Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA.
BMC Biol. 2021 Feb 10;19(1):28. doi: 10.1186/s12915-021-00963-z.
The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector's genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution.
To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role.
Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.
致倦库蚊是亚洲城市疟疾的传播媒介，最近已入侵非洲。研究媒介传播能力的遗传基础和工程遗传干预都受到载体基因组组装的限制。致倦库蚊现有的基因组组装是草图质量的，包含数千个序列缺口，可能缺失对其生物学和进化重要的遗传元件。
为了访问以前难以处理的基因组区域，我们生成了参考级别的基因组组装和完整的转录注释，为疾病媒介的参考基因组建立了新的标准。在这里，我们报告了新的种特异性转座元件（TE）家族和功能基因元件中的插入，证明了 TEs 在基因组进化和表型变异中的广泛作用。我们发现了 29 个以前隐藏的杀虫剂抗性基因成员，揭示了致倦库蚊中广泛存在的杀虫剂抗性的新候选遗传元件。我们鉴定了 2.4 Mb 的 Y 染色体和七个新的雄性连锁基因候选物，这代表了任何蚊子中 Y 染色体的最广泛覆盖。通过跟踪吸血后超过 15 天的全长 mRNA，我们发现了以前未表征的基因在血液代谢和雌性生殖中的不同作用。Y 连锁异染色质景观揭示了长末端重复反转录转座子在这条染色体的进化和退化过程中的广泛积累。最后，我们鉴定了一种新的 Y 连锁假定转录因子，它在雄性发育和成年期持续表达，表明其具有重要作用。
总之，这些结果和资源突出了以前隐藏的基因组元件在疟疾蚊子生物学中的重要性，并将加速疟疾传播遗传控制策略的发展。
