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
sinensis_213830_contig7863_p182_GAsinensis_213830_contig7863_p182_GAgenetic_marker
sinensis_213830_contig7865_p241_TCsinensis_213830_contig7865_p241_TCgenetic_marker
sinensis_213830_contig7865_p429_TCsinensis_213830_contig7865_p429_TCgenetic_marker
sinensis_213830_contig7865_p494_GCsinensis_213830_contig7865_p494_GCgenetic_marker
sinensis_213830_contig7865_p580_GTsinensis_213830_contig7865_p580_GTgenetic_marker
sinensis_213830_contig7865_p736_TGsinensis_213830_contig7865_p736_TGgenetic_marker
sinensis_213830_contig7865_p761_GTsinensis_213830_contig7865_p761_GTgenetic_marker
sinensis_213830_contig7865_p832_ACsinensis_213830_contig7865_p832_ACgenetic_marker
sinensis_213830_contig7880_p115_CAsinensis_213830_contig7880_p115_CAgenetic_marker
sinensis_213830_contig7880_p282_TCsinensis_213830_contig7880_p282_TCgenetic_marker
sinensis_213830_contig7880_p361_TCsinensis_213830_contig7880_p361_TCgenetic_marker
sinensis_213830_contig7880_p418_TGsinensis_213830_contig7880_p418_TGgenetic_marker
sinensis_213830_contig7880_p517_CTsinensis_213830_contig7880_p517_CTgenetic_marker
sinensis_213830_contig7880_p607_CTsinensis_213830_contig7880_p607_CTgenetic_marker
sinensis_213830_contig7889_p196_GAsinensis_213830_contig7889_p196_GAgenetic_marker
sinensis_213830_contig7889_p421_A-sinensis_213830_contig7889_p421_A-genetic_marker
sinensis_213830_contig7892_p1033_CTsinensis_213830_contig7892_p1033_CTgenetic_marker
sinensis_213830_contig7892_p1222_-Tsinensis_213830_contig7892_p1222_-Tgenetic_marker
sinensis_213830_contig7892_p1247_CAsinensis_213830_contig7892_p1247_CAgenetic_marker
sinensis_213830_contig7903_p284_TCsinensis_213830_contig7903_p284_TCgenetic_marker
sinensis_213830_contig7903_p509_TAsinensis_213830_contig7903_p509_TAgenetic_marker
sinensis_213830_contig7903_p52_GTsinensis_213830_contig7903_p52_GTgenetic_marker
sinensis_213830_contig7903_p706_CTsinensis_213830_contig7903_p706_CTgenetic_marker
sinensis_213830_contig7903_p720_-Tsinensis_213830_contig7903_p720_-Tgenetic_marker
sinensis_213830_contig7903_p819_GTsinensis_213830_contig7903_p819_GTgenetic_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