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_contig16194_p380_AGclementina_122005_contig16194_p380_AGgenetic_marker
clementina_122005_contig16194_p416_CTclementina_122005_contig16194_p416_CTgenetic_marker
clementina_122005_contig16195_p188_AGclementina_122005_contig16195_p188_AGgenetic_marker
clementina_122005_contig16196_p490_TAclementina_122005_contig16196_p490_TAgenetic_marker
clementina_122005_contig16197_p319_GTclementina_122005_contig16197_p319_GTgenetic_marker
clementina_122005_contig162_p222_GAclementina_122005_contig162_p222_GAgenetic_marker
clementina_122005_contig162_p280_CGclementina_122005_contig162_p280_CGgenetic_marker
clementina_122005_contig162_p374_TCclementina_122005_contig162_p374_TCgenetic_marker
clementina_122005_contig162_p518_TCclementina_122005_contig162_p518_TCgenetic_marker
clementina_122005_contig162_p531_CGclementina_122005_contig162_p531_CGgenetic_marker
clementina_122005_contig162_p548_CAclementina_122005_contig162_p548_CAgenetic_marker
clementina_122005_contig162_p700_ACclementina_122005_contig162_p700_ACgenetic_marker
clementina_122005_contig16201_p180_GAclementina_122005_contig16201_p180_GAgenetic_marker
clementina_122005_contig16201_p520_TCclementina_122005_contig16201_p520_TCgenetic_marker
clementina_122005_contig16201_p581_CTclementina_122005_contig16201_p581_CTgenetic_marker
clementina_122005_contig16206_p640_GCclementina_122005_contig16206_p640_GCgenetic_marker
clementina_122005_contig16206_p687_AGclementina_122005_contig16206_p687_AGgenetic_marker
clementina_122005_contig16206_p703_GTclementina_122005_contig16206_p703_GTgenetic_marker
clementina_122005_contig16207_p211_-Aclementina_122005_contig16207_p211_-Agenetic_marker
clementina_122005_contig16207_p224_ACclementina_122005_contig16207_p224_ACgenetic_marker
clementina_122005_contig16207_p264_TCclementina_122005_contig16207_p264_TCgenetic_marker
clementina_122005_contig16207_p389_ATclementina_122005_contig16207_p389_ATgenetic_marker
clementina_122005_contig16207_p496_CTclementina_122005_contig16207_p496_CTgenetic_marker
clementina_122005_contig16217_p632_GTclementina_122005_contig16217_p632_GTgenetic_marker
clementina_122005_contig16217_p719_CTclementina_122005_contig16217_p719_CTgenetic_marker

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