Dataset Information

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.

ABSTRACT: BACKGROUND: The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft 'Lovell' peach sequence as well as sufficient depth of coverage for 'in silico' SNP discovery. DESCRIPTION: The sequences were aligned to the 'Lovell' peach genome released April 01, 2010 by the International Peach Genome Initiative (IPGI). 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle' were sequenced to add SNPs segregating in two breeding populations, Pop DF ('Dr. Davis' × 'F8, 1-42') and Pop DG ('Dr. Davis' × 'Georgia Belle'). Roche 454 sequencing produced 980,000 total reads with 236 Mb sequence for 'Dr. Davis' and 735,000 total reads with 172 Mb sequence for 'F8, 1-42'. 84 bp × 84 bp paired end Illumina/Solexa sequences yielded 25.5, 21.4, 25.5 million sequences for 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle', respectively. BWA/SAMtools were used for alignment of raw reads and SNP detection, with custom PERL scripts for SNP filtering. Velvet's Columbus module was used for sequence assembly. Comparison of aligned and overlapping sequences from both Roche 454 and Illumina/Solexa resulted in the selection of 6654 high quality SNPs for 'Dr. Davis' vs. 'F8, 1-42' and 'Georgia Belle', distributed on eight major peach genome scaffolds as defined from the 'Lovell' assembly. CONCLUSION: The eight scaffolds contained about 215-225 Mb of peach genomic sequences with one SNP/~ 40,000 bases. All sequences from Roche 454 and Illumina/Solexa have been submitted to NCBI for public use in the Short Read Archive database. SNPs have been deposited in the NCBI SNP database.

SUBMITTER: Ahmad R

PROVIDER: S-EPMC3253712 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.

Ahmad Riaz R Parfitt Dan E DE Fass Joseph J Ogundiwin Ebenezer E Dhingra Amit A Gradziel Thomas M TM Lin Dawei D Joshi Nikhil A NA Martinez-Garcia Pedro J PJ Crisosto Carlos H CH

BMC genomics 20111122

<h4>Background</h4>The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft 'Lovell' peach sequence as well as sufficient depth of coverage for 'in silico' SNP discovery.<h4>Description</h4>The sequences were aligned to the 'Lovell' peach genome releas ...[more]

PMID: 22108025

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Project description:MicroRNAs (miRNAs) are a group of non-coding RNAs that have functions in post-transcriptional gene regulation in plants. Although the most important economic component of peach trees (Prunus persica) is the fruit, not much is known about miRNAs in this organ. In this study, miRNAs and their targets were identified and characterized from libraries of small RNAs of peach fruit through Solexa based-sequencing and bioinformatics approaches. A total of 557 known peach miRNAs belonging to 34 miRNA families were identified, and some of these miRNAs were found to be highly conserved in at least four other plant species. Using the most current criteria for miRNA annotation, 275 putative novel miRNAs were predicted, and the sequencing frequencies of these novel miRNAs were less than those of the conserved miRNAs. In total, 3959 and 1614 target genes for 349 known and 193 novel miRNAs, respectively, were predicted with the criteria that a single target gene can be targeted by different miRNAs and that a single miRNA can also have a large number of target genes. Three targets were even found to be targeted by 13 novel miRNAs that contained the same complete miRNA sequence at different locations and had different scaffolds. The proteins predicted to be targeted by the miRNAs identified in this study encompass a wide range of transcription factors and are involved in many biological processes and pathways, including development, metabolism, stress responses and signal transduction. A total of 115 and 101 target genes were identified to be cleaved by 60 known miRNAs and 27 novel miRNAs through degradome sequencing, respectively. These miRNAs induce cleavage of their targets precisely at the position between nucleotides 10 and 11 of the miRNA sequences from the 5' to the 3' end. Thirty conserved miRNAs and 19 novel miRNAs exhibited differential expression profiles in the peach, and the expression patterns of some miRNAs appeared to be tissue- or developmental stage-specific. The findings of this study provide an important basis for the analysis of miRNAs, their targets and the functions of these targets in peach fruit.

Project description:BackgroundMADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes.ResultsWe identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248 ± 72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 and FLC lineages in woody perennial species.ConclusionsMost Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.

Dataset Information

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.

Publications

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.

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