De novo transcriptome assembly of the Mediterranean sea-rock pool mosquitoes Aedes mariae and Aedes zammitii

Abstract

Understanding the genomic consequences of hybridization is an essential research focus in global change biology. Species adapted to rapidly changing environments can offer valuable, yet largely underexplored insights in this context. Here, we present the first de novo transcriptomes of the sea-rock pools mosquitoes Aedes mariae and Aedes zammitii, two species adapted to highly variable habitats. Using RNA-seq data obtained from larval stages, we assembled and annotated 95,059,578 reads for Ae. mariae and 101,050,236 reads for Ae. zammitii, detecting 49,352 transcripts with N50 of 2,615 for the former and 43,461 transcripts with N50 of 2,570 for the latter. Validation by BUSCO confirmed the high quality of our resources. Homology alignments of predicted ORFs showed that 21,842 sequences from Ae. mariae and 21,944 sequences from Ae. zammitii mapped to the Nr, SwissProt, and TrEMBL databases, while 19,208 and 19,393 predicted ORFs, respectively, were functionally annotated using the COG and KEGG databases. These high-quality transcriptomes will provide valuable resources to investigate the role of hybridization in species adaptation to changing environments.

Fig. 1

Workflow of the Bioinformatic for the de novo transcriptome assembly of Aedes mariae and Aedes zammitii. The pipeline starts from raw data, leads to annotated transcripts and includes transcriptome comparison.

Fig. 2

BUSCO assessment results for Aedes mariae.

Fig. 3

BUSCO assessment results for Aedes zammitii.

Fig. 4

For each sample, the representation of the total paired-reads is shown in blue (in light blue there is raw paired reads mapped back against transcriptome; the percentage value is relative to the total paired-read), the representation of trimmed paired-reads is shown in green. In yellow trimmed paired reads mapped back against transcriptome (Bowtie2) and in fuchsia trimmed paired reads mapped back against transcriptome (BOWTIE2); the percentage value is correlate to the trimmed paired-reads).

Fig. 5

Venn diagrams showing for the number of contigs annotated with DIAMOND using Aedes mariae BLASTX (Panel A) and Aedes zammitii BLASTX (Panel B) against the three databases: Nr, SwissProt, TrEMBL.

Fig. 6

Top ten best species (A) and protein (B) hits in Aedes mariae present in the reference databases (Nr, BLASTX).

Fig. 7

Top ten best species (A) and protein (B) hits in Aedes zammitii present in the reference databases (Nr, BLASTX).

Fig. 8

Upset diagram representing the number of species-specific and overlapping protein orthogroups between the six transcriptomes (intersection size>50, full detail in figshare). The number of orthogroups was identified with OrthoFinder.

Fig. 9

Ortholog multiplicity of transcriptomes. The values in percentual were identified with OrthoFinder.