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

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.

Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes

“…A unique feature of our study was the use of ultralong nanopore reads for creating manually curated scaffolds for most of the assembly, since the repetitive and complex structure of pea centromeres makes them prone to misassemblies. This makes our CEN6 assembly superior in completeness and contiguity even to the novel high-quality genome assembly of the pea cultivar ZW6 (Yang et al 2022) (data not shown), which was published during preparation of this manuscript.…”

Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes

“…A unique feature of our study was the use of ultralong nanopore reads for creating manually curated scaffolds for most of the assembly, since the repetitive and complex structure of pea centromeres makes them prone to misassemblies. This makes our CEN6 assembly superior in completeness and contiguity even to the novel high-quality genome assembly of the pea cultivar ZW6 [ 27 ], which was published during preparation of this manuscript.…”

Genome-wide characterization of AINTEGUMENTA-LIKE family in Medicago truncatula reveals the significant roles of AINTEGUMENTAs in leaf growth

“…The OsAILs protein sequences were obtained from the Rice Genome Annotation Project ( ) and National Center for Biotechnology Information ( ). The GmAILs and LjAILs protein sequences were obtained in Phytozome, and the PsAILs protein sequences were obtained in the Pea Genome Database ( ) ( Yang et al., 2022 ).…”