Evidence map›Paper›PMID 33099628›Full record

ArticleGigaScience2020

Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome.

Yan Li, Guangliang Gao, Yu Lin, Silu Hu, Yi Luo, Guosong Wang, Long Jin, Qigui Wang, Jiwen Wang, Qianzi Tang and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.

0numbers the graph read from it
0cells of the map it votes in
26citing papers in PubMed
1.8field-weighted citation impact, top 14% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

26 citing papers in PubMed, 64 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 2 institutions in 2 countries.

Yan LiInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Guangliang GaoInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Yu LinInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Silu HuInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Yi LuoInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Guosong WangInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Long JinInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Qigui WangInstitute of Poultry Science, Chongqing Academy of Animal Science, No. 51 Changlong Avenue, Rongchang District, Chongqing 402460, China.
Jiwen WangInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Qianzi TangInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Mingzhou LiInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China.
Sichuan Agricultural University · CNChongqing Academy of Animal Science · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

GeeseGenomeAnimalsChromosomesFemaleGenomicsHigh-Throughput Nucleotide SequencingMolecular Sequence Annotationannotationchromosome-length assemblygoose genomeHi-Chybrid de novo assembly approachesPacBio

Identifiers

PMID33099628
PMCPMC7585555
OpenAlexW3094090602

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.