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Abstract The aye-aye (Daubentonia madagascariensis) is the only extant member of the Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, the predominant usage of short-read sequencing has resulted in limited assembly contiguity and completeness, and no protein-coding gene annotations have yet been released. Here, we present a novel, fully annotated, chromosome-level hybrid de novo assembly for the species based on a combination of Oxford Nanopore Technologies long reads and Illumina short reads and scaffolded using genome-wide chromatin interaction data—a community resource that will improve future conservation efforts as well as primate comparative analyses.
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Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri
The hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and they are one of only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming to reconstruct a high-coverage protein-coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of the gene models promise a high utility in various comparative analyses including phylogenomics and phylome exploration.
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- Award ID(s):
- 1818012
- PAR ID:
- 10432052
- Date Published:
- Journal Name:
- F1000Research
- Volume:
- 11
- ISSN:
- 2046-1402
- Page Range / eLocation ID:
- 1270
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.12688/f1000research.124719.1
