Published July 23, 2018 | Version 1.0
Dataset Open

Actinidia eriantha Accession EA01_01 low coverage genome assembly

Authors/Creators

  • 1. Plant and Food Research

Description

Draft assembly scaffolds of kiwifruit Actinidia eriantha 'EA01_01'. This is a female vine derived from seed collected on Qi-Yuan Mt., Min-Qing, Fukien on 15/11/75 by Li Lai-Yung, Professor of Subtropical Pomology, University of Fukien, Peoples Republic of China and provided to the New Zealand DSIR in 1975

Notes

Scaffolds file split to meet Zenodo upload limits.Paired-end small insert libraries of nuclear DNA of accession  'EA01-01' was sequenced on the Illumina HiSeq 2000 platform to circa  62x coverage. Reads were error-corrected with the Allpaths LG error corrector(Butler 2008) ,trimmed using Fastq-Mcf (https://github.com/ExpressionAnalysis/ea-utils)  with parameters  q=20 t=0.0001 and assembled using Soap Denovo2 (http://soap.genomics.org.cn/soapdenovo.html) with kmers 53/63/73. Following  gap closure with GapCloser with two iterations, scaffolds were shredded , reassembled with Newbler (parameters -het -large -mi 90 -ml 40)  and subjected to a reference-based scaffolding against draft assembly of Red5 (Pilkington 2018) with SSPACE (Boetzer 2010).

Files

Files (779.2 MB)

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md5:765e14deb86ec463122a0db4912d1613
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md5:d2c53b6f8cc9a72fafd4a7d8d93baf31
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Additional details

References

  • Genomic Analysis of a Super-High Vitamin C Trait in Polyploid Hybrids of Kiwifruit (Actinidia spp.). John McCallum, Susan Thomson ,William Laing, Mareike Knaebel,Jibran Tahir, Simon Deroles, Sean Bulley, Ross Crowhurst , Elena Hilario, Andrew Catanach, Alan Seal. (2018) Submitted