Author:
Meredith Robert W.,Milián-García Yoamel,Gatesy John,Russello Michael A.,Amato George
Abstract
Abstract
Objectives
The new data provide an important genomic resource for the Critically Endangered Cuban crocodile (Crocodylus rhombifer). Cuban crocodiles are restricted to the Zapata Swamp in southern Matanzas Province, Cuba, and readily hybridize with the widespread American crocodile (Crocodylus acutus) in areas of sympatry. The reported de novo assembly will contribute to studies of crocodylian evolutionary history and provide a resource for informing Cuban crocodile conservation.
Data description
The final 2.2 Gb draft genome for C. rhombifer consists of 41,387 scaffolds (contigs: N50 = 104.67 Kb; scaffold: N50-518.55 Kb). Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 92.3% of the 3,354 genes in the vertebrata_odb10 database. Approximately 42% of the genome (960Mbp) comprises repeat elements. We predicted 30,138 unique protein-coding sequences (17,737 unique genes) in the genome assembly. Functional annotation found the top Gene Ontology annotations for Biological Processes, Molecular Function, and Cellular Component were regulation, protein, and intracellular, respectively. This assembly will support future macroevolutionary, conservation, and molecular studies of the Cuban crocodile.
Funder
National Science Foundation
Rufford Foundation for Nature Conservation
Mitacs Elevate Program
Natural Sciences and Engineering Research Council of Canada
Publisher
Springer Science and Business Media LLC
Reference34 articles.
1. IUCN. The IUCN Red List of Threatened Species. IUCN Red List of Threatened Species. 2023. https://www.iucnredlist.org/en. Accessed 19 Apr 2023.
2. Milián-García Y, Ramos-Targarona R, Pérez-Fleitas E, Sosa-Rodríguez G, Guerra-Manchena L, Alonso-Tabet M, et al. Genetic evidence of hybridization between the critically endangered Cuban crocodile and the American crocodile: implications for population history and in situ/ex situ conservation. Heredity. 2015;114:272–80.
3. Morgan GS, Franz R, Crombie RI. The Cuban crocodile, Crocodylus rhombifer, from late Quaternary fossil deposits on Grand Cayman. 1993;:12.
4. Steadman DW, Franz R, Morgan GS, Albury NA, Kakuk B, Broad K, et al. Exceptionally well preserved late quaternary plant and vertebrate fossils from a blue hole on Abaco, the Bahamas. PNAS. 2007;104:19897–902.
5. Targarona RR. Ecologia y conservación del cocodrilo Cubano (Crocodylus rhombifer) en la Ciénaga De Zapata, Cuba. Universitat d’Alacant - Universidad de Alicante; 2013. http://purl.org/dc/dcmitype/Text.