The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

Abstract

Background: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes.

Methods: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes.

Results: The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence.

Conclusion: Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).

Keywords: Criollo B97–61/B2 genome; GBS; Genome Assembly; Mate Paired sequences; Theobroma cacao.

Fig. 1

CIRCOS graphical representation of paired reads mapping on a misassembled contig. The blue circle represents the contig sequence. In the inner circle, grey lines represent concordant links (orientation and insert size) between read pairs. The black arrow points to the misassembled region

Fig. 2

Chromosome reconstruction. Linkage dot plots between markers along non-ordered scaffolds (a) and ordered scaffolds (b) on chromosome 1. Each dot represents the recombination frequency between two markers. The intensity of the linkage is color coded. Warm colors indicate strong linkage and cold colors indicate weak linkage. Grey bars in the dot plots divide markers belonging to a same scaffold

Fig. 3

Scaffolds anchored to the 10 Theobroma cacao chromosomes. Black boxes represent scaffolds with orientation. Gene and SNP marker densities are in blue and orange, respectively, and were computed with a window size of 400 kb

Fig. 4

Comparison of Theobroma cacao Criollo assembly version 1 and version 2. a Graphical representation of insertions and reduction of the unknown chromosome version 1 (Tc00) in chromosomes version 2 (chr1–10). b Graphical representation of regions previously anchored to a different chromosome in the first version of the assemblies. “Tc” chromosomes refer to assembly version 1 and “chr” chromosomes to assembly version 2

Fig. 5

Dot plot comparing Criollo B97–61/B2 version 2 and Amelonado Matina 1–6 genomes computed with Last [29]. Red and blue dots indicate forward and reverse alignments, respectively