A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta).

Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. Results: We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. Conclusions: mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.

背景：环尾狐猴（Lemur catta）是一种具有独特魅力的原猴亚目灵长类动物，是马达加斯加特有的物种。鉴于其作为旗舰物种的地位以及在大众媒体中的广泛宣传，这些狐猴备受关注。不幸的是，近期其种群数量下降，导致野生个体数量普查降至不足2500只，并且该物种被世界自然保护联盟（IUCN）列为濒危物种。与大多数原猴亚目灵长类动物的情况一样，对环尾狐猴进行的基因组研究数量有限，部分原因是缺乏基因组资源。 结果：我们为环尾狐猴生成了一个新的高质量参考基因组组装（mLemCat1），该组装符合脊椎动物基因组计划的标准。这个新的长读长组装由太平洋生物科学公司的连续长读长（CLR数据）、光学图谱Bionano读长、Arima HiC数据以及10X连锁读长组成。该组装的连续性和完整性极高，支架和重叠群的N50值分别为90.982 Mb和10.570 Mb。此外，与其他高质量的灵长类动物组装相比，环尾狐猴的Alu元件数量报告值最低，这主要是由于缺乏AluS和AluY元件。 结论：mLemCat1不仅是环尾狐猴群体的优质基因组资源，也是狐猴科其他成员的优质资源，并且是首个原猴亚目的超长读长组装。