Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus

Publication Overview
TitleMining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus
AuthorsChen C and Gmitter FG.
TypeJournal Article
Journal NameBMC Genomics
Volume14
Year2013
Page(s)746
CitationChen C and Gmitter FG. Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus. BMC Genomics. 2013. 14: 746.

Abstract

BACKGROUND: Single nucleotide polymorphisms (SNPs), the most abundant variations in a genome, have been widely used in various studies. Detection and characterization of citrus haplotype-based expressed sequence tag (EST) SNPs will greatly facilitate further utilization of these gene-based resources. RESULTS: In this paper, haplotype-based SNPs were mined out of publicly available citrus expressed sequence tags (ESTs) from different citrus cultivars (genotypes) individually and collectively for comparison. There were a total of 567,297 ESTs belonging to 27 cultivars in varying numbers and consequentially yielding different numbers of haplotype-based quality SNPs. Sweet orange (SO) had the most (213,830) ESTs, generating 11,182 quality SNPs in 3,327 out of 4,228 usable contigs. Summed from all the individually mining results, a total of 25,417 quality SNPs were discovered - 15,010 (59.1%) were transitions (AG and CT), 9,114 (35.9%) were transversions (AC, GT, CG, and AT), and 1,293 (5.0%) were insertion/deletions (indels). A vast majority of SNP-containing contigs consisted of only 2 haplotypes, as expected, but the percentages of 2 haplotype contigs varied widely in these citrus cultivars. BLAST of the 25,417 25-mer SNP oligos to the Clementine reference genome scaffolds revealed 2,947 SNPs had "no hits found", 19,943 had 1 unique hit / alignment, 1,571 had one hit and 2+ alignments per hit, and 956 had 2+ hits and 1+ alignment per hit. Of the total 24,293 scaffold hits, 23,955 (98.6%) were on the main scaffolds 1 to 9, and only 338 were on 87 minor scaffolds. Most alignments had 100% (25/25) or 96% (24/25) nucleotide identities, accounting for 93% of all the alignments. Considering almost all the nucleotide discrepancies in the 24/25 alignments were at the SNP sites, it served well as in silico validation of these SNPs, in addition to and consistent with the rate (81%) validated by sequencing and SNaPshot assay. CONCLUSIONS: High-quality EST-SNPs from different citrus genotypes were detected, and compared to estimate the heterozygosity of each genome. All the SNP oligo sequences were aligned with the Clementine citrus genome to determine their distribution and uniqueness and for in silico validation, in addition to SNaPshot and sequencing validation of selected SNPs.
Features
This publication contains information about 25,417 features:
Feature NameUniquenameType
clementina_122005_contig3013_p261_CTclementina_122005_contig3013_p261_CTgenetic_marker
clementina_122005_contig3013_p288_CTclementina_122005_contig3013_p288_CTgenetic_marker
clementina_122005_contig3013_p301_AGclementina_122005_contig3013_p301_AGgenetic_marker
clementina_122005_contig3013_p354_AGclementina_122005_contig3013_p354_AGgenetic_marker
clementina_122005_contig3013_p486_AGclementina_122005_contig3013_p486_AGgenetic_marker
clementina_122005_contig3013_p630_AGclementina_122005_contig3013_p630_AGgenetic_marker
clementina_122005_contig3015_p217_CTclementina_122005_contig3015_p217_CTgenetic_marker
clementina_122005_contig3015_p377_CTclementina_122005_contig3015_p377_CTgenetic_marker
clementina_122005_contig3015_p464_TCclementina_122005_contig3015_p464_TCgenetic_marker
clementina_122005_contig3015_p618_GAclementina_122005_contig3015_p618_GAgenetic_marker
clementina_122005_contig3017_p413_T-clementina_122005_contig3017_p413_T-genetic_marker
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clementina_122005_contig3028_p131_GCclementina_122005_contig3028_p131_GCgenetic_marker
clementina_122005_contig3028_p174_CTclementina_122005_contig3028_p174_CTgenetic_marker
clementina_122005_contig3028_p579_CTclementina_122005_contig3028_p579_CTgenetic_marker
clementina_122005_contig3028_p95_AGclementina_122005_contig3028_p95_AGgenetic_marker
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Pages

Stocks
This publication contains information about 23 stocks:
Stock NameUniquenameType
Alemow pepadaAlemow pepadaaccession
Amakusa tangorAmakusa tangoraccession
Carrizo CitrangeCarrizo Citrangeaccession
ClementineClementineaccession
CleopatraCleopatraaccession
Etrog 861-S1Etrog 861-S1accession
Fortune tangorFortune tangoraccession
Hassaku mandarinHassaku mandarinaccession
Hayata mandarinHayata mandarinaccession
Kankitsu Chukanbohon Nou 6 Gou tangorKankitsu Chukanbohon Nou 6 Gou tangoraccession
MexicanMexicanaccession
Orah tangorOrah tangoraccession
Palestine sweet limePalestine sweet limeaccession
PonkanPonkanaccession
Rangur limeRangur limeaccession
Rixiangxia mandarinRixiangxia mandarinaccession
Rough LemonRough Lemonaccession
Satsuma mandarinSatsuma mandarinaccession
summer orangesummer orangeaccession
Sweet OrangeSweet Orangeaccession
Swingle citrumeloSwingle citrumeloaccession
Tahiti limeTahiti limeaccession
Trifoliate orangeTrifoliate orangeaccession
Properties
Additional details for this publication include:
Property NameValue
URLhttp://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-746