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
aurantifolia_8219_contig323_p1499_CAaurantifolia_8219_contig323_p1499_CAgenetic_marker
aurantifolia_8219_contig323_p1548_AGaurantifolia_8219_contig323_p1548_AGgenetic_marker
aurantifolia_8219_contig323_p180_GAaurantifolia_8219_contig323_p180_GAgenetic_marker
aurantifolia_8219_contig323_p227_TCaurantifolia_8219_contig323_p227_TCgenetic_marker
aurantifolia_8219_contig323_p382_CTaurantifolia_8219_contig323_p382_CTgenetic_marker
aurantifolia_8219_contig323_p533_CTaurantifolia_8219_contig323_p533_CTgenetic_marker
aurantifolia_8219_contig323_p587_ACaurantifolia_8219_contig323_p587_ACgenetic_marker
aurantifolia_8219_contig330_p212_AGaurantifolia_8219_contig330_p212_AGgenetic_marker
aurantifolia_8219_contig69_p419_AGaurantifolia_8219_contig69_p419_AGgenetic_marker
aurantifolia_8219_contig74_p33_CTaurantifolia_8219_contig74_p33_CTgenetic_marker
aurantium_14584_contig100_p809_CTaurantium_14584_contig100_p809_CTgenetic_marker
aurantium_14584_contig100_p97_-Aaurantium_14584_contig100_p97_-Agenetic_marker
aurantium_14584_contig103_p159_CTaurantium_14584_contig103_p159_CTgenetic_marker
aurantium_14584_contig103_p246_CGaurantium_14584_contig103_p246_CGgenetic_marker
aurantium_14584_contig103_p322_AGaurantium_14584_contig103_p322_AGgenetic_marker
aurantium_14584_contig103_p490_AGaurantium_14584_contig103_p490_AGgenetic_marker
aurantium_14584_contig103_p586_TGaurantium_14584_contig103_p586_TGgenetic_marker
aurantium_14584_contig103_p685_CGaurantium_14584_contig103_p685_CGgenetic_marker
aurantium_14584_contig1034_p405_TCaurantium_14584_contig1034_p405_TCgenetic_marker
aurantium_14584_contig1038_p359_TCaurantium_14584_contig1038_p359_TCgenetic_marker
aurantium_14584_contig104_p308_TCaurantium_14584_contig104_p308_TCgenetic_marker
aurantium_14584_contig104_p500_TAaurantium_14584_contig104_p500_TAgenetic_marker
aurantium_14584_contig104_p89_AGaurantium_14584_contig104_p89_AGgenetic_marker
aurantium_14584_contig1089_p154_TGaurantium_14584_contig1089_p154_TGgenetic_marker
aurantium_14584_contig1089_p270_CTaurantium_14584_contig1089_p270_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