The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

Abstract

BackgroundThe polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes.ResultsThe genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150–250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations.ConclusionsWe show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-819) contains supplementary material, which is available to authorized users.

Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

“…The annotation produced a reasonable number of protein-coding genes. This is comparable to C. tentans from the same genus as well as Drosophila melanogaster (15 120 and 13 907 protein-coding genes, respectively; dos Santos et al 2015; Table S7, Supporting Information; Kutsenko et al 2014). The difference of approximately 30 MB of sequence length between the presented and the estimated genome size of 200 MB (Schmidt-Ott et al 2009) is in the most part likely to be due to centromers, telomers and other large repetitive clusters that cannot be assembled with the existing data.…”

“…; Table , Supporting Information; Kutsenko et al . ). The difference of approximately 30 MB of sequence length between the presented and the estimated genome size of 200 MB (Schmidt‐Ott et al .…”

Chironomus riparius(Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

“…From a BUSCO analysis we could assume that the genome is almost complete in terms of its gene set (93 % of core arthropod genes found). The annotation further resulted in a reasonable number of protein-coding genes that is comparable to C. tentans from the same genus as well as Drosophila melanogaster (15,120 and 13,907 protein-coding genes respectively; Supplementary Table S7; dos Santos et al 2015;Kutsenko et al 2014). The delta of roughly 30 MB of sequence between the presented and the estimated genome size of 200 MB (Schmidt-Ott et al 2009), therefore, is likely mostly due to centromers, telomers, and other large repetitive clusters that cannot be assembled with the existing data.…”

Entomology moves into the genomics era

“…http://engine.scichina.com/doi/10.1360/N052016-00222 摇蚊(Chironomus tentans)基因组鉴定了多线染色体 相关的 Balbiani ring(BR)基因和 BR 位点的组织形 式 [66] ; 南极摇蚊(Belgica antarctica)基因组展示了极 度紧凑的基因组及其对极端环境的适应 [67] ; 竹节虫 两种生态型的比较基因组揭示了寄主植物对昆虫平 行物种进化的作用 [17] ; 榕小蜂(Ceratosolen solmsi)基 因组揭示了榕小蜂-榕树特殊的协同进化 [68] ; 37 种苍 蝇的比较基因组学研究揭示了性染色体在双翅目昆 虫中的多态性及其核型的演化 [69] ; 蛱蝶属 3 个近缘 种的比较基因组学研究了与拟态相关的基因组区域 的频繁交流, 推测近缘种之间的杂交和基因交流可 能在适应性扩散过程中具有重要作用 [70] . 这些昆虫 基因组学的研究加深了人们对昆虫中一些独特表型 的决定基因及其进化机制的认识.…”