation":[{"name":"School of Biological Sciences, Monash University , Victoria ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily K","family":"Belcher","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Monash University , Victoria ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0454-0552","authenticated-orcid":false,"given":"Crist\u00f3bal","family":"Gallegos","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Monash University , Victoria ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn A","family":"Hodgins","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Monash University , Victoria ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keyne","family":"Monro","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Monash University , Victoria ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,4,22]]},"reference":[{"key":"2025090410513954600_CIT0001","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1111\/1755-0998.13160","article-title":"MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics","volume":"20","author":"Allio","year":"2020","journal-title":"Mol Ecol Resour"},{"key":"2025090410513954600_CIT0002","doi-asserted-by":"publisher","first-page":"2860","DOI":"10.1093\/molbev\/msv157","article-title":"Articulating \u201cArchiannelids\u201d: phylogenomics and annelid relationships, with emphasis on meiofaunal taxa","volume":"32","author":"Andrade","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2025090410513954600_CIT0088","article-title":"k-means++: the advantages of careful seeding","volume-title":"Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms","author":"Arthur","year":"2007"},{"key":"2025090410513954600_CIT0004","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1093\/nar\/28.1.304","article-title":"The ENZYME database in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2025090410513954600_CIT0005","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.ympev.2012.08.023","article-title":"MITOS: improved de novo metazoan mitochondrial genome annotation","volume":"69","author":"Bernt","year":"2013","journal-title":"Mol Phylogenet Evol"},{"key":"2025090410513954600_CIT0006","doi-asserted-by":"publisher","first-page":"lqaa108","DOI":"10.1093\/nargab\/lqaa108","article-title":"BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database","volume":"3","author":"Br\u016fna","year":"2021","journal-title":"NAR Genom Bioinform."},{"key":"2025090410513954600_CIT0007","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat Methods"},{"key":"2025090410513954600_CIT0008","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf"},{"key":"2025090410513954600_CIT0009","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":"2013","journal-title":"Plant Physiol"},{"key":"2025090410513954600_CIT0010","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2025090410513954600_CIT0087","doi-asserted-by":"publisher","first-page":"null","DOI":"10.1002\/imt2.107","article-title":"Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp","volume":"2","author":"Chen","year":"2023","journal-title":"iMeta"},{"key":"2025090410513954600_CIT0086","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0011","doi-asserted-by":"publisher","first-page":"gkaf018","DOI":"10.1093\/nar\/gkaf018","article-title":"edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets","volume":"53","author":"Chen","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2025090410513954600_CIT0012","doi-asserted-by":"publisher","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":"2025090410513954600_CIT0013","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1038\/s41587-022-01261-x","article-title":"Haplotype-resolved assembly of diploid genomes without parental data","volume":"40","author":"Cheng","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2025090410513954600_CIT0014","doi-asserted-by":"publisher","first-page":"194","DOI":"10.7882\/az.2015.034","article-title":"Predicting biodiversity changes due to loss of bioengineers from an intertidal landscape, a case study from Sydney Harbour","volume":"39","author":"Cole","year":"2018","journal-title":"Aust Zool"},{"key":"2025090410513954600_CIT0015","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"Consortium","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025090410513954600_CIT0016","doi-asserted-by":"publisher","first-page":"2123","DOI":"10.1017\/9781009325844.018","article-title":"Cross-chapter paper 1: biodiversity hotspots","volume-title":"Climate change 2022 \u2013 impacts, adaptation and vulnerability: working group II contribution to the sixth assessment report of the intergovernmental panel on climate change","author":"Costello","year":"2023."},{"key":"2025090410513954600_CIT0017","article-title":"AGAT: another Gff analysis toolkit to handle annotations","author":"Dainat","year":"2023"},{"key":"2025090410513954600_CIT0018","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"2025090410513954600_CIT0019","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1242\/jcs.s3-101.56.395","article-title":"The chromosome numbers and nuclear cytology of some common British serpulids","volume":"S3-101","author":"Dasgupta","year":"1960","journal-title":"J Cell Sci"},{"key":"2025090410513954600_CIT0020","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1093\/jhered\/esac044","article-title":"A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting","volume":"113","author":"DeBiasse","year":"2022","journal-title":"J Hered"},{"key":"2025090410513954600_CIT0021","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1017\/S0025315400048220","article-title":"Reproductive biology of the serpulid Ficopomatus (Mercierella) enigmaticus in the Thames Estuary, S.E. England","volume":"61","author":"Dixon","year":"1981","journal-title":"J Mar Biol Assoc U K"},{"key":"2025090410513954600_CIT0022","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1017\/S0025315400044362","article-title":"Karyotypic differences between two species of Pomatoceros, P. Triqueter and P. Lamarckii (Polychaeta: Serpulidae)","volume":"78","author":"Dixon","year":"1998","journal-title":"J Mar Biol Assoc"},{"key":"2025090410513954600_CIT0089","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2012","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0024","doi-asserted-by":"crossref","DOI":"10.1007\/978-94-017-2887-4","volume-title":"Reproductive strategies and developmental patterns in annelids","author":"Dorresteijn","year":"1999"},{"key":"2025090410513954600_CIT0025","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1007\/978-1-0716-2819-5_16","article-title":"Phased genome assemblies","volume-title":"Haplotyping: methods in molecular biology","author":"Duitama","year":"2023"},{"key":"2025090410513954600_CIT0026","doi-asserted-by":"publisher","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":"2025090410513954600_CIT0027","doi-asserted-by":"publisher","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 USA"},{"key":"2025090410513954600_CIT0028","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.tree.2021.11.008","article-title":"The era of reference genomes in conservation genomics","volume":"37","author":"Formenti","year":"2022","journal-title":"Trends Ecol Evol"},{"key":"2025090410513954600_CIT0029","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1186\/s12859-021-04482-0","article-title":"TSEBRA: transcript selector for BRAKER","volume":"22","author":"Gabriel","year":"2021","journal-title":"BMC Bioinf"},{"key":"2025090410513954600_CIT0030","doi-asserted-by":"publisher","first-page":"1990","DOI":"10.1111\/mec.16848","article-title":"Climate adaptation and vulnerability of foundation species in a global change hotspot","volume":"32","author":"Gallegos","year":"2023","journal-title":"Mol Ecol"},{"key":"2025090410513954600_CIT0031","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1093\/evolut\/qpae012","article-title":"Temperature and sex shape reproductive barriers in a climate change hotspot","volume":"78","author":"Gallegos","year":"2024","journal-title":"Evolution"},{"key":"2025090410513954600_CIT0032","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/hdy.2008.62","article-title":"Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species","volume":"101","author":"Gissi","year":"2008","journal-title":"Heredity"},{"key":"2025090410513954600_CIT0033","doi-asserted-by":"publisher","first-page":"btae450","DOI":"10.1093\/bioinformatics\/btae450","article-title":"Drawing mitochondrial genomes with circularMT","volume":"40","author":"Goodman","year":"2024","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0034","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1086\/688018","article-title":"Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions","volume":"188","author":"Hoban","year":"2016","journal-title":"Am Naturalist"},{"key":"2025090410513954600_CIT0035","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1007\/s11160-013-9326-6","article-title":"Identification of global marine hotspots: sentinels for change and vanguards for adaptation action","volume":"24","author":"Hobday","year":"2014","journal-title":"Rev Fish Biol Fish"},{"key":"2025090410513954600_CIT0036","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1093\/bioinformatics\/btv661","article-title":"BRAKER1: unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS","volume":"32","author":"Hoff","year":"2016","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0037","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/978-1-4939-9173-0_5","article-title":"Whole-genome annotation with BRAKER","volume-title":"Gene prediction: methods and protocols","author":"Hoff","year":"2019"},{"key":"2025090410513954600_CIT0038","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1023\/A:1008871430178","article-title":"Biodiversity and functioning of Polychaetes in benthic sediments","volume":"7","author":"Hutchings","year":"1998","journal-title":"Biodivers Conserv"},{"key":"2025090410513954600_CIT0039","doi-asserted-by":"publisher","first-page":"e10313","DOI":"10.7717\/peerj.10313","article-title":"High-quality genome assembly of Metaphire vulgaris","volume":"8","author":"Jin","year":"2020","journal-title":"PeerJ"},{"key":"2025090410513954600_CIT0040","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0041","article-title":"Ggpubr: \u201cGgplot2\u201d based publication ready plots","author":"Kassambara","year":"2023","journal-title":"R package version 0.6.0"},{"key":"2025090410513954600_CIT0042","doi-asserted-by":"publisher","first-page":"398","DOI":"10.3390\/d15030398","article-title":"Phylogeny of Serpulidae (Annelida, Polychaeta) inferred from morphology and DNA sequences, with a new classification","volume":"15","author":"Kupriyanova","year":"2023","journal-title":"Diversity"},{"key":"2025090410513954600_CIT0043","first-page":"1","article-title":"Life-history patterns in serpulimorph polychaetes: ecological and evolutionary perspectives","volume":"39","author":"Kupriyanova","year":"2001","journal-title":"Oceanograph Marine Biol"},{"key":"2025090410513954600_CIT0044","doi-asserted-by":"publisher","first-page":"msae172","DOI":"10.1093\/molbev\/msae172","article-title":"Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians","volume":"41","author":"Lewin","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2025090410513954600_CIT0045","doi-asserted-by":"publisher","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":"2025090410513954600_CIT0046","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1146\/annurev-animal-020518-115034","article-title":"Multiple facets of marine invertebrate conservation genomics","volume":"7","author":"Lopez","year":"2019","journal-title":"Annu Rev Anim Biosci"},{"key":"2025090410513954600_CIT0047","doi-asserted-by":"publisher","first-page":"20212443","DOI":"10.1098\/rspb.2021.2443","article-title":"Evolution in changing seas","volume":"288","author":"Lotterhos","year":"2021","journal-title":"Proc Biol Sci"},{"key":"2025090410513954600_CIT0048","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/j.aquatox.2017.08.008","article-title":"Exposure of spermatozoa to dibutyl phthalate induces abnormal embryonic development in a marine invertebrate Galeolaria caespitosa (Polychaeta: Serpulidae)","volume":"191","author":"Lu","year":"2017","journal-title":"Aquat Toxicol"},{"key":"2025090410513954600_CIT0049","doi-asserted-by":"publisher","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":"2025090410513954600_CIT0050","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/s41559-020-01327-6","article-title":"Conservative route to genome compaction in a miniature annelid","volume":"5","author":"Mart\u00edn-Dur\u00e1n","year":"2021","journal-title":"Nat Ecol Evol"},{"key":"2025090410513954600_CIT0051","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1038\/s41586-022-05636-7","article-title":"Annelid functional genomics reveal the origins of bilaterian life cycles","volume":"615","author":"Mart\u00edn-Zamora","year":"2023","journal-title":"Nature"},{"key":"2025090410513954600_CIT0052","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1016\/j.tree.2020.03.002","article-title":"A roadmap for understanding the evolutionary significance of structural genomic variation","volume":"35","author":"M\u00e9rot","year":"2020","journal-title":"Trends Ecol Evol"},{"key":"2025090410513954600_CIT0053","doi-asserted-by":"publisher","first-page":"i142","DOI":"10.1093\/bioinformatics\/bty266","article-title":"Versatile genome assembly evaluation with QUAST-LG","volume":"34","author":"Mikheenko","year":"2018","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0054","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/bs.amb.2022.06.001","article-title":"Chapter one - serpulid reefs and their role in aquatic ecosystems: a global review","volume-title":"Advances in","author":"Montefalcone","year":"2022"},{"key":"2025090410513954600_CIT0055","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1126\/science.abm8127","article-title":"Reference genomes for conservation","volume":"377","author":"Paez","year":"2022","journal-title":"Science"},{"key":"2025090410513954600_CIT0056","unstructured":"Palmer J, Stajich J. \u00a0Funannotate: automated eukaryotic genome annotation pipeline (1.7.1). Zenodo. 2019. https:\/\/doi.org\/10.5281\/zenodo.3548120"},{"key":"2025090410513954600_CIT0057","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fevo.2023.1185566","article-title":"Assembling animals: trees, genomes, cells, and contrast to plants","volume":"11","author":"Paps","year":"2023","journal-title":"Front Ecol Evol"},{"key":"2025090410513954600_CIT0058","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2025090410513954600_CIT0059","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1093\/cz\/zow096","article-title":"Genetic load in marine animals: a review","volume":"62","author":"Plough","year":"2016","journal-title":"Curr Zool"},{"key":"2025090410513954600_CIT0060","doi-asserted-by":"publisher","first-page":"giad077","DOI":"10.1093\/gigascience\/giad077","article-title":"Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas","volume":"12","author":"Qi","year":"2023","journal-title":"GigaScience"},{"key":"2025090410513954600_CIT0061","doi-asserted-by":"publisher","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":"2025090410513954600_CIT0062","doi-asserted-by":"publisher","first-page":"2488","DOI":"10.1111\/1365-2435.14398","article-title":"When is warmer better? Disentangling within- and between-generation effects of thermal history on early survival","volume":"37","author":"Rebolledo","year":"2023","journal-title":"Funct Ecol"},{"key":"2025090410513954600_CIT0063","doi-asserted-by":"publisher","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":"2025090410513954600_CIT0064","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1007\/s002440010201","article-title":"A 48-h larval development toxicity test using the marine polychaete Galeolaria caespitosa Lamarck (Fam. Serpulidae)","volume":"40","author":"Ross","year":"2001","journal-title":"Arch Environ Contam Toxicol"},{"key":"2025090410513954600_CIT0065","doi-asserted-by":"publisher","first-page":"2006","DOI":"10.1101\/2023.06.06.543960","article-title":"Haplotype-resolved, chromosome-level assembly of white clover (Trifolium repens L., Fabaceae)","volume":"15","author":"Santangelo","year":"2023","journal-title":"Genome Biol Evol"},{"key":"2025090410513954600_CIT0066","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1093\/jhered\/esad054","article-title":"A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides","volume":"115","author":"Schiebelhut","year":"2023","journal-title":"J Hered"},{"key":"2025090410513954600_CIT0067","doi-asserted-by":"publisher","DOI":"10.1101\/2024.05.12.593736","article-title":"Acceleration of genome rearrangement in clitellate annelids","author":"Schultz","year":"2024.","journal-title":"bioRxiv"},{"key":"2025090410513954600_CIT0068","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.gene.2016.12.024","article-title":"Mitochondrial genome of the Christmas tree worm Spirobranchus giganteus (Annelida: Serpulidae) reveals a high substitution rate among annelids","volume":"605","author":"Seixas","year":"2017","journal-title":"Gene"},{"key":"2025090410513954600_CIT0069","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/s42003-023-04471-4","article-title":"The metazoan landscape of mitochondrial DNA gene order and content is shaped by selection and affects mitochondrial transcription","volume":"6","author":"Shtolz","year":"2023","journal-title":"Commun Biol"},{"key":"2025090410513954600_CIT0070","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0071","author":"Smit","year":"2013-2015"},{"key":"2025090410513954600_CIT0072","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1093\/bioinformatics\/btn013","article-title":"Using native and syntenically mapped cDNA alignments to improve de novo gene finding","volume":"24","author":"Stanke","year":"2008","journal-title":"Bioinformatics"},{"key":"2025090410513954600_CIT0073","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/1471-2105-7-62","article-title":"Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources","volume":"7","author":"Stanke","year":"2006","journal-title":"BMC Bioinf."},{"key":"2025090410513954600_CIT0074","doi-asserted-by":"publisher","first-page":"925","DOI":"10.1093\/sysbio\/syad023","article-title":"Mitochondrial genome evolution in Annelida\u2014a systematic study on conservative and variable gene orders and the factors influencing its evolution","volume":"72","author":"Struck","year":"2023","journal-title":"Syst Biol"},{"key":"2025090410513954600_CIT0075","doi-asserted-by":"publisher","first-page":"W397","DOI":"10.1093\/nar\/gkad313","article-title":"OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes","volume":"51","author":"Sun","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025090410513954600_CIT0076","doi-asserted-by":"publisher","first-page":"107124","DOI":"10.1016\/j.ympev.2021.107124","article-title":"Another blow to the conserved gene order in Annelida: evidence from mitochondrial genomes of the calcareous tubeworm genus Hydroides","volume":"160","author":"Sun","year":"2021","journal-title":"Mol Phylogenet Evol"},{"key":"2025090410513954600_CIT0077","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/dnares\/dsac035","article-title":"A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster","volume":"29","author":"Takeuchi","year":"2022","journal-title":"DNA Res"},{"key":"2025090410513954600_CIT0078","doi-asserted-by":"publisher","first-page":"e78","DOI":"10.1093\/nar\/gkv227","article-title":"Identification of protein coding regions in RNA transcripts","volume":"43","author":"Tang","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025090410513954600_CIT0079","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1186\/s12859-023-05385-y","article-title":"MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads","volume":"24","author":"Uliano-Silva","year":"2023","journal-title":"BMC Bioinf"},{"key":"2025090410513954600_CIT0080","doi-asserted-by":"publisher","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":"2025090410513954600_CIT0081","article-title":"Read, manipulate and visualize \u201cPairwise mApping Format\u201d","author":"Winter","year":"2022","journal-title":"Data"},{"key":"2025090410513954600_CIT0082","doi-asserted-by":"publisher","first-page":"2425","DOI":"10.1002\/ecy.1932","article-title":"Disturbance-mediated facilitation by an intertidal ecosystem engineer","volume":"98","author":"Wright","year":"2017","journal-title":"Ecology"},{"key":"2025090410513954600_CIT0083","doi-asserted-by":"publisher","first-page":"5923","DOI":"10.1111\/mec.16146","article-title":"Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies","volume":"30","author":"Yamaguchi","year":"2021","journal-title":"Mol Ecol"},{"key":"2025090410513954600_CIT0084","doi-asserted-by":"publisher","first-page":"evac008","DOI":"10.1093\/gbe\/evac008","article-title":"The genome of the poecilogonous annelid Streblospio benedicti","volume":"14","author":"Zakas","year":"2022","journal-title":"Genome Biol Evol."},{"key":"2025090410513954600_CIT0085","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac808","article-title":"YaHS: yet another Hi-C scaffolding tool","volume":"39:0.","author":"Zhou","year":"2022","journal-title":"Bioinformatics"}],"container-title":["Journal of Heredity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article-pdf\/116\/5\/702\/62996081\/esaf025.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jhered\/article-pdf\/116\/5\/702\/62996081\/esaf025.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jhered\/article-pdf\/116\/5\/702\/62996081\/esaf025.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T14:51:56Z","timestamp":1756997516000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jhered\/article\/116\/5\/702\/8118891"}},"subtitle":[],"editor":[{"given":"Taras","family":"Oleksyk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,4,22]]},"references-count":87,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,4,22]]},"published-print":{"date-parts":[[2025,8,23]]}},"URL":"https:\/\/doi.org\/10.1093\/jhered\/esaf025","relation":{},"ISSN":["0022-1503","1465-7333"],"issn-type":[{"value":"0022-1503","type":"print"},{"value":"1465-7333","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,9]]},"published":{"date-parts":[[2025,4,22]]}}}