Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System.
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| Formato: | Artículo científico |
| Lenguaje: | en |
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Molecular biology and evolution
2025
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| author | Castellano, Kate R Neitzey, Michelle L Starovoitov, Andrew Barrett, Gabriel A Reid, Noah M Vuruputoor, Vidya S Webster, Cynthia N Storer, Jessica M Pauloski, Nicole R Ameral, Natalie J McEvoy, Susan L McManus, M Conor Puritz, Jonathan B Wegrzyn, Jill L O'Neill, Rachel J |
| author_facet | Castellano, Kate R Neitzey, Michelle L Starovoitov, Andrew Barrett, Gabriel A Reid, Noah M Vuruputoor, Vidya S Webster, Cynthia N Storer, Jessica M Pauloski, Nicole R Ameral, Natalie J McEvoy, Susan L McManus, M Conor Puritz, Jonathan B Wegrzyn, Jill L O'Neill, Rachel J Castellano, Kate R Neitzey, Michelle L Starovoitov, Andrew Barrett, Gabriel A Reid, Noah M Vuruputoor, Vidya S Webster, Cynthia N Storer, Jessica M Pauloski, Nicole R Ameral, Natalie J McEvoy, Susan L McManus, M Conor Puritz, Jonathan B Wegrzyn, Jill L O'Neill, Rachel J |
| collection | PubMed - marine biology |
| contents | Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System. Castellano, Kate R Neitzey, Michelle L Starovoitov, Andrew Barrett, Gabriel A Reid, Noah M Vuruputoor, Vidya S Webster, Cynthia N Storer, Jessica M Pauloski, Nicole R Ameral, Natalie J McEvoy, Susan L McManus, M Conor Puritz, Jonathan B Wegrzyn, Jill L O'Neill, Rachel J Animals Horseshoe Crabs Sex Chromosomes Centromere Fossils Genome Gene Duplication DNA Transposable Elements Phylogeny Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species. |
| format | Artículo científico |
| id | pubmed_39907027 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Molecular biology and evolution |
| record_format | pubmed |
| spellingShingle | Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System. Castellano, Kate R Neitzey, Michelle L Starovoitov, Andrew Barrett, Gabriel A Reid, Noah M Vuruputoor, Vidya S Webster, Cynthia N Storer, Jessica M Pauloski, Nicole R Ameral, Natalie J McEvoy, Susan L McManus, M Conor Puritz, Jonathan B Wegrzyn, Jill L O'Neill, Rachel J Animals Horseshoe Crabs Sex Chromosomes Centromere Fossils Genome Gene Duplication DNA Transposable Elements Phylogeny Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System. Castellano, Kate R Neitzey, Michelle L Starovoitov, Andrew Barrett, Gabriel A Reid, Noah M Vuruputoor, Vidya S Webster, Cynthia N Storer, Jessica M Pauloski, Nicole R Ameral, Natalie J McEvoy, Susan L McManus, M Conor Puritz, Jonathan B Wegrzyn, Jill L O'Neill, Rachel J Animals Horseshoe Crabs Sex Chromosomes Centromere Fossils Genome Gene Duplication DNA Transposable Elements Phylogeny Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species. |
| title | Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System. |
| topic | Animals Horseshoe Crabs Sex Chromosomes Centromere Fossils Genome Gene Duplication DNA Transposable Elements Phylogeny |
| url | https://pubmed.ncbi.nlm.nih.gov/39907027/ |