Chromosome-level genome assembly of the coastal horseshoe crab (Tachypleus gigas).
chromosome-scale genome assembly
coastal horseshoe crab
conservation
living-fossil
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Nov 2020
Nov 2020
Historique:
received:
30
04
2020
revised:
14
07
2020
accepted:
21
07
2020
pubmed:
30
7
2020
medline:
10
8
2021
entrez:
30
7
2020
Statut:
ppublish
Résumé
Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole-genome sequences are currently available for three species. In this study, we have generated a chromosome-level genome assembly of the fourth species, the Asian coastal horseshoe crab (Tachypleus gigas; genome size 2.0 Gb). The genome assembly has a scaffold N50 value of 140 Mb with ~97% of the assembly mapped to 14 scaffolds representing 14 chromosomes of T. gigas. In addition, we have generated the complete mitochondrial genome sequence and deep-coverage transcriptome assemblies for four tissues. A total of 26,159 protein-coding genes were predicted in the genome. The T. gigas genome contains five Hox clusters similar to the mangrove horseshoe crab (Carcinoscorpius rotundicauda), suggesting that the common ancestor of horseshoe crabs already possessed five Hox clusters. Phylogenomic and divergence time analysis suggested that the American and Asian horseshoe crab lineages shared a common ancestor around the Silurian period (~436 Ma). Comparison of the T. gigas genome with those of other horseshoe crab species with chromosome-level assemblies provided insights into the chromosomal rearrangement events that occurred during the emergence of these species. The genomic resources of T. gigas will be useful for understanding their genetic diversity and population structure and would help in designing strategies for managing and conserving their stocks across Asia.
Identifiants
pubmed: 32725950
doi: 10.1111/1755-0998.13233
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1748-1760Subventions
Organisme : National Research Foundation, Prime Minister's Office, Singapore under its Marine Science Research and Development programme
ID : MSRDP-P19
Informations de copyright
© 2020 John Wiley & Sons Ltd.
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