Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana

Abstract

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

Keywords: Anura; Phyllomedusidae; amphibian; genome; mitogenome; transcriptome.

Fig. 1.

a) Photo of Phyllomedusa bahiana (by Pedro P. G. Taucce). b) Map with the approximate distribution range of P. bahiana (blue shading), with indication on sampling location for the specimens used for reference genome and transcriptome assemblies (Jequié, Bahia, Brazil). Distribution map was adapted from Pombal and Haddad (1992), while the topographic map was retrieved from Natural Earth (https://www.naturalearthdata.com). c) Comparison between ours and other anuran assemblies regarding assembly size and contig N50 (natural logarithm transformed for ease of visualization). The position of P. bahiana is highlighted in blue (see Supplementary Figs. 1 and 2 for names of all species). d) Relationship between genome size (Gbp) and the proportion of repetitive sequence for all anuran species with published genomes. Repetitive sequence content was calculated for each genome using a de novo, unbiased repeat detection method. e) Frequency distribution of genome-wide values of nucleotide diversity (π) and Tajima’s D for P. bahiana and P. burmeisteri, based on pool-sequencing data. Each statistic was calculated in 10-kb nonoverlapping windows across the whole genome. For better visualization, a small number of windows with nucleotide diversity values above 3.0% was omitted.