GenomiCOM: ClimOliveMed Genomic resources for research on adaptation of olive tree to climate change
To understand biological processes, genetic and molecular mechanisms involved in olive tree adaptation to climate change, especially to a deficit of winter cold temperature affecting flowering processes and to drought, ClimOliveMed project is aiming to develop a large panel of genomic resources on olive tree. Four types of genomic data will be developed and implemented within GenomicCOM database. I. Target sequencing data on wild and cultivated olive trees The cultivated Olea europaea var. europaea (cv. Farga) Oe9 genome assembly (Julca et al. 2020) was used as a reference to design target sequencing probes.Baits were designed according to the following parameters: place 80 bp probes with 0.5x tilling targeting the first 640 bp of each of the 55,595 annotated genes available. For each gene, 1 to 4 baits were designed depending on its length. Based on a total set of 210,367 baits representing 55,452 unique loci and a captured length of 16.8 Mb, target sequencing data have been obtained on 375 wild olive trees sampled in natural environment of 27 western (6 from South France, 4 from Corsica, 9 from Spain and 8 from Morocco) and one eastern (South Turkey). Using the identical methodology, target-sequencing data have been obtained on xxx accessions from the Worldwide Olive Germplasm Bank of Marrakech.  II. Long read sequencing to construct the reference olive genome for the dominant Moroccan cultivar “Picholine marocaine” GenomCOM database will include genomic resources on a new assembly of the reference olive genome for “Picholine marocaine” cultivar. This new reference olive genome will be assembled based on long-read sequencing using PacBio technologies. Based on RAD-seq data analysis, hybrids issued from crossing between Picholine marocaine (PM) as a female parent and Picholine du Langedoc (PL) as a male parent, have been genetically evidenced (El Bakkali et al, Unpublished). ClimOliveMed project is aiming to obtain long read sequencing on one hybrid issued from crossing PM x PL. As the whole genome of these two cultivars will be available through short-read sequencing using NovaSeq Illumina  technology, It will be possible to identify each of the two haplotypes of the new assembly reference olive genome.   III. Re-sequencing the whole genome of 200 olive accessions (50 wild olive trees and 150 olive cultivars) ClimOliveMed project is aiming to collect genomic data related to the whole genome of 200 accessions including 50 wild olive trees and 150 olive cultivars. These data will obtained by short-read resequencing using NovaSeq Illumina  technology  IV. RNA-seq of bud and leave samples collected on two olive cultivars under different temperature regimes To understand the relationships between the cold winter temperature and flowering and particularly to draw the gene pathways involved in these biological processes, ClimOliveMed project aims to investigate RNA-seq of bud and leave samples collected on two olive cultivars under different temperature regimes.