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.
Stocks
This publication contains information about 23 stocks:
Stock NameUniquenameType
Alemow pepadaAlemow pepadacultivar
Amakusa tangorAmakusa tangorcultivar
Carrizo CitrangeCarrizo Citrangebreeding_research_material
ClementineClementinebreeding_research_material
CleopatraCleopatracultivar
Etrog 861-S1Etrog 861-S1breeding_research_material
Fortune tangorFortune tangorcultivar
Hassaku mandarinHassaku mandarincultivar
Hayata mandarinHayata mandarincultivar
Kankitsu Chukanbohon Nou 6 Gou tangorKankitsu Chukanbohon Nou 6 Gou tangorcultivar
MexicanMexicancultivar
Orah tangorOrah tangorcultivar
Palestine sweet limePalestine sweet limebreeding_research_material
PonkanPonkancultivar
Rangur limeRangur limecultivar
Rixiangxia mandarinRixiangxia mandarincultivar
Rough LemonRough Lemoncultivar
Satsuma mandarinSatsuma mandarincultivar
summer orangesummer orangecultivar
Sweet OrangeSweet Orangebreeding_research_material
Swingle citrumeloSwingle citrumelocultivar
Tahiti limeTahiti limecultivar
Trifoliate orangeTrifoliate orangecultivar
Features
This publication contains information about 25,417 features:
Feature NameUniquenameType
aurantium_14584_contig437_p121_TGaurantium_14584_contig437_p121_TGgenetic_marker
aurantium_14584_contig437_p251_AGaurantium_14584_contig437_p251_AGgenetic_marker
aurantium_14584_contig437_p380_GAaurantium_14584_contig437_p380_GAgenetic_marker
aurantium_14584_contig437_p551_GAaurantium_14584_contig437_p551_GAgenetic_marker
aurantium_14584_contig437_p725_GAaurantium_14584_contig437_p725_GAgenetic_marker
aurantium_14584_contig437_p754_AGaurantium_14584_contig437_p754_AGgenetic_marker
aurantium_14584_contig437_p797_GAaurantium_14584_contig437_p797_GAgenetic_marker
aurantium_14584_contig442_p374_GAaurantium_14584_contig442_p374_GAgenetic_marker
aurantium_14584_contig453_p266_GCaurantium_14584_contig453_p266_GCgenetic_marker
aurantium_14584_contig453_p284_-Taurantium_14584_contig453_p284_-Tgenetic_marker
aurantium_14584_contig453_p371_GAaurantium_14584_contig453_p371_GAgenetic_marker
aurantium_14584_contig453_p409_GCaurantium_14584_contig453_p409_GCgenetic_marker
aurantium_14584_contig453_p448_CTaurantium_14584_contig453_p448_CTgenetic_marker
aurantium_14584_contig47_p791_CGaurantium_14584_contig47_p791_CGgenetic_marker
aurantium_14584_contig510_p550_CAaurantium_14584_contig510_p550_CAgenetic_marker
aurantium_14584_contig541_p227_GAaurantium_14584_contig541_p227_GAgenetic_marker
aurantium_14584_contig551_p187_ATaurantium_14584_contig551_p187_ATgenetic_marker
aurantium_14584_contig551_p271_GAaurantium_14584_contig551_p271_GAgenetic_marker
aurantium_14584_contig551_p303_CTaurantium_14584_contig551_p303_CTgenetic_marker
aurantium_14584_contig551_p325_CGaurantium_14584_contig551_p325_CGgenetic_marker
aurantium_14584_contig551_p441_CTaurantium_14584_contig551_p441_CTgenetic_marker
aurantium_14584_contig551_p584_TCaurantium_14584_contig551_p584_TCgenetic_marker
aurantium_14584_contig551_p600_CTaurantium_14584_contig551_p600_CTgenetic_marker
aurantium_14584_contig551_p656_TCaurantium_14584_contig551_p656_TCgenetic_marker
aurantium_14584_contig560_p464_A-aurantium_14584_contig560_p464_A-genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
URLhttp://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-746