Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome
| Autor: | Mingzhou Li, Yan Li, Qianzi Tang, Silu Hu, Guangliang Gao, Jiwen Wang, Long Jin, Yi Luo, Yu Lin, Guosong Wang, Qigui Wang |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Anser cygnoides
chromosome-length assembly AcademicSubjects/SCI02254 Sequence assembly goose genome Health Informatics Anser anser Data Note Genome DNA sequencing Chromosomes 03 medical and health sciences 0302 clinical medicine food Goose Hi-C biology.animal Geese Animals Domestic goose 030304 developmental biology PacBio 0303 health sciences Graylag goose biology hybrid de novo assembly approaches High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Genomics biology.organism_classification food.food Computer Science Applications annotation Evolutionary biology AcademicSubjects/SCI00960 Female 030217 neurology & neurosurgery |
| Zdroj: | GigaScience |
| ISSN: | 2047-217X |
| Popis: | BackgroundThe domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing.FindingsWe generated a 1.11-Gb goose genome with contig and scaffold N50 values of 1.85 and 33.12 Mb, respectively. The assembly contains 39 pseudo-chromosomes (2n = 78) accounting for ∼88.36% of the goose genome. Compared with previous goose assemblies, our assembly has more continuity, completeness, and accuracy; the annotation of core eukaryotic genes and universal single-copy orthologs has also been improved. We have identified 17,568 protein-coding genes and a repeat content of 8.67% (96.57 Mb) in this genome assembly. We also explored the spatial organization of chromatin and gene expression in the goose liver tissues, in terms of inter-pseudo-chromosomal interaction patterns, compartments, topologically associating domains, and promoter-enhancer interactions.ConclusionsWe present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese. |
| Databáze: | OpenAIRE |
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