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_contig17377_p340_GAsinensis_213830_contig17377_p340_GAgenetic_marker
sinensis_213830_contig17377_p364_GTsinensis_213830_contig17377_p364_GTgenetic_marker
sinensis_213830_contig17377_p513_T-sinensis_213830_contig17377_p513_T-genetic_marker
sinensis_213830_contig17377_p554_TCsinensis_213830_contig17377_p554_TCgenetic_marker
sinensis_213830_contig17377_p594_CGsinensis_213830_contig17377_p594_CGgenetic_marker
sinensis_213830_contig1739_p148_TCsinensis_213830_contig1739_p148_TCgenetic_marker
sinensis_213830_contig17395_p475_AGsinensis_213830_contig17395_p475_AGgenetic_marker
sinensis_213830_contig174_p1077_AGsinensis_213830_contig174_p1077_AGgenetic_marker
sinensis_213830_contig174_p1102_ATsinensis_213830_contig174_p1102_ATgenetic_marker
sinensis_213830_contig174_p1321_GAsinensis_213830_contig174_p1321_GAgenetic_marker
sinensis_213830_contig174_p1514_GAsinensis_213830_contig174_p1514_GAgenetic_marker
sinensis_213830_contig174_p1571_CAsinensis_213830_contig174_p1571_CAgenetic_marker
sinensis_213830_contig174_p1654_GTsinensis_213830_contig174_p1654_GTgenetic_marker
sinensis_213830_contig174_p1681_ATsinensis_213830_contig174_p1681_ATgenetic_marker
sinensis_213830_contig174_p1704_A-sinensis_213830_contig174_p1704_A-genetic_marker
sinensis_213830_contig174_p1758_TAsinensis_213830_contig174_p1758_TAgenetic_marker
sinensis_213830_contig174_p702_GAsinensis_213830_contig174_p702_GAgenetic_marker
sinensis_213830_contig174_p940_GAsinensis_213830_contig174_p940_GAgenetic_marker
sinensis_213830_contig17401_p1028_AGsinensis_213830_contig17401_p1028_AGgenetic_marker
sinensis_213830_contig17401_p811_GAsinensis_213830_contig17401_p811_GAgenetic_marker
sinensis_213830_contig17401_p961_CTsinensis_213830_contig17401_p961_CTgenetic_marker
sinensis_213830_contig17411_p413_CTsinensis_213830_contig17411_p413_CTgenetic_marker
sinensis_213830_contig17411_p440_AGsinensis_213830_contig17411_p440_AGgenetic_marker
sinensis_213830_contig17430_p227_ACsinensis_213830_contig17430_p227_ACgenetic_marker
sinensis_213830_contig17430_p633_GAsinensis_213830_contig17430_p633_GAgenetic_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