Abstract
BackgroundAltica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far.ResultsThe genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation.ConclusionsThe genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.
Highlights
Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation
We generated and assembled 187.3× coverage from Illumina short reads and 72.7× coverage via PacBio long reads from 157 female adults, creating a draft genome reference assembly of 864.8 Megabase pairs (Mb) consisting of contig and scaffold N50s of 92.8 kb and 557.2 kb, respectively
The draft genome assembly of A. viridicyanea was contained within 17,580 contigs that were assembled into 4490 scaffolds, with the longest scaffold size of 5.6 Mb
Summary
Studies of three closely related species, Altica viridicyanea, A. cirsicola, and A. fragariae, have demonstrated that these species are broadly sympatric and quite similar in morphology, they feed on distantly related host plants from different plant families [6]. Their divergence is likely the result of dietary shifts to unrelated host plants [6]. Their close relationship is supported by crossing studies that show that interspecific hybrids can be generated under laboratory conditions [4,5,6, 8, 10], and phylogenetic analysis indicates that these species diverged
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