Hauff Lindsey, Rasoanaivo Noa Elosmie, Razafindrakoto Andriamahery, Ravelonjanahary Hajanirina, Wright Patricia C, Rakotoarivony Rindra, Bergey Christina M
Department of Ecology, Evolution, and Natural Resources Rutgers University New Brunswick New Jersey USA.
Center for Human Evolutionary Studies Rutgers University New Brunswick New Jersey USA.
Ecol Evol. 2025 Jan 6;15(1):e70734. doi: 10.1002/ece3.70734. eCollection 2025 Jan.
As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next-generation sequencing technologies and the resulting reduction in associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first published reference genome for the endangered red-fronted brown lemur () from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived specimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.157 gigabase, 2980-contig nuclear assembly with an N50 of 101.6 Mb and a 17,108 bp mitogenome. The nuclear assembly had 30× average coverage and was comparable in completeness to other primate reference genomes, with a 96.1% BUSCO completeness score for primate-specific genes. As the first published reference genome for and the only annotated genome available for the speciose genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.
作为最受威胁的哺乳动物类群之一，马达加斯加的狐猴正面临前所未有的人为压力。为应对诸如此类的保护需求，研究人员越来越依赖保护基因组学来识别特别受关注的种群。然而，许多这些基因组方法需要高质量的基因组。虽然下一代测序技术的出现以及相关成本的降低导致了基因组数据和高质量参考基因组的激增，但基因组测序能力的全球差异往往导致来自生物多样性丰富的宿主国家的生物样本被出口到全球北方的机构，在基因组研究的获取和培训方面造成不平等。在此，我们展示了首个公开的濒危红额褐狐猴（）参考基因组，该基因组是在宿主国家完全使用便携式牛津纳米孔测序进行测序工作获得的。我们使用一个存档的标本，在马达加斯加农村拉努马法纳国家公园附近的瓦勒生物研究中心进行了长读长纳米孔测序，从10个MinION流动槽中产生了超过750 Gb的测序数据。仅使用这些长读长数据，我们组装了一个2.157千兆碱基、2980个重叠群的核基因组，N50为101.6 Mb，还有一个17,108 bp的线粒体基因组。该核基因组平均覆盖度为30×，在完整性上与其他灵长类参考基因组相当，灵长类特异性基因的BUSCO完整性评分达到96.1%。作为首个公开的红额褐狐猴参考基因组以及狐猴属中唯一可用的注释基因组，这一资源对于保护基因组学研究将至关重要，同时我们的努力展示了该方案在解决研究不平等和建立基因组能力方面的潜力。
