Genome Sequence of a Novel Iflavirus from mRNA Sequencing of the Butterfly Heliconius erato

Abstract

Here, we report the genome sequence of a novel iflavirus strain recovered from the neotropical butterfly Heliconius erato. The coding DNA sequence (CDS) of the iflavirus genome was 8,895 nucleotides in length, encoding a polyprotein that was 2,965 amino acids long.

GENOME ANNOUNCEMENT

Heliconius butterflies are a diverse group of around 40 neotropical species that are widely studied for their wing color pattern diversity and Müllerian mimicry, and display a striking pattern of both divergent and convergent evolution in wing phenotypes (1, 2). Heliconius erato is native to Central and South America where a huge diversity of wing phenotypes are expressed across races from different geographic locations (3). Iflaviruses are single-stranded RNA viruses that infect insect hosts, often leading to developmental problems and the death of the host (4). However, little is known about the viral (and bacterial) assemblages infecting Heliconius butterflies.

We sequenced the mRNA of one male and one female of H. erato, obtained from a Costa Rican butterfly farm, Suministros Entomológicos Costarricenses, S.A. RNA was extracted from two individuals for each of four tissue types (the antenna, mouth-parts, head, and legs) using TRIzol (Life Technologies). RNA sequencing libraries were prepared using the mRNA-Seq sample preparation kit (Illumina) and sequenced using an Illumina HiSeq 2000 sequencer by the UCI Genomics High-Throughput Facility. In total, eight libraries were sequenced, producing an average library size of approximately 24 million 100-bp paired-end reads, after quality control filters were applied. Paired-end libraries were then de novo assembled into putative mRNA transcripts using Trinity (5). The Trinity-assembled nucleotide (nt) contigs were translated into amino acid (aa) sequences, and a BLASTp comparison to the NCBI NR protein database (6) revealed the presence of a viral polyprotein.

The best BLASTp hit for the discovered viral polyprotein matched a strain of iflavirus previously described from the Chinese oak silkmoth, Antheraea pernyi. The H. erato iflavirus polyprotein amino acid sequence demonstrated a 63% pairwise similarity to the Chinese oak moth iflavirus polyprotein. The coding DNA sequence (CDS) of the H. erato iflavirus was 8,895 nucleotides in length, encoding a 2,965-aa polyprotein. The entire iflavirus genome was 9,910 nucleotides long, which included a 906-nt 5′ untranslated region (UTR) and 110-nt 3′ UTR, and had a G+C content of 35.3%.

Iflavirus genomes typically encode a single polyprotein that is comprised of conserved domains for structural proteins in the N-terminal region, and non-structural proteins, RNA helicase, protease, and RNA-dependent RNA polymerase (RdRp) proteins in the C-terminal region (4). The 2,965-aa polyprotein of the H. erato iflavirus strain contained an arrangement of conserved domains common to that of previously described insect iflavirus genomes (7). This included two rhv-like picornavirus capsid protein domain-like motifs (Pfam entry, cd00205), an RdRp motif (Pfam entry, cd01699), RNA helicase (Pfam entry, PF00910), a cricket paralysis virus (CRPV) capsid protein-like motif (Pfam entry, PF08762), and a 3-C cysteine protease motif (Pfam entry, PF00548).

We present the complete genome of a novel strain of iflavirus isolated from H. erato. This H. erato iflavirus genomic sequence encodes a full and complete polyprotein when compared to other iflavirus genomes. The increasing availability of mRNA sequencing data from a wide range of insect species promises to aid in the understanding of the ecology and evolution of insect viral infection.

Nucleotide sequence accession number.

The genome sequence was deposited at DDBJ/EMBL/GenBank under accession no. KJ679438.