Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

Abstract

17Pigs (Sus scrofa) exhibit diverse phenotypes in different breeds shaped by the 18 combined effects of various local adaptation and artificial selection. To 19 comprehensively characterize the genetic diversity of pigs, we construct a pig pan-20 genome by comparing genome assemblies of 11 representative pig breeds with the 21 reference genome (Sscrofa11.1). Approximately 72.5 Mb non-redundant sequences 22 were identified as pan-sequences which were absent from the Sscrofa11.1. On 23 average, 41.7 kb of spurious heterozygous SNPs per individual are removed and 12.9 24 kb novel SNPs per individual are recovered using pan-genome as the reference for 25 SNP calling, thereby providing enhanced resolution for genetic diversity in pigs. 26Homolog annotation and analysis using RNA-seq and Hi-C data indicate that these 27 pan-sequences contain protein-coding regions and regulatory elements. These pan-28 sequences can further improve the interpretation of local 3D structure. The pan-29 genome as well as the accompanied web-based database will serve as a primary 30 resource for exploration of genetic diversity and promote pig breeding and biomedical 31 research. 32 65level. 66Here we carried out an in-depth comparison between 11 de novo assemblies 67 and the reference genome by analysis of the assembly-versus-assembly alignment. 68The final pan-genome comprises 39,744 (total length: 72.5 Mb) newly added 69 sequences and of which 607 demonstrate coding potential. Furthermore, the three-70 dimensional (3D) spatial structure of pan-genome was depicted by revealing the 71 characteristics of pan-genome in A/B compartment (generally euchromatic and 72 heterochromatic regions) and topologically associating domain (TAD). We also build 73 a pig pan-genome database (PIGPAN, 74 http://animal.nwsuaf.edu.cn/code/index.php/panPig) which can serve as a 75 fundamental resource for unlocking variations within diverse pig breeds.76 5 Results 77Initial characterization of pan-sequences in the pig genome 78 To construct the pig pan-genome, we first aligned 11 assemblies from 11 genetically 79 distinct breeds (five from Europe, and six from China) against Sscrofa11.1 using 80 BLASTN to generate the unaligned sequences ( Fig. 1a and Supplementary Fig. 2). 81 The length of the unaligned sequences in the Chinese pigs was significantly longer 82 than those in the European pigs (P <0.01) since the reference genome is from a 83 European pig (Fig. 1a). As expected, the Wuzhishan assembly had the largest number 84 of sequences because this sample is the only male individual among the 11 assemblies 85 and can provide many male-specific sequences ( Fig. 1a and Supplementary Table 86 2). After removing redundant sequences, we obtained 39,744 sequences with a total 87 length of 72.5 Mb (Fig. 1b), which were absent from Sscrofa11.1 and thus were 88 defined as pan-sequences. The content of the repetitive elements (45.91%) and GC 89 (44.61%) in these sequences were slightly higher than those in Sscrofa11.1 (45.19% 90 and 41.5%, respectively) ( Fig. 1...

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

“…Interestingly, in contrast to the observations in human, the repeat content of the newly assembled pan-sequences was similar to that of the reference pig genome assembly, and newly assembled repeats were more evenly distributed across categories [53]. This study also identified TIG3, an essential regulator of adipocyte lipolysis which displays presence/absence variation in pig populations, and could contribute to differences in physiology among pigs [53]. A previous study which analysed nine non-reference pig genomes reported 137 Mb of additional sequence harbouring 1,737 genes [54].…”

“…The pangenome was constructed using 12 pig genomes, and 72.5 Mb of novel sequence was found, corresponding to ~3% of the genome. Interestingly, in contrast to the observations in human, the repeat content of the newly assembled pan-sequences was similar to that of the reference pig genome assembly, and newly assembled repeats were more evenly distributed across categories [53]. This study also identified TIG3, an essential regulator of adipocyte lipolysis which displays presence/absence variation in pig populations, and could contribute to differences in physiology among pigs [53].…”

“…To our knowledge the only other mammal for which a pangenome has been reported is Sus scrofa (pig) [53]. The pangenome was constructed using 12 pig genomes, and 72.5 Mb of novel sequence was found, corresponding to ~3% of the genome.…”

“…In bacteria accessory genes are mostly derived from HGT, whereas in eukaryotes they can mostly be traced to local and whole genome duplications, as well as de novo gene birth [28,59,60]. While accessory genes constitute a substantial proportion of bacterial, fungal and plant pangenomes, mammalian pangenomes are dominated by core genes (up to 96.88% of human genes are reported as core) [3,53]. However, a substantial proportion (25%) of accessory genes found in Mediterranean mussel demonstrates that the current animal gene space is far from complete, especially for species with high adaptive capabilities, high levels of heterozygosity, high levels of repetitive elements and histories of whole genome duplication events [55].…”

Reference-based QUantification Of gene Dispensability (QUOD)

“…Additionally, QUOD is not restricted to plants, but could be applied to other species (e.g. pig [37]). However, an accurate determination of gene dispensability scores free of systematic biases might rely on a uniform selection of genomes from the respective taxonomic group and on uniform read coverage of genes.…”