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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #395781
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Pan-genome resources for grapevine

Author
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item MOREIRA, BRUNO CONTRERAS - Embl-Ebi
item NAAMATI, GUY - Embl-Ebi
item DYER, SARAH - Embl-Ebi
item PAPATHEODOROU, IRENE - Embl-Ebi
item GEORGE, NANCY - Embl-Ebi
item ELSER, JUSTIN - Oregon State University
item NAITHANI, SUSHMA - Oregon State University

Submitted to: Acta Horticulture Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 9/30/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary: Grape is one of the most important fruit crops of the world and has a large and expanding worldwide market. Recent advances in genome sequencing and assembly technologies are now making it possible to generate many accurate high quality reference genome assemblies. With this increase in the number of genomes, there is a need to integrate the information to support pan-genomes and provide access to reference assemblies, facilitating the identification and characterization of common and variable regions. Here we present the GrapeVine pan-genome site (https://vitis.gramene.org), a web portal for comparative plant genomics focused on GrapeVine.

Technical Abstract: Capturing and characterizing the gene space within a species and linking to agronomic traits will be critical to improving agricultural practices and accelerating crop improvement. Recent advances in genome sequencing and assembly technologies are now making it possible to generate many accurate high quality reference genome assemblies for each species. The GrapeVine community is no longer limited to the single PN40024 reference assembly, but has access to many high-quality reference assemblies for table and wine grapes. With this increase in the number of genomes, there is a need to integrate the information to support the transition from single reference to pan-genome research approaches. Here, we present a pan-genome resource for grapevine (https://vitis.gramene.org) that includes 10 reference genomes representing wild and cultivated grape genomes. In addition, there are seven genomes as outgroups that provide a powerful phylogenetic framework constructed with 594,645 input proteins from 553,999 individual genes, resulting in 24,050 protein-coding gene family trees of which 8,881 are grapevine specific. Pinot noir PN40024 V3 was used as a reference genome for gene expression and orthology-based pathway projections. This resource allows exploration of pan gene sets for the species, characterizing potential gene gain and loss between different accessions of grapevine reference assemblies based on the gene trees