Actinidia chinensis Red5 genome assembly (version 2) and annotation files

We present version 2 of the genome assembly for Actinidia chinensis var. chinensis genotype Red5. The Red5 genome was originally assembled using short read Illumina data (Pilkington et al, 2018; https://doi.org/10.1186/s12864-018-4656-3). In version 2 we employed Pacific BioSciences Sequel Single Molecule Real Time (SMRT) sequencing technology in place of Illumina paired end read sequencing for the main assembly but leveraged that short read data (Pilkington et al, 2018) for post assembly base correction of long read assembly contigs. Additionally the Illumina long insert libraries from Pilkington et al (2018) were used for post assembly scaffolding of contigs. Scaffold assignment to linkage groups leveraged the genetic map described in Pilkington et al (2018) as well as consensus evidence from DNA synteny comparisons to existing whole genome sequences from Actinidia.

To meet the file size restrictions some dataset components have been split into multiple parts.

Assembly

The assembly work flow used the FALCON/FALCON-unzip assembly suite is described in Red5_version_2_genome_assembly.md. The assembly yielded both primary and haplotig contig data sets, the metrics for which are documented in this file. The CDS and predicted peptide fasta and GFF3 gene annotation for the primary and haplotig sets are provided in separate files.

File Descriptions

Files named chr1.fasta to chr29.fasta represent the primary assembly linkage group level assembly units

Files named haplotig_part_1.fasta to haplotig_part_10.fasta represent the haplotig contig sets split into 10 parts to meet upload file size restrictions

Files named primary_assembly.primary.gff3 and haplotig.gff3 contain the gene model annotations for the primary and haplotig assembly datasets respectively

primary_assembly.cds.fasta and primary_assembly.pep.fasta contain the CDS and peptide sequences for the annotations on the primary contigs

haplotig.cds.fasta and haplotig.pep.fasta contain the CDS and peptide sequences for the annotations on the haplotig contigs

haplotigs.placements.tsv and haplotigs.reassignments.tsv describe the placement of haplotigs relative to the primary contigs as derived from purge_haplotigs

The file Red5_version_2_genome_assembly.md describes the assembly work flow and code steps used as well as assembly metrics

Files HYV3_1.v.R5V2_1.png to HYV3_29.v.R5V2_29.png depict Circos plots of DNA:DNA synteny based on 1coords alignment filter of nucmer alignments using dnadiff

See Red5_version_2_genome_assembly.md for description of assembly methods and assembly metrics.

Funding

This work was funded by Kiwifruit Royalty Investment Program by The New Zealand Institute for Plant & Food Research Ltd. with support from Zespri, and the CORE grant Endeavour Smart Idea Fund (UOOX1801) from the New Zealand Ministry of Business, Innovation and Employment (MBIE). The funding bodies had no role in the design of the study, the collection, analysis, or interpretation of data or writing this manuscript.