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

Abstract

Background The 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. Findings We 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. Conclusions We present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese.

Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese

“…We also used all three published geese genomes and 12 other chromosome-level bird genomes to carry out BUSCO 19 analyses to delve into the completeness of the XGG genome. The results showed that 95.7% of complete genes and 1.0% of fragments of genes were identified from the 8,338 core genes in the Aves dataset, better than the evaluation results of TFG 3 (Fig. 2a ).…”

“…To further assess the accuracy of the scaffolded genome, we realigned the Illumina paired-end reads to the XGG genome with high mapping (99.19%) and high coverage rates (97.96%), generally reflecting the base accuracy of the reliable genome (Supplementary Table 6 ). The genome was further evaluated by CEGMA 18 , and 92.3% of 248 core genes from six eukaryotic model organisms could be identified (Supplementary Table 7 ), a value that was significantly higher than the evaluation results (85.08%) of TFG 3 . We also used all three published geese genomes and 12 other chromosome-level bird genomes to carry out BUSCO 19 analyses to delve into the completeness of the XGG genome.…”

“…2a ). In particular, our constructed genome for XGG displayed 2.35-fold, 14.99-fold, and 15.28-fold improvements in scaffold contiguity over that of a currently reported hybrid goose (TFG) 3 and the other two Chinese indigenous geese breeds (SCW and ZDW) 4 , 5 (Table 1 ).…”

“…Under the influences of diverse economic cultures and geographical structures, 30 Chinese indigenous geese breeds with different phenotypic features and production performance have gradually been formed 2 . The genome assemblies of three domestic geese have been recently completed, but only the hybrid Tianfu goose (TFG) was assembled to the chromosome level 3 . Chinese indigenous geese (the Sichuan white goose [SCW] and the Zhedong white goose [ZDW]) assemblies are still at the scaffold level 4 , 5 .…”

Genome-Wide Gene Expression Profiles Reveal Distinct Molecular Characteristics of the Goose Granulosa Cells

“…After removing the adaptors, the sequences with uncertain bases, low-quality sequences, and sequences of less than 50 bp, as well as the high-quality data from the 45 libraries were mapped to the goose genome, which was assembled by our lab ( Li et al, 2020 ) by alignment tool STAR (version 2.6.0c) ( Dobin and Gingeras, 2015 ; Dobin and Gingeras, 2016 ) with the parameters of ENCODE standard RNA-seq pipeline. Then, the transcripts were reconstructed with parameters of -g -u -b --library-type fr-first strand using the Cufflinks (2.2.1) ( Pollier et al, 2013 ; Ghosh and Chan, 2016 ).…”