Department of Biology, University of Fribourg, Switzerland.
Swiss Institute of Bioinformatics, Fribourg, Switzerland.
Genome Biol Evol. 2020 Jul 1;12(7):1167-1173. doi: 10.1093/gbe/evaa102.
Rapid evolution of weed biological control agents (BCAs) to new biotic and abiotic conditions is poorly understood and so far only little considered both in pre-release and post-release studies, despite potential major negative or positive implications for risks of nontargeted attacks or for colonizing yet unsuitable habitats, respectively. Provision of genetic resources, such as assembled and annotated genomes, is essential to assess potential adaptive processes by identifying underlying genetic mechanisms. Here, we provide the first sequenced genome of a phytophagous insect used as a BCA, that is, the leaf beetle Ophraella communa, a promising BCA of common ragweed, recently and accidentally introduced into Europe. A total 33.98 Gb of raw DNA sequences, representing ∼43-fold coverage, were obtained using the PacBio SMRT-Cell sequencing approach. Among the five different assemblers tested, the SMARTdenovo assembly displaying the best scores was then corrected with Illumina short reads. A final genome of 774 Mb containing 7,003 scaffolds was obtained. The reliability of the final assembly was then assessed by benchmarking universal single-copy orthologous genes (>96.0% of the 1,658 expected insect genes) and by remapping tests of Illumina short reads (average of 98.6 ± 0.7% without filtering). The number of protein-coding genes of 75,642, representing 82% of the published antennal transcriptome, and the phylogenetic analyses based on 825 orthologous genes placing O. communa in the monophyletic group of Chrysomelidae, confirm the relevance of our genome assembly. Overall, the genome provides a valuable resource for studying potential risks and benefits of this BCA facing environmental novelties.
杂草生物防治剂（BCAs）快速适应新的生物和非生物条件的机制尚未被充分了解，到目前为止，无论是在释放前还是释放后研究中，都很少考虑到这一点，尽管这可能对非目标攻击的风险或分别为尚未适合的栖息地的定殖带来重大的负面影响或积极影响。提供遗传资源，如组装和注释基因组，对于通过识别潜在的遗传机制来评估潜在的适应性过程至关重要。在这里，我们提供了第一个被用作 BCA 的植食性昆虫的测序基因组，即普通豚草叶甲（Ophraella communa），这是最近意外引入欧洲的普通豚草的一种很有前途的 BCA。使用 PacBio SMRT-Cell 测序方法获得了 33.98 Gb 的原始 DNA 序列，代表约 43 倍的覆盖率。在测试的五个不同的组装器中，然后使用 Illumina 短读序列对 SMARTdenovo 组装器显示出的最佳分数进行校正。最终获得了包含 7003 个支架的 774 Mb 基因组。然后通过基准测试通用单拷贝直系同源基因（> 1658 个预期昆虫基因的 96.0%）和重新映射 Illumina 短读序列（过滤前平均为 98.6 ± 0.7%）来评估最终组装的可靠性。75642 个编码蛋白的基因数量，代表已发表的触角转录组的 82%，以及基于 825 个直系同源基因的系统发育分析，将 O. communa 置于 Chrysomelidae 的单系群中，证实了我们基因组组装的相关性。总的来说，该基因组为研究这种 BCA 面临环境新奇时的潜在风险和益处提供了有价值的资源。
