The Pecari tajacu genome: A tool for its conservation and the study of the Suoidea superfamily

Abstract

The goal of this study is the development of a high-quality assembly for the Pecari tajacu species. The Suoidea superfamily groups 2 families: Suidae and Tayassuidae. Suidae species inhabit Africa and Eurasia, occupying a wide range of habitats. The same applies to the Tayassuidae species that live in the Americas and were the first from Suoidea to diverge from their common ancestor in North America ~36 Ma. Lineages of Tayassuidae from South America diverged around 10 Ma. Divergence between peccary genera is estimated as early as the late Myocene. Tayassu pecari and Catagonus wagneri are more closely related to each other than to Pecari tajacu. Despite their significance, the genomes of the Tayassuidae family remain poorly characterized. Their conservation status ranges from least concern (P. tajacu), to vulnerable (T. pecari), to endangered (C. wagneri). Developing high-quality reference genomes is essential for the understanding of the evolution and genetics of these species and for enhancing conservation efforts. Blood samples were collected from a female zoo specimen and flash-frozen in liquid nitrogen. High molecular weight DNA was isolated for Oxford Nanopore (100×) and PacBio HiFi sequencing (70×), alongside Dovetail Omni-C data generation. Assembly and scaffolding of nanopore reads was performed using a pipeline that included canu-medata-salsa2. Assembly and scaffolding of Hi-Fi reads was performed using hifiasm and yahs. The HiFi assembly achieved higher contiguity (N50: 121 Mbp) and lower error rate then the Nanopore assembly (N50: 46 Mpb). The HiFi assembly reconstructed both pseudo haplotypes at chromosome level, whereas the Nanopore data yielded a close to chromosome level single pseudo-haplotype assembly. Comparative analysis of the P. tajacu and the S. scrofa genome (Sscrofa11.1) confirmed that the chromosome level assemblies are consistent with expected homology based on previous ZOO-FISH analyses. This high-quality, haplotype-resolved reference genome offers a robust framework for further studies regarding the species genetic structure and diversity.