Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat

Abstract

Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with the 45,791 predicted protein-coding genes. Analysis of comparative genomics indicated that loquat shared a common ancestor with apple and pear, and a recent whole-genome duplication event occurred in loquat prior to its divergence. Genome re-sequencing showed that the loquat germplasms were distinctly classified into wild and cultivated groups, and the commercial cultivars experienced allelic admixture. Compared with the cultivated loquats, the wild loquat genome showed very few selected genomic regions and had higher levels of genetic diversity. However, whole-genome scans of selective sweeps were mainly related to fruit quality, size, and flesh color during the domestication process. Large-scale transcriptome and metabolome analyses were further performed to identify the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in the wild and cultivated loquats, at various fruit development stages. Unlike that in wild loquat, the key DEGs and DAMs involved in carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, and carotenoid biosynthesis were significantly regulated in cultivated loquats during fruit development. These high-quality reference genome, re-sequencing, and large-scale transcriptome/metabolome data provide valuable resources for elucidating fruit domestication and molecular breeding in loquat.

Wampee chromosome-level reference genome elucidates fruit sugar-acid metabolism

“…Wampee and sweet orange exhibited very good collinearity, possibly because of their relatively recent divergence ( Figure 2E and S3 ). Additionally, 1:2 collinearity was observed between C. lansium and E. japonica , confirming a recent WGD event in E. japonica ( Figure 2D and 2E ), as reported previously 12 .…”

EjFAD8 Enhances the Low-Temperature Tolerance of Loquat by Desaturation of Sulfoquinovosyl Diacylglycerol (SQDG)

“…After selecting EjFAD8 (EVM0014726) from the transcriptome data, they were compared with the sequencing results of Jing et al [ 44 ]. The coding sequence (CDS) of EjFAD8 was found in the loquat coding sequence database, and a pair of gene-specific primers was designed based on its sequence [ 45 ].…”

Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication

“…To distinguish diverse subgenomes in Brassica species, we redesignated the subgenomes as follows: B. rapa genome as BraA, B. nigra genome as BniB, B. oleracea genome as BolC, B. juncea A and B subgenomes as BjuA and BjuB, respectively, B. napus A and C subgenomes as BnaA and BnaC, respectively, B. carinata B and C subgenomes as BcaB and BcaC, respectively. The interspecific all OGPs were determined using OrthoFinder2 ( Emms and Kelly, 2018 ; Jing et al., 2023 ) platform (BLASTP all- vs -all, 10e-3, orthofinder -f./dataset -t 16 -a 8 -M msa -S blast -A mafft) in the combinations among different subgenome of Brassica species (BraA-BnaA, BraA-BjuA, BniB-BjuB, BniB-BcaB, BolC-BnaC and BolC-BcaC) and combinations between A. thaliana and Brassica species (Ath-BraA, Ath-BniB and Ath-BolC). The rates of nonsynonymous substitution (Ka) and the rates of synonymous substitution (Ks) values for each pair of homologous genes were estimated using ParaAT 2.0 ( https://bigd.big.ac.cn/tools/ ).…”