Long‐read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds

Ma, Haiming; Juan, José; He, Jun; Liu, Huifang; Han, Lingling; Gong, Yan; Li, Biao; Zhang, Yu; Tang, Shengguo; Zhang, Yuebo; Duan, Yehui; Yin, Yulong; Zeng, Qinghua; Yi, Jiacheng; He, X. M.; Zeng, Yongbo; Kim, Kung Seok; Xu, Kang; Liang, Fan; He, Jun

doi:10.1111/1755-0998.13550

Cited by 19 publications

(10 citation statements)

References 63 publications

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“…Despite the fundamental role of genome assemblies in biological studies, high‐quality assemblies are limited to well‐known domestic pig breeds. For example, all currently available chromosome‐level assemblies were from domestic breeds, including Duroc (Groenen et al, 2012; Warr et al, 2020), Bama (Zhang et al, 2019a), Luchuan (Yang et al, 2019), Ningxiang (Ma et al, 2022) and Meishan (Zhou et al, 2021), whereas the scaffold‐level assemblies also came from domestic breeds, including Wuzhishan (Fang et al, 2012), Large White, Landrace, Berkshire, Hampshire, Pietrain, Bamei, Jinhua, Rongchang and Tibetan (Li et al, 2017). For wild boars, there are some short‐read Illumina sequences (Bosse et al, 2015; Frantz et al, 2015; Groenen, 2016), but no assembly of a genome based on long‐reads or long‐range sequencing.…”

Section: Introductionmentioning

confidence: 99%

The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications

Chen

Zhong

et al. 2022

Animal Genetics

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The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long‐range information provided by 10× Linked‐Reads sequencing. We achieved a high‐quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference‐assistant scaffolding method. Using the ‘assembly‐to‐assembly’ approach, we identified intra‐chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (R2 > 0.64, p < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large‐scale inter‐chromosomal evolution, by resolving parental‐derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (p < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (p < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter‐chromosomal interaction between the sex chromosome and autosomes.

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Section: Introductionmentioning

confidence: 99%

The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications

Chen

Zhong

et al. 2022

Animal Genetics

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“…When we combined the analysis of SV distribution and the location of gene gain and loss on the 3D4/21 cell chromosome, it was found that there was a close relationship between structural variation and gene function, which was consistent with previous reports. It has been found that the deletion of 281 bp in the first intron of MYL4 in Ningxiang pigs promoted the formation of subcutaneous fat [ 39 ], and the deletion of the intron of IGF2R in Tibetan pigs inhibited its growth rate [ 27 ]. By further combining Hi-C data, we found that the deletion of large fragments resulted in the change in 3D genomic domains in 3D4/21 cells, leading to gene dysfunction.…”

Section: Discussionmentioning

confidence: 99%

Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells

Zhang

Luo

et al. 2022

Genes

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The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the CD163 had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection.

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“…Previously, the second-generation sequencing was the most commonly used method to analyze gene molecular mechanism in pig ( Liu et al, 2019b ; Tang et al, 2017 ). Recently, third-generation sequencing has been increasingly employed in studying the functional genomics and epigenetics in pig ( Beiki et al, 2019 ; Ma et al, 2021 ; Zhang et al, 2020 ). However, the AS and APA events in the pig ovary are rarely reported.…”

Section: Discussionmentioning

confidence: 99%

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing

Wang

et al. 2022

PeerJ

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Background In intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells. Methods Combined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells’ transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR. Results The present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs.

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Long‐read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds

Cited by 19 publications

References 63 publications

The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications

The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications

Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing

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