De novo transcriptome assembly and annotation for gene discovery in the streamside salamander (Ambystoma barbouri)

<ns5:p> Although amphibian populations are declining globally, few species possess foundational genomic resources needed to conduct conservation genetics studies and inform species status assessments. We sequenced, assembled, and annotated the first <ns5:italic>de novo</ns5:italic> transcriptome of <ns5:italic>Ambystoma barbouri</ns5:italic> from larval individuals exposed to two temperature treatments as well as adult heart, liver, spleen, and tail tissue samples. RNA reads were assembled with Trinity and rnaSPAdes, and resulting assemblies were merged using EvidentialGene followed by CD-HIT-est for redundancy reduction. This produced a transcriptome with 850,204 unigenes. The assembly possessed 98.1% of complete vertebrate BUSCO markers, an N50 of 1,628 bp, and an L50 of 130,416. TransDecoder identified 534,476 protein coding sequences, of which 276,770 possessed annotation information within one or more of the databases employed (EggNM, GO, Infernal, KEGG, Ko Fam, Pfam, SignalP, SwissProt). This assembly provides a reference for gene expression and population-level studies as well as conservation genetics within <ns5:italic>Ambystoma</ns5:italic> and in amphibians and broader evolutionary and comparative studies. </ns5:p>