Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, 60020-181, Brasil.
Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, 333 - Quitandinha, Petrópolis, RJ, 25651-076, Brasil.
BMC Genom Data. 2024 Sep 3;25(1):81. doi: 10.1186/s12863-024-01262-6.
The two oyster species studied hold considerable economic importance for artisanal harvest (Crassostrea rhizophorae) and aquaculture (Crassostrea gasar). Their draft genomes will play an important role in the application of genomic methods such as RNAseq, population-based genomic scans aiming at addressing expression responses to pollution stress, adaptation to salinity and temperature variation, and will also permit investigating the genetic bases and enable marker-assisted selection of economically important traits like shell and mantle coloration and resistance to temperature and disease.
The draft assembly size of Crassostrea gasar is 506 Mbp, and of Crassostrea rhizophorae is 584 Mbp with scaffolds N50 of 11,3 Mbp and 4,9 Mbp, respectively. The general masked bases by RepeatMasker in both genomes were highly similar using different datasets. The masked bases varied from 9.41% in C. gasar to 10.05% in C. rhizophorae and 42.85% in C. gasar to 44.44% in C. rhizophorae using Dfam and RepeatModeler datasets, respectively. Functional annotation with eggNog resulted in 34,693 annotated proteins in C. rhizophorae and 26,328 in C. gasar. BUSCO analysis shows that almost 99% of genes (5,295) are complete in relation to the mollusk orthologous genes dataset (mollusca_odb10).
研究的两种牡蛎物种在手工收获（红树牡蛎）和水产养殖（海湾牡蛎）方面具有重要的经济价值。它们的草图基因组将在应用基因组方法（如 RNAseq）方面发挥重要作用，基于群体的基因组扫描旨在解决对污染胁迫、适应盐度和温度变化的表达反应，还将允许研究遗传基础，并实现对经济重要性状（如贝壳和套膜颜色以及对温度和疾病的抗性）的标记辅助选择。
海湾牡蛎的草图组装大小为 506 Mbp，红树牡蛎的草图组装大小为 584 Mbp，支架 N50 分别为 11.3 Mbp 和 4.9 Mbp。使用不同的数据集时，重复掩蔽器在两个基因组中的一般掩蔽碱基高度相似。使用 Dfam 和 RepeatModeler 数据集时，掩蔽碱基在 C. gasar 中的比例分别从 9.41%变化到 10.05%，在 C. rhizophorae 中的比例分别从 42.85%变化到 44.44%。使用 eggNog 进行功能注释，在红树牡蛎中得到了 34693 个注释蛋白，在海湾牡蛎中得到了 26328 个注释蛋白。BUSCO 分析表明，几乎 99%的基因（5295 个）与软体动物同源基因数据集（mollusca_odb10）完全对应。
