The Pan-genome of the Cultivated Soybean (PanSoy) Reveals an Extraordinarily Conserved Gene Content

  Davoud Torkamaneh, Marc-Andre Lemay and François Belzile. The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content. Plant Biotechnology J. 2021 Sept;19:(9):1852-1862. doi: 10.1111/pbi.13600. PMID: 33942475

Studies on structural variation in plants have revealed the inadequacy of a single reference genome for an entire species and suggest that it is necessary to build a species-representative genome, called a pan-genome to better capture the extent of both structural and nucleotide variation. Here, we present a pan-genome of cultivated soybean (Glycine max), termed PanSoy, constructed using the de novo genome assembly of 204 phylogenetically and geographically representative improved accessions selected from the larger GmHapMap collection. PanSoy uncovers 108 Mb (~11%) of novel nonreference sequences encompassing 3,621 protein-coding genes (including 1,659 novel genes) absent from the soybean Williams 82 reference genome. Nonetheless, the core genome represents an exceptionally large proportion of the genome, with >90.6% of genes being shared by >99% of the accessions. A majority of PAVs encompassing genes could be confirmed with long-read sequencing on a subset of accessions. The PanSoy is a major step towards capturing the extent of genetic variation in cultivated soybean and provides a resource for soybean genomics research and breeding.

Link to FigShare Repository

Link to Data Store directory

glyma.Wm82.gnm4.pan.W46N.GmHapMap_IDs.xlsx: Identifiers, plant introduction numbers, and countries of origin for accessions from the 1007 accessions described in the GmHapMap project, Torkamaneh, Laroche et al. (2020; DOI: 10.1111/pbi.13466), from which the 204 accessions in the data set in this collection derive.

glyma.Wm82.gnm4.pan.W46N.PanSoy.ptpg.gtf.gz: Predicted genes from the PanSoy genomic data, file PanSoy_genes_not_in_Wm82.fna. This includes both genes identified in Wm82.gnm4 and genes in the PanSoy complement.

glyma.Wm82.gnm4.pan.W46N.PanSoy_cds_not_in_Wm82.fna.gz: Coding sequence (CDS) predicted from the PanSoy genomic sequence, not in Wm84.gnm4.

glyma.Wm82.gnm4.pan.W46N.PanSoy_seq_not_in_Wm82.fna.gz: The PanSoy genomic sequence, present in one or more of the 204 accessions described in Torkamaneh, Lemay, Belzile (2021) but not in the reference Wm82.gnm4.

glyma.Wm82.gnm4.pan.W46N.PanSoy_supp_tables.xlsx: Supplementary tables S1-S7 from Torkamaneh, Lemay, Belzile (2021), including gene presence-absence variation for genes predicted in Wm82.gnm4.ann1 and in the 204 accessions described in this study.