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

Abstract

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.

The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations

“…When focusing on the long SVs over 1000bp, we found that X chromosome was the most extreme outlier of the linear pattern that shapes autosomes (Figure 1D, p < 0.001). This pattern indicates the “faster-X divergence” in principle [63], which is consistent with a previous observation in other mammalian species based on segmental duplication identified using only SyRI [27].…”

“…which is consistent with a previous observation in other mammalian species based on segmental duplication identified using only SyRI [27].…”

“…In this study, we are particularly interested in whether genomic SVs could be shaped by chromosomal distribution, methylation frequencies, recombination rates, and evolutionary forces. The distribution of SVs and the related evolutionary forces could provide a new empirical evidence for the "faster-X effect", an evolutionary pattern caused by differences between autosomes and hemizygous sex chromosomes [27][28][29][30]. The relationship between SVs and DNA methylation is a still unclear, which could be addressed with the nanopore long-read sequencing due to its direct signals of epigenome-wide methylation [31,32].…”

The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative

“…Although the “assembly-to-assembly” approach has been successfully used to identify SVs in other species ( Chen et al, 2022b ; Goel et al, 2019 ), we failed to obtain results from this method, probably due to the known phenomenon of higher rearrangements in plants than in animals. We further identified structural variations (SVs) using Sniffles V2.0.3 ( Sedlazeck et al, 2018 ) and a dual-alignment strategy implemented in Vulcan ( Fu et al, 2021 ).…”

Inference of ancestral alleles in the pig reference genome

“…We first used reference sequences of six suids for genome alignment: the domestic Duroc (Sscrofa11.1) and Diannan small‐ear pig, the European wild boar (also belonging to S. scrofa ), Visayan warty pig ( Sus cebifrons ), and the African common warthog and red river hog (Chen et al, 2022; Liu et al, 2022; Warr et al, 2020; Xie et al, 2022). Cattle (Rosen et al, 2020) and horse (Kalbfleisch et al, 2018) served as outgroups (Appendix S1).…”