Department of Biology, University of Maryland, USA.
Mol Biol Evol. 2011 Apr;28(4):1339-48. doi: 10.1093/molbev/msq293. Epub 2010 Nov 1.
With the advent of transcriptome data, it has become clear that mRNA-like noncoding RNAs (mlncRNAs) are widespread in eukaryotes. Although their functions are poorly understood, these transcripts may play an important role in development and could thus be involved in determining developmental complexity and phenotypic diversification. However, few studies have assessed their potential roles in the divergence of closely related species. Here, we identify and study patterns of sequence and expression divergence in ten novel candidate mlncRNAs from Drosophila pseudoobscura and its close relative D. persimilis. The candidate mlncRNAs were identified by randomly sequencing a group of 734 cDNA clones from a microarray that showed either no difference in expression (187 clones) or differential expression (547 clones) in comparisons between D. pseudoobscura and D. persimilis and between these two species and their F(1) hybrids. Candidate mlncRNAs are overrepresented among differentially expressed transcripts between males of D. pseudoobscura and D. persimilis, and although they have high sequence conservation between these two species, seven of them have no putative homologs in any of the other ten Drosophila species whose genomes have been sequenced. Expression of eight of the ten candidate mlncRNAs was detected either in whole bodies (adults) or testes using a custom-designed oligonucleotide microarray. Three of the ten candidate mlncRNAs are highly expressed (in the top 4% of the male transcriptome), differentially expressed between species, and show extreme levels of sex-bias, with one transcript having the highest level of male bias in the whole transcriptome. Proteomic data from testes show no traces of any predicted peptides from the candidate mlncRNAs. Our results suggest that these mlncRNAs may be important in male-specific processes related to sexual dimorphism and species divergence in this species group.
随着转录组数据的出现，人们已经清楚地认识到，mRNA 样非编码 RNA（mlncRNA）在真核生物中广泛存在。尽管它们的功能还不太清楚，但这些转录物可能在发育过程中发挥着重要作用，因此可能参与决定发育的复杂性和表型的多样化。然而，很少有研究评估它们在密切相关物种分化中的潜在作用。在这里，我们鉴定并研究了来自黑腹果蝇及其近缘种 D. persimilis 的 10 个新候选 mlncRNA 的序列和表达分化模式。这些候选 mlncRNA 是通过随机测序微阵列上的一组 734 个 cDNA 克隆来鉴定的，该微阵列在黑腹果蝇和 D. persimilis 之间以及这两个物种与其 F(1)杂种之间的表达差异比较中显示出无差异（187 个克隆）或差异表达（547 个克隆）。候选 mlncRNA 在黑腹果蝇和 D. persimilis 雄蝇之间差异表达的转录本中所占比例较高，尽管它们在这两个物种之间具有很高的序列保守性，但其中 7 个在其他 10 个已测序的黑腹果蝇种中没有假定的同源物。使用定制设计的寡核苷酸微阵列，在整个身体（成虫）或睾丸中检测到这 10 个候选 mlncRNA 中的 8 个的表达。这 10 个候选 mlncRNA 中的 3 个表达水平较高（在雄转录组的前 4%），在物种之间存在差异表达，并且表现出极端的性别偏向，其中一个转录本在整个转录组中具有最高的雄性偏向性。睾丸的蛋白质组学数据显示不出候选 mlncRNA 预测肽的任何痕迹。我们的结果表明，这些 mlncRNA 可能在与性二态性和该物种组中物种分化有关的雄性特有的过程中很重要。
