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Annotation of the Protein Coding Regions of the Equine Genome.

Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN - PLoS ONE (2015)

Bottom Line: From these, we derived the structures of 68,594 transcripts.In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2.Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.

View Article: PubMed Central - PubMed

Affiliation: Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America.

ABSTRACT
Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.

No MeSH data available.


Related in: MedlinePlus

An example of a deletion (chr1:42863989, CC > C) that extends the ORF in the gene DKK1.In UCSC (A), the full constructed transcript is shown as the top track, followed by a BLAT track showing the ORF with (ORF_with_del_228-1031) and without (ORF_with_no_var_1509_814) the deletion. The transcript structure can be seen to resemble the known annotations, and the ORF is similar to annotation only when including the deletion. In IGV [11] (B) it can be seen that the deletion event is present in three out of five Sanger reads, as well as most Illumina genomic resequencing and RNA-seq reads. Note: though the position of the deletion is the first C in a stretch of C’s within the genomic reads and the last C in the RNA-seq reads, this gives the same result.
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pone.0124375.g004: An example of a deletion (chr1:42863989, CC > C) that extends the ORF in the gene DKK1.In UCSC (A), the full constructed transcript is shown as the top track, followed by a BLAT track showing the ORF with (ORF_with_del_228-1031) and without (ORF_with_no_var_1509_814) the deletion. The transcript structure can be seen to resemble the known annotations, and the ORF is similar to annotation only when including the deletion. In IGV [11] (B) it can be seen that the deletion event is present in three out of five Sanger reads, as well as most Illumina genomic resequencing and RNA-seq reads. Note: though the position of the deletion is the first C in a stretch of C’s within the genomic reads and the last C in the RNA-seq reads, this gives the same result.

Mentions: Twenty percent of the ORF extending SNPs found by RNA-seq were confirmed in the Twilight genomic data (Table 2). Additionally, 66% of the ORF extending insertions and 71% of the ORF extending deletions found in the RNA-seq data were supported by genomic analyses (Table 2). Of the 780 variants that were identified as homozygous in the reference animal and extended the open-reading frame of the transcript they reside in (S1 Dataset), most were not SNPs, but small indels. One such example is a 1bp deletion (chr1:42863989 CC > C) within the DKK1 gene loci, supported by 67 of 77 RNA-seq reads and all 23 genomic reads (vcf AD fields) (Fig 4).


Annotation of the Protein Coding Regions of the Equine Genome.

Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN - PLoS ONE (2015)

An example of a deletion (chr1:42863989, CC > C) that extends the ORF in the gene DKK1.In UCSC (A), the full constructed transcript is shown as the top track, followed by a BLAT track showing the ORF with (ORF_with_del_228-1031) and without (ORF_with_no_var_1509_814) the deletion. The transcript structure can be seen to resemble the known annotations, and the ORF is similar to annotation only when including the deletion. In IGV [11] (B) it can be seen that the deletion event is present in three out of five Sanger reads, as well as most Illumina genomic resequencing and RNA-seq reads. Note: though the position of the deletion is the first C in a stretch of C’s within the genomic reads and the last C in the RNA-seq reads, this gives the same result.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4481266&req=5

pone.0124375.g004: An example of a deletion (chr1:42863989, CC > C) that extends the ORF in the gene DKK1.In UCSC (A), the full constructed transcript is shown as the top track, followed by a BLAT track showing the ORF with (ORF_with_del_228-1031) and without (ORF_with_no_var_1509_814) the deletion. The transcript structure can be seen to resemble the known annotations, and the ORF is similar to annotation only when including the deletion. In IGV [11] (B) it can be seen that the deletion event is present in three out of five Sanger reads, as well as most Illumina genomic resequencing and RNA-seq reads. Note: though the position of the deletion is the first C in a stretch of C’s within the genomic reads and the last C in the RNA-seq reads, this gives the same result.
Mentions: Twenty percent of the ORF extending SNPs found by RNA-seq were confirmed in the Twilight genomic data (Table 2). Additionally, 66% of the ORF extending insertions and 71% of the ORF extending deletions found in the RNA-seq data were supported by genomic analyses (Table 2). Of the 780 variants that were identified as homozygous in the reference animal and extended the open-reading frame of the transcript they reside in (S1 Dataset), most were not SNPs, but small indels. One such example is a 1bp deletion (chr1:42863989 CC > C) within the DKK1 gene loci, supported by 67 of 77 RNA-seq reads and all 23 genomic reads (vcf AD fields) (Fig 4).

Bottom Line: From these, we derived the structures of 68,594 transcripts.In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2.Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.

View Article: PubMed Central - PubMed

Affiliation: Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America.

ABSTRACT
Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.

No MeSH data available.


Related in: MedlinePlus