A draft genome sequence of the common, or spectacled caiman Caiman crocodilus

Introduction

The common, or spectacled, caiman, Caiman crocodilus, is one of the most widely distributed and abundant crocodilian species, ranging continuously from Mexico to Argentina (Busack and Pandya 2001; US Fish and Wildlife Service 2018). A generalist predator, C. crocodilus is remarkably adaptable, occupying a wide range of habitats from urban to seasonal savannahs to tropical rainforests (Medem 1981, 1983), and has recently been introduced to Cuba, Puerto Rico and Florida where it is considered an invasive species (US Fish and Wildlife Service 2018). The broad distribution and diversity of habitats has facilitated considerable intraspecific diversification within C. crocodilus; a recent analysis by Roberto et al. (2020) identified between seven and ten lineages within C. crocodilus across differing biogeographic regions and watersheds throughout Central and South America. Within-species diversity is also morphologically apparent, with skull shape in particular exhibiting systematic patterns of regional differentiation (Medem 1955; Gans 1980; Medem 1981, 1983; Ayarzaguena 1984; Escobedo-Galván et al. 2015). These intraspecific patterns of cranial shape variation within C. crocodilus have been shown to parallel patterns of interspecific cranial diversity found in extant crocodilians (Okamoto et al. 2015).

Additionally, C. crocodilus is a species of commercial importance, chiefly in the leather industry. While the hides of C. crocodilus contain osteoderms that render the manufacturing process more difficult than for other crocodilians, a majority of the approximately 1.5 million crocodilian skins traded globally come from C. crocodilus (Brazaitis et al. 1998; Caldwell 2015). As with other crocodilians, most legal hides come from commercial farming operations, and the market for caiman hides is estimated to be over US $85 million (Caldwell 2015). Wild populations of C. crocodilus are also hunted for meat and even fishing bait (Da Silveira and Thorbjarnarson 1999; Brum et al. 2015; Pimenta et al. 2018) and provide ecosystem services including nutrient cycling and biological control (Valencia-Aguilar et al. 2013; Marley et al. 2019). Due to its role as an apex predator, C. crocodilus exhibits considerable bioaccumulation, with genotoxic analyses demonstrating molecular signatures of pollution on the C. crocodilus genome (Oliveira et al. 2021).

Thus, a draft genome sequence for C. crocodilus can not only assist with improved husbandry, ecotoxicology and wildlife management, but also has the potential to provide insight into evolutionary processes driving intraspecific diversification in continental systems more broadly.

Materials and methods

DNA was extracted from a tissue sample belonging to a single Caiman crocodilus museum specimen (UF-FLMNH 171438) using the DNeasy ™kit from Qiagen (Hilden, Germany). DNA was quantitated using Thermofisher’s (Waltham, MA, USA) Picogreen ™kit (for a final Picogreen concentration of 77.78 ng/$\mu$L). Tecan’s (Männedorf, Switzerland) NuGEN Celero ™kit was then used to construct a paired-end library, which was subsequently sequenced on a single Illumina (San Diego, CA, USA) NovaSeq S4 lane. This yielded 239,911,946 paired-end reads of 2 × 150 bp each. Nucleic acid isolation, quantitation, library generation and raw-read sequencing were performed at the University of Minnesota Genomics Center.

The paired-end reads (as of October 2021, accessible at doi.org/10.5281/zenodo.5598241) were assembled de novo using the Iterative de Bruijn Graph Assembler (IDBA-UD; Peng et al. 2012). To assess the reliability of our pipeline from sequencing to de novo assembly using IDBA-UD, we repeated the sequencing and assembly using a museum-derived tissue sample from a single Alligator mississippiensis individual (UF-FLMNH 175565). This resulted in 249,325,204 paired-end reads of 2 × 150 bp each. As was the case for the C. crocodilus individual, the reads were then de novo assembled using IDBA-UD, and we used QUAST (Gurevich et al. 2013) to determine that the IDBA assembly of A. missippiensis captured approximately 94.2% of a recently published A. missippiensis assembly (GCA_000281125.4; Rice et al. 2017), with an NG50 of 21172 based on de novo assembled contigs alone.

We scaffolded the resulting draft C. crocodilus contigs using a two-step procedure. First, we scaffolded the caiman’s contigs against a Crocodylus porosus assembly (GCF_001723895.1; Ghosh et al. 2020) using ragtag (Alonge et al. 2019). We then re-scaffolded the resulting contigs/scaffolds against the confamilial Alligator mississipiensis assembly (GCA_000281125.4), again using ragtag. The draft assembly was then submitted to the National Center for Biotechnology Information (NCBI).

Contaminants, mitochondrial DNA, vectors, adapters, and sequences shorter than 200 bp identified by NCBI were manually removed using seqkit (Shen et al. 2016) and custom scripts (available at http://github.com/kewok/ncbi_scrubber). As of July 2021, this draft assembly can be accessed at doi.org/10.5281/zenodo.4755063.

The resulting scaffold (10.5281/zenodo.4755063) was then masked using RepeatMasker (Smit et al. 2015) relying on the HMMER database (Finn et al. 2011) and with “alligator” specified as species. Finally, liftoff (Shumate and Salzberg 2020) was used to generate a draft annotation based on the masked assembly using the annotations associated with A. mississipiensis (GCA_000281125.4; Rice et al. 2017) as a reference.

table 2asn_gff (National Center for Biotecnology Information 2020) was used to generate a Sequin file (National Center for Biotechnology Information (US) 2014), and features flagged as errors were manually removed using custom scripts (available at https://github.com/kewok/ncbi_scrubber); as of July 2021 the draft annotation is available at 10.5281/zenodo.4755063).

Results and conclusions

Our assembly yielded a draft assembly of length 2,341,057,913 bp with 465,471 scaffolds and contigs, and an N50 of 70,464,410 bp (Proch::N50 - Telatin 2018). A total of 297,374 gene features were predicted.

Here we have described the first draft assembly and annotation of the C. crocodilus genome. We feel these data can assist natural resource management, ecotoxicology, agriculture, as well as research into broader questions about the interplay between microevolutionary and macroevolutionary processes across broad biogeographic scales.

Competing interests

The authors declare no competing interests.

Data availability

The draft assembly has been submitted to the National Center for Biotechnology Information and both assembly and annotation are currently available for review at (doi.org/10.5281/zenodo.4755063).