G3: Genes, Genomes, Genetics

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Open Access Publication



FileS2.pdf (2258 kB)
Sequence assembly synteny in the alignment of the Gallus_gallus-4.0 and Gallus_gallus-5.0 assembled versions of the chicken genome.

FileS3.pdf (144 kB)
Alignment of Gallus_gallus-5.0 chromosomes to the Cheng et al. 1995) chicken genetic linkage map.

FileS9.pdf (723 kB)
Novel chicken linkage groups E101 to E129 created with SNPs genotyped against unplaced Gallus_gallus-5.0 assembled scaffolds.

FileS1.xls (4834 kB)
The predicted protein sequences corresponding to newly predicted coding genes retrieved from the NCBI proteome ( and scanned for conserved Interpro signatures in eleven databases of protein predictive models.

FileS4.xls (381 kB)
The most common conserved domains among all categories of novel genes.

FileS5.xls (482 kB)
InterProScan (Mitchell et al. 2015) assignments to unique gene ontology (GO) annotation based on functional domain conservation.

FileS6.xls (186 kB)
Total counts among novel genes by unique gene ontology (GO) annotation classification based on biological processes.

FileS7.xls (82 kB)
Total counts among novel genes by unique gene ontology (GO) annotation classification based on cellular component.

FileS8.xls (122 kB)
Total counts among novel genes by unique gene ontology (GO) annotation classification based on molecular function.

FileS10.xlsx (302 kB)
A summary of newly developed SNP markers with Affymetrix SNP indentification, assigned linkage group, associated flanking sequence of each SNP and position with each Gallus_gallus-5.0 unplaced assembly scaffold.

FigureS1.docx (556 kB)
Measured sequence representation and discrepancies in chicken MHC.

FigureS2.docx (592 kB)
Measured base total by individual chromosome for Gallus_gallus-5.0 when compared to Gallus_gallus-4.0.

FigureS3.docx (160 kB)
Gallus_gallus-5.0 sequence coverage of aligned reference sequences (bird #256; accession SRR3954707).

FigureS4.docx (64 kB)
Distribution of total GC bases for individual Gallus_gallus-5.0 chromosomes.

FigureS5.docx (94 kB)
Subread distribution for all long read that served as input for de novo assembly.

TableS1.docx (57 kB)
Assembly contiguity metrics of iterative builds of the Gallus_gallus-5.0 reference.

TableS2.docx (100 kB)
Classification of chicken protein coding genes in Gallus_gallus-5.0.

TableS3.docx (119 kB)
Mammalian or lizard genes that are not present in other sequenced birds with annotated gene sets.

TableS4.docx (157 kB)
Mammalian or lizard genes that are found in sequenced birds but not Gallus_gallus-5.0.

TableS5.docx (134 kB)
Genes now present in Gallus_gallus-5.0 that were not predicted in Gallus_gallus-4.0.

TableS6.docx (120 kB)
Genes unplaced in Gallus_gallus-4.0 that now have improved predictions and/or chromosomal placements in Gallus_gallus-5.0.

TableS7.docx (53 kB)
A summary of newly identified genetic linkage groups.