Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds

Abstract

Background Anatidae contains numerous waterfowl species with great economic value, but the genetic diversity basis remains insufficiently investigated. Here, we report a chromosome-level genome assembly of Lion-head goose (Anser cygnoides), a native breed in South China, through the combination of PacBio, Bionano, and Hi-C technologies. Findings The assembly had a total genome size of 1.19 Gb, consisting of 1,859 contigs with an N50 length of 20.59 Mb, generating 40 pseudochromosomes, representing 97.27% of the assembled genome, and identifying 21,208 protein-coding genes. Comparative genomic analysis revealed that geese and ducks diverged approximately 28.42 million years ago, and geese have undergone massive gene family expansion and contraction. To identify genetic markers associated with body weight in different geese breeds, including Wuzong goose, Huangzong goose, Magang goose, and Lion-head goose, a genome-wide association study was performed, yielding an average of 1,520.6 Mb of raw data that detected 44,858 single-mucleotide polymorphisms (SNPs). Genome-wide association study showed that 6 SNPs were significantly associated with body weight and 25 were potentially associated. The significantly associated SNPs were annotated as LDLRAD4, GPR180, and OR, enriching in growth factor receptor regulation pathways. Conclusions We present the first chromosome-level assembly of the Lion-head goose genome, which will expand the genomic resources of the Anatidae family, providing a basis for adaptation and evolution. Candidate genes significantly associated with different goose breeds may serve to understand the underlying mechanisms of weight differences.

Chromosome-level genome sequencing and multi-omics of the Hungarian White Goose (Anser anser domesticus) reveals novel miRNA-mRNA regulation mechanism of waterfowl feather follicle development

“…This study used sequencing strategies to construct the Hungarian white goose genome. We got a high-quality genome assembly, which has a total length of 1115.82 Mb, 39 pairs of chromosomes, 92.98% of the BUSCO index and a higher level of contig N50 and scaffold N50 separately up to 2.32 Mb and 60.69 Mb compared with other goose genomes, indicating that this genome had good continuity and integrity ( Li et al, 2020 ; Zhao et al, 2022 ). The chromosome level of the genome can provide a fundamental resource for functional genomic research and help to illustrate biological and evolutionary features.…”

“…It has widely been claimed that the Chinese goose was inherited from the swan goose ( Anser cygnoides ), while the European geese were thought to have originated from the greylag goose ( Anser anser ) ( Ouyang et al, 2022 ). Using high-quality assembly sequences allows us to scientifically and completely decode the genetic variety of species, investigate disease processes, and comprehend the evolution of species ( Zhao et al, 2022 ). In recent years, advances in genomics technology have allowed us to better understand and identify genetic variations associated with desirable phenotypic traits, including feather production and development, using combined genome and transcriptome sequencing data ( Li et al, 2019 ; Deng et al, 2021 ).…”

“…In recent years, advances in genomics technology have allowed us to better understand and identify genetic variations associated with desirable phenotypic traits, including feather production and development, using combined genome and transcriptome sequencing data ( Li et al, 2019 ; Deng et al, 2021 ). However, with the improvement of genomic techniques, a growing number of avian genomes are being assembled, including those of Indian peafowl ( Pavo cristatus ) ( Liu et al, 2022 ), domestic chicken ( Gallus gallus ) ( International Chicken Genome Sequencing Consortium, 2004 ), domestic turkey ( Meleagris gallopavo ) ( Dalloul et al, 2010 ), the zebra finch ( Taeniopygia guttata ) ( Smith et al, 2013 ) and some of the goose species, such as the bar-headed goose ( Wang et al, 2020 ; Zhang et al, 2022 ), pink-footed goose ( Pujolar et al, 2018 ), lion-head goose ( Zhao et al, 2022 ) and the swan goose ( Anser cygnoides ) ( Lu et al, 2015 ). One of the most excellent European goose breeds is the Hungarian white goose ( Anser Anser ), which was imported to China in 2010, known for its high productivity and adaptability to different climatic conditions, as well as its significantly high feather production and other exclusive features that have drawn the interest of researchers and scientists.…”

High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis

“… 18 , 19 High-quality genome assembly sequences enable comprehensive and scientific decoding of genetic diversity in various organisms. 20 They have been extensively utilized to study invasion dynamics, identify molecular mechanisms underlying adaptability, and discover promising genes for biotechnology-based control strategies. 21 To fill the gap, in this study, we successfully assembled a high-quality chromosome-level genome of A. amurensis using Illumina, PacBio and Hi-C sequencing technologies resulting in 22 pseudochromosomes.…”

Metagenomic and Antibiotic Resistance Analysis of the Gut Microbiota in Larus relictus and Anatidae Species Inhabiting the Honghaizi Wetland of Ordos, Inner Mongolia, from 2021 to 2023

“…There exist four relatively independent breeding populations worldwide, of which Erdos City in Inner Mongolia is the largest and most important for maintaining global numbers [6]. Anatidae collectively refer to Anseries birds belonging to the order Anseriformes, a diverse avian family constituting ducks, geese and swans [7], with a wide range of species and abundance in Inner Mongolia, and interesting group dynamics and distribution patterns.…”