transcriptome_evaluation.txt

Marsupials exhibit highly specialized patterns of reproduction and development, making them uniquely valuable for comparative genomics studies with their sister lineage, eutherian (also known as placental) mammals. However, marsupial genomic resources still lag far behind those of eutherian mammals, limiting our insight into mammalian diversity. Here, we present a series of novel genomic resources for the fat-tailed dunnart (<em>Sminthopsis crassicaudata</em>), a mouse-like marsupial that, due to its ease of husbandry and <em>ex-utero</em> development, is emerging as a laboratory model. To enable wider use, we have generated a multi-tissue <em>de novo</em> transcriptome assembly of dunnart RNA-seq reads spanning 15 tissues. This highly representative transcriptome is comprised of 2,093,982 assembled transcripts, with a mean transcript length of 830 bp. The transcriptome mammalian BUSCO completeness score of 93% is the highest amongst all other published marsupial transcriptomes. Additionally, we report an improved fat-tailed dunnart genome assembly which is 3.23 Gb long, organized into 1,848 scaffolds, with a scaffold N50 of 72.64 Mb. The genome annotation, supported by assembled transcripts and <em>ab initio</em> predictions, revealed 21,622 protein-coding genes. Altogether, these resources will contribute greatly towards characterizing marsupial biology and mammalian genome evolution.

有袋类动物展现出高度特化的繁殖与发育模式，使其在与姊妹类群真兽类（eutherian，又称胎盘类）哺乳动物的比较基因组学研究中具有独特价值。然而，有袋类动物的基因组资源仍远落后于真兽类哺乳动物，限制了我们对哺乳动物多样性的深入理解。在此，我们为肥尾袋鼬（<em>Sminthopsis crassicaudata</em>）——一种类似小鼠的有袋类动物，因其易于饲养和宫外（ex-utero）发育的特性而逐渐成为实验室模型——提供了一系列新的基因组资源。为促进其更广泛应用，我们对该袋鼬15种组织的RNA-seq数据进行了多组织从头（de novo）转录组组装。该转录组具有高度代表性，包含2,093,982条组装转录本，平均转录本长度为830 bp。其哺乳动物BUSCO完整性评分为93%，在所有已发表的有袋类转录组中最高。此外，我们报道了一个改进的肥尾袋鼬基因组组装版本，长度为3.23 Gb，包含1,848个scaffold，scaffold N50为72.64 Mb。该基因组注释结合了组装转录本和从头算（ab initio）预测的结果，共鉴定出21,622个蛋白编码基因。总之，这些资源将极大地推动有袋类生物学特征解析及哺乳动物基因组演化研究。