ArticleBMC biology2017
Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).
Article in BMC biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 78 citations in OpenAlex.
- Rapid centromere turnover and the adaptive radiation of lemurs.bioRxiv : the preprint server for biology · 2026Article
- Species-Specific Responses to Paleoclimatic Changes and Landscape Barriers Drive Contrasting Phylogeography of Co-Distributed Lemur Species in Northeastern Madagascar.Molecular ecology · 2025Article
- Relaxation of selective constraint on the sweet-taste receptor gene TAS1R2 in lorisiform primates.Scientific reports · 2025Article
- A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (II) Fast One-Step Assembly of Highly Continuous Chromosome Sequences.Animals : an open access journal from MDPI · 2025Article
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- In vivo self-renewal and expansion of quiescent stem cells from a non-human primate.Nature communications · 2025Article
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- Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar.Nature ecology & evolution · 2025Article
- eLemur: A cellular-resolution 3D atlas of the mouse lemur brain.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A hybrid genome assembly of the endangered aye-aye (Daubentonia madagascariensis).G3 (Bethesda, Md.) · 2024Article
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- Diversification processes in Gerp's mouse lemur demonstrate the importance of rivers and altitude as biogeographic barriers in Madagascar's humid rainforests.Ecology and evolution · 2023Article
- Identification of highly variable sequence fragments in unmapped reads for rapid bacterial genotyping.BMC genomics · 2022Article
- CebidaeLife (Basel, Switzerland) · 2022Article
- Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results.Proceedings. Biological sciences · 2022Article
- From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.Science (New York, N.Y.) · 2022Article
- Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar.BMC ecology and evolution · 2021Article
Corrections and comments
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Authors and funding
20 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundThe de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly.
methodsWe used a combination of advanced genomic technologies to iteratively resolve conflicts and super-scaffold the M. murinus genome.
resultsWe improved the M. murinus genome assembly to a scaffold N50 of 93.32 Mb. Whole genome alignments between our primary super-scaffolds and 23 human chromosomes revealed patterns that are congruent with historical comparative cytogenetic data, thus demonstrating the accuracy of our de novo scaffolding approach and allowing assignment of scaffolds to M. murinus chromosomes. Moreover, we utilized our independent datasets to discover and characterize sequences associated with centromeres across the mouse lemur genome. Quality assessment of the final assembly found 96% of mouse lemur canonical transcripts nearly complete, comparable to other published high-quality reference genome assemblies.
conclusionsWe describe a new assembly of the gray mouse lemur (Microcebus murinus) genome with chromosome-scale scaffolds produced using a hybrid bioinformatic and sequencing approach. The approach is cost effective and produces superior results based on metrics of contiguity and completeness. Our results show that emerging genomic technologies can be used in combination to characterize centromeres of non-model species and to produce accurate de novo chromosome-scale genome assemblies of complex mammalian genomes.
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