Genome-wide discovery and analysis of single nucleotide polymorphisms and insertions/ deletions in Juglans regia L. by high-throughput pyrosequencing

• Published in: Plant omics Vol. 7; no. 6; pp. 445 - 449
• Main Authors: Zhuoyi Liao, Kai Feng, Yingnan Chen, Xiaogang Dai, Shuxian Li, Tongming Yin
• Format: Journal Article
• Published: 01.12.2014
• Subjects: Analysis; Genomes; Nucleotides; Single nucleotide polymorphisms; Walnut
• ISSN: 1836-0661; 1836-3644

Walnut (Juglans regia L.) is one of the most widespread economic trees in the world. In this study, genome sequencing of J regia was performed with Roche 454 GS-FLX sequencer. A total of 541,176 high-quality reads were produced with an avemge read length of 359 bp. We obtained 31,362 contigs (>= l00 bp) after assembling with the Roche Newbler de novo Assembler (Version 2.8); the total length of the assembly was 15.1 Mb. We then mapped all the sequence reads against the J regia genome assembly. Totally, 49,202 nucleotide variations were detected including 48,165 single nucleotide polymorphisms (SNP5) and 1,037 insertions/deletions (InDels). Among the detected SNPs, the number of transitions (35,480) was much more than that of transversions (12,685), with a ratio of 2.79:1. Within transitions, C/T transitions were slightly more abundant than that of U/A. Among transversions, AJT transversions were much more common than the other three types of transversions. As for the detected InDels, single nucleotide changes accounted for 52.65% of all InDels. Additionally, the InDel numbers were negatively correlated with the InDel lengths.