Summary
Publication
Pilkington, S. M., Crowhurst, R., Hilario, E., Nardozza, S., Fraser, L., Peng, Y., … Schaffer, R. J. (2018). A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. BMC Genomics, 19, 257. Source.
Name
Actinidia chinensis - Reference Genome
Resource Type
Genome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Actinidia chinensis

A “PseudoSanger”-like approach was used to assemble two paired-end read libraries which were assembled using Newbler 2.9. After processing the final assembly consisted of 3887 scaffolds with a total length of 550.5 Mb and an N50 of 623.8 kb with L50 of 240 scaffolds. Note, 1206 unanchored scaffolds were concatenated to form a composite entity known as ‘Chr30’ that was submitted as individual (non-concatenated) scaffolds in NCBI Genbank. Genome accuracy was evaluated by comparing the assembled contigs for 22 clones from a BAC library of A. chinensis Red Female 1. This resulted from using a different technology and different assembly path (Newbler). BUSCO analysis was used to evaluate genome completeness for comparison of the published chromosomal sequences for ‘Hongyang'. Red5 contained 1364 (94.7%) ‘complete’ BUSCOs and in comparison, ‘Hongyang’ contained 1358 (94.3%) ‘complete’ BUSCOs. Of the 47,384 A. chinensis EST sequences that were mapped to the Red5 chromosomes, only 580 had no homology. In comparison, when the ESTs were aligned to the published chromosomes of ‘Hongyang’, 3295 had no homology to any region, suggesting Red5 and Hongyang have a comparable gene space assembly.

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Source:

Pilkington, S. M., Crowhurst, R., Hilario, E., Nardozza, S., Fraser, L., Peng, Y., … Schaffer, R. J. (2018). A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. BMC Genomics, 19, 257. http://doi.org/10.1186/s12864-018-4656-3

Details
Program, Pipeline, Workflow or Method Name
Newbler
Program Version
2.9 [03-Oct-2018]
Date Performed
Monday, October 22, 2018 - 17:13
Data Source
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