■假基因是已经丧失转录RNA分子或编码截短但可能有功能的蛋白质的能力的序列。虽然它们曾经被认为是进化的毫无意义的残余,最近的研究表明,假基因在各种生物过程中起着重要作用。然而,家蚕假基因的研究,一个重要的模式生物,是有限的,专注于单个或仅几个特定基因。
■为了填补这些空白,我们对家蚕的假基因进行了系统的全基因组研究。
■我们利用家蚕基因组组件鉴定了家蚕中的假基因,转录组,家蚕及其近缘种的蛋白质序列。然后我们使用来自832RNA-seq分析的转录组数据集来构建这些假基因的时空表达谱。此外,我们鉴定了组织特异性表达和差异表达的假基因,以进一步了解它们的特征。最后,系统分析了假基因作为lncRNAs的功能作用。
■我们总共鉴定了4410个假基因,分为4组,包括重复(DUP),单一伪基因(单一),加工假基因(逆转录假基因,RETs),和碎片(FRAG)。家蚕中的假基因大多数是在野生和家蚕分歧之前产生的,然而,驯化还可能涉及假基因的积累。这些假基因清楚地分为2个簇,一个高度表达和低调表达,后丝腺是组织特异性假基因最多的组织(199),暗示这些假基因可能参与了丝腺的发育和功能。我们在这些假基因中鉴定出3299个lncRNAs,这些lncRNAs在家蚕假基因中的靶基因被富集在卵形成和嗅觉功能中。
■这项研究补充了家蚕的基因组注释,为假基因的生物学作用提供有价值的见解。这也将有助于我们理解家蚕中复杂的基因调控网络,也可能对其他生物产生影响。
UNASSIGNED: Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes.
UNASSIGNED: To fill these gaps, we present a systematic genome-wide studies of pseudogenes in the silkworm.
UNASSIGNED: We identified the pseudogenes in the silkworm using the silkworm genome assemblies, transcriptome, protein sequences from silkworm and its related species. Then we used transcriptome datasets from 832 RNA-seq analyses to construct spatio-temporal expression profiles for these pseudogenes. Additionally, we identified tissue-specifically expressed and differentially expressed pseudogenes to further understand their characteristics. Finally, the functional roles of pseudogenes as lncRNAs were systematically analyzed.
UNASSIGNED: We identified a total of 4410 pseudogenes, which were grouped into 4 groups, including duplications (DUPs), unitary pseudogenes (Unitary), processed pseudogenes (retropseudogenes, RETs), and fragments (FRAGs). The most of pseudogenes in the domestic silkworm were generated before the divergence of wild and domestic silkworm, however, the domestication may also involve in the accumulation of pseudogenes. These pseudogenes were clearly divided into 2 cluster, a highly expressed and a lowly expressed, and the posterior silk gland was the tissue with the most tissue-specific pseudogenes (199), implying these pseudogenes may be involved in the development and function of silkgland. We identified 3299 lncRNAs in these pseudogenes, and the target genes of these lncRNAs in silkworm pseudogenes were enriched in the egg formation and olfactory function.
UNASSIGNED: This study replenishes the genome annotations for silkworm, provide valuable insights into the biological roles of pseudogenes. It will also contribute to our understanding of the complex gene regulatory networks in the silkworm and will potentially have implications for other organisms as well.