The southern muriqui (Brachyteles arachnoides) is the largest neotropical primate. This species is endemic to Brazil and is currently critically endangered due to its habitat destruction. The genetic basis underlying adaptive traits of New World monkeys has been a subject of interest to several investigators, with significant concern about genes related to the immune system. In the absence of a reference genome, RNA-seq and de novo transcriptome assembly have proved to be valuable genetic procedures for accessing gene sequences and testing evolutionary hypotheses. We present here a first report on the sequencing, assembly, annotation and adaptive selection analysis for thousands of transcripts of B. arachnoides from two different samples, corresponding to 13 different blood cells and fibroblasts. We assembled 284,283 transcripts with N50 of 2,940 bp, with a high rate of complete transcripts, with a median high scoring pair coverage of 88.2%, including low expressed transcripts, accounting for 72.3% of complete BUSCOs. We could predict and extract 81,400 coding sequences with 79.8% of significant BLAST hit against the Euarchontoglires SwissProt dataset. Of these 64,929 sequences, 34,084 were considered homologous to Supraprimate proteins, and of the remaining sequences (30,845), 94% were associated with a protein domain or a KEGG Orthology group, indicating potentially novel or specific protein-coding genes of B. arachnoides. We use the predicted protein sequences to perform a comparative analysis with 10 other primates. This analysis revealed, for the first time in an Atelid species, an expansion of APOBEC3G, extending this knowledge to all NWM families. Using a branch-site model, we searched for evidence of positive selection in 4,533 orthologous sets. This evolutionary analysis revealed 132 amino acid sites in 30 genes potentially evolving under positive selection, shedding light on primate genome evolution. These genes belonged to a wide variety of categories, including those encoding the innate immune system proteins (APOBEC3G, OAS2, and CEACAM1) among others related to the immune response. This work generated a set of thousands of complete sequences that can be used in other studies on molecular evolution and may help to unveil the evolution of primate genes. Still, further functional studies are required to provide an understanding of the underlying evolutionary forces modeling the primate genome.

南部穆里基（短臂蜘蛛）是最大的新热带灵长类动物。该物种是巴西特有种，由于栖息地遭到破坏，目前正处于极度濒危的境地。新世界猴的适应性状特征的遗传基础已成为一些研究者关注的主题，他们对与免疫系统相关的基因非常关注。在没有参考基因组的情况下，RNA-seq和从头转录组装配已被证明是用于访问基因序列和测试进化假设的有价值的遗传程序。我们在这里提出了有关数千个转录本的测序，装配，注释和自适应选择分析的第一份报告。花生来自两个不同的样本，分别对应于13个不同的血细胞和成纤维细胞。我们组装了284,283个N50为2,940 bp的转录本，完整转录本的比率很高，中位数的高得分对覆盖率达88.2％，其中包括低表达的转录本，占完整BUSCO的72.3％。我们可以预测和提取针对Euarchontoglires SwissProt数据集的79.8％重大BLAST命中的81,400个编码序列。在这64,929个序列中，有34,084个被认为与Supraprimate蛋白同源，而在其余序列（30,845个）中，有94％与蛋白质结构域或KEGG Orthology组相关，表明潜在的新的或特定的蛋白质编码基因花生。我们使用预测的蛋白质序列与其他10个灵长类动物进行比较分析。该分析首次揭示了在Atelid物种中APOBEC3G，将此知识扩展到所有NWM家庭。使用分支站点模型，我们搜索了4,533个直系同源集中阳性选择的证据。这项进化分析揭示了在正选择下可能进化的30个基因中的132个氨基酸位点，为灵长类动物基因组进化提供了线索。这些基因属于多种类别，包括那些编码先天免疫系统蛋白的基因（APOBEC3G， OAS2和 CEACAM1）以及其他与免疫反应有关的信息。这项工作产生了成千上万的完整序列，可用于其他有关分子进化的研究，并可能有助于揭示灵长类动物基因的进化。尽管如此，仍需要进一步的功能研究以提供对灵长类动物基因组建模的潜在进化力的理解。