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. 2022 Oct;54(10):1553-1563.
doi: 10.1038/s41588-022-01172-2. Epub 2022 Sep 22.

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Tao Yang #  1 , Rong Liu #  1 , Yingfeng Luo #  2 , Songnian Hu #  2   3 , Dong Wang #  1   4 , Chenyu Wang  1 , Manish K Pandey  5 , Song Ge  6   3 , Quanle Xu  7 , Nana Li  4   8 , Guan Li  1 , Yuning Huang  1 , Rachit K Saxena  5 , Yishan Ji  1 , Mengwei Li  1 , Xin Yan  1 , Yuhua He  9 , Yujiao Liu  10   11 , Xuejun Wang  12 , Chao Xiang  13 , Rajeev K Varshney  14   15 , Hanfeng Ding  16   17 , Shenghan Gao  18 , Xuxiao Zong  19
Affiliations

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Tao Yang et al. Nat Genet. 2022 Oct.

Abstract

Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Overview of the pea genome assembly.
The outer layer of colored blocks is a circular representation of seven chromosomes. a = the genetic markers, b = repeat density, c = gene density calculated in 1,000-kb windows sliding in 500-kb steps, d = tandem duplicated genes, e = Mendel’s genes (red lines); f, g and h = the nucleotide diversity (π) of the three species within Pisum (P. sativum (64), P. fulvum (22) and P. abyssinicum (15)) based on population genetic structure analyses, and i = transcription factors. The innermost layer shows interchromosomal synteny.
Fig. 2
Fig. 2. The comparative and functional characterization of repeats.
a, Nucleotide identity distribution of long terminal region of the complete LTR retrotransposons. b, Length distribution of the complete LTR-RTs in pea genome. c, Comparison of gene length between P. sativum (ZW6) and M. truncatula. d, Expression characterization of pea genes with different length.
Fig. 3
Fig. 3. Summary of SVs for 118 representatives cultivated and wild pea in Pisum.
a, Density plot of variation frequency for different SV size. b, Density plot of SV length for different SV type. DNA_TE, DNA transposable elements; LTR, long terminal repeat; nonLTR Retro TE, non-LTR retrotransposable elements. c, Distribution of repeat types in SVs of deletions and duplications. d, Stacked bar plot of SV number and type for each accession. DEL, deletion; DUP, duplication; INS, insertion.
Fig. 4
Fig. 4. Population genomic analyses of 118 representative cultivated and wild pea in Pisum based on SNPs and SVs.
a, SNP-based phylogenetic tree. b, SNP-based ADMIXTURE analysis at K = 5. c, SV-based ADMIXTURE analysis at K = 5. d, SV-based phylogenetic tree. e, SNP-based principal-component (PC) analysis. f, SV-based principal-component analysis. Colors and shapes indicate the genetic groups and taxonomic species in Pisum of each accession, respectively.
Fig. 5
Fig. 5. Results of QTL analysis for 12 agronomic traits in pea as well as candidate gene and selective signals in three QTLs associated with three Mendel’s traits.
a , 25 QTLs were identified to be associated with 12 agronomic traits, and red bars indicate four QTLs in related to the three Mendel’s traits of seed shape (SS), stem length (SL) and pod form (PF). b–d, distribution of LOD score, PVE and candidate genes in SS3 (b), SL5 (c) and PF5 (d), with the red solid and broken lines representing thresholds of 0.01 and 0.05, respectively. e–g, Candidate selective signals in SS3 (e), SL5 (f) and PF5 (g) based on results of XP-CLR analysis between species within Pisum, with the red line representing P. fulvum versus P. sativum with α0.05 = 2.18 and the blue line representing P. fulvum versus P. abyssinicum with α0.05 = 0.39.
Fig. 6
Fig. 6. A pan-genome based on 116 representatives cultivated and wild pea in Pisum (including ZW6 and excluding three accessions).
a, Modeling of core genome (red curve) and pan genome (blue curve). b, Number of genes present in 116 pea genomes (blue) and 27 representative sequenced plant genomes (red). The size of circle represents the number of genes, and the width of the violin plot represents the frequency of genes. c, Presence (green) and absence (light yellow) variation pattern of pan-genome orthologues and A–H = eight clusters according to preferred orthogroups in all accessions. Colors and shapes indicate the genetic groups and taxonomic species in Pisum of each accession, respectively.
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