International Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya.
Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362-00902, Kikuyu, Kenya.
Sci Rep. 2019 Dec 4;9(1):18355. doi: 10.1038/s41598-019-54989-z.
The fruit fly species, Ceratitis rosa sensu stricto and Ceratitis quilicii, are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of C. rosa with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled de novo into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In C. quilicii females, bacterial transcripts of Pectobacterium spp., Enterobacterium buttiauxella, Enterobacter cloacae and Klebsiella variicola were upregulated compared to the C. rosa s.s. females. Comparison of expression levels of the host transcripts revealed a heavier investment by C. quilicii (compared with C. rosa s.s.) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.
果实蝇种 Ceratitis rosa sensu stricto 和 Ceratitis quilicii 是分别局限于低地和高地地区的近缘种。直到最近，这些近缘种被认为是 C. rosa 的异地种群，具有明显的生物学特征。我们使用深度下一代测序 (NGS) 技术对来自这两个近缘种的个体完整肠道进行测序，以比较它们的转录谱，同时了解肠道微生物组和宿主分子过程，并确定这两个物种之间的区别遗传差异。由于这两个物种的基因组以前都没有发表过，因此我们从头组装转录本。通过使用 OrthoMCL 从转录本中过滤搜索微生物数据库，将微生物特异性转录本直系同源物从组装中分离出来。然后，我们使用宿主特异性转录本（即去除微生物特异性转录本后剩余的转录本）和来自两个近缘种的微生物特异性转录本的差异表达分析，鉴定仅存在于一种或另一种果实蝇物种中的定义种特异性转录本，但不存在于两种物种中。在 C. quilicii 雌蝇中，与 C. rosa s.s. 雌蝇相比，果胶杆菌属、肠杆菌属、肠杆菌属和克氏柠檬酸杆菌的细菌转录本上调。宿主转录本表达水平的比较表明，与 C. rosa s.s. 相比，C. quilicii （与 C. rosa s.s. 相比）在免疫、能量产生、细胞增殖、杀虫剂抗性、繁殖和增殖以及与应激反应和水果代谢物降解有关的通常与氧化还原反应相关的方面投入更多。
