YamOmics

Introduction

Yams (Dioscorea spp.) are a highly important class of horticultural crops, serving as a staple food for millions of people in Africa and contributing significantly to food security. They are also widely cultivated in East Asia as medicinal herbs, bringing substantial economic incomes. YamOmics is a one-stop multi-omics data resource that provides support for yam basic biology research and breeding.

Genome

5 genomic assemblies for D. alata, D. dumetorum, D. rotundata, D. tokoro, D. zingiberensis

Transcriptome

14 de novo transcriptomic assemblies for D. polystachya, D. japonica, nipponica and more

Plastome

41 complete chloroplast genomic assemblies and corresponding species phylogenic tree

Variome

935 yam germplasms of D. rotundata and D. alata, together with 14 million SNPs and small InDels

Pathway

479,819 genes of 19 yam species are organized in 145 signal pathways for exploring their functions

Family

Genes are classified into families and sub families based on Arabidopsis thaliana sequence similarity

Collinearity

six pair pariwise genome collinearity analysis for four yam genomes with chromosome-level assembly

BLAST

BLAST program is equipped for users to explore genes by sequence similarity

Expression analysis

191 RNA-seq samples collected for differential gene expression and co-expression analysis

CRISPR sgRNAs

CRISPR tool for designing CRISPR sgRNAs and estimate efficiency in genome editing

Enrichment analysis

Clusterfile is integrated to conduct functional enrichment analysis for specified gene set

Kinship ideentification

Identification of kinship through construction of phylogenetic tree based on chloroplast genomes