Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

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dc.citation.journalTitleGigaScienceen_US
dc.citation.volumeNumber3en_US
dc.contributor.authorNossa, Carlos W.en_US
dc.contributor.authorHavlak, Paulen_US
dc.contributor.authorYue, Jia-Xingen_US
dc.contributor.authorLv, Jieen_US
dc.contributor.authorVincent, Kimberly Y.en_US
dc.contributor.authorBrockmann, H.Janeen_US
dc.contributor.authorPutnam, Nicholas H.en_US
dc.date.accessioned2014-10-09T15:38:25Zen_US
dc.date.available2014-10-09T15:38:25Zen_US
dc.date.issued2014en_US
dc.description.abstractHorseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses. Here we apply a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab, Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes. Comparison with other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications 300 million years ago, followed by extensive chromosome fusion. These results provide a counter-example to the often noted correlation between whole genome duplication and evolutionary radiations. The new, low-cost genetic mapping method for obtaining a chromosome-scale view of non-model organism genomes that we demonstrate here does not require laboratory culture, and is potentially applicable to a broad range of other species.en_US
dc.identifier.citationNossa, Carlos W., Havlak, Paul, Yue, Jia-Xing, et al.. "Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication." <i>GigaScience,</i> 3, (2014) BioMed Central: http://dx.doi.org/10.1186/2047-217X-3-9.en_US
dc.identifier.doihttp://dx.doi.org/10.1186/2047-217X-3-9en_US
dc.identifier.urihttps://hdl.handle.net/1911/77503en_US
dc.language.isoengen_US
dc.publisherBioMed Centralen_US
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/2.0/en_US
dc.subject.keywordgenotyping-by-sequencing (GBS)en_US
dc.subject.keywordgenetic linkage mappingen_US
dc.subject.keywordgenome evolutionen_US
dc.subject.keywordlimulus polyphemusen_US
dc.titleJoint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplicationen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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