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Table 5 New and previously known OGSv3.2 genes

From: Finding the missing honey bee genes: lessons learned from a genome upgrade

 

All OGSv3.2

Type I new genes

Type II new genes

Previously known genes

 

Number of genes (% of total OGSv3.2 genes)

15,314 (100%)

782 (5.1%)

3,953 (25.8%)

10,579 (69.1%)

Scaffold analysis

Number of genes within mapped scaffolds (% of no. of gene type)

13,285 (86.8%)

544 (69.6%)

3,199 (80.9%)

9,542 (90.2%)

Number of genes within un-mapped scaffolds (% of no. of gene type)

2,029 (13.2%)

238 (30.4%)

754 (19.1%)

1,037 (9.8%)

CDS analysis

Average CDS length

1,266

1,172

330

1,622

Average no. CDS Exons

5.3

5.6

2.1

6.5

Number of single CDS exon genes (% of no. of gene type)

2,059 (13.4%)

101 (12.9%)

1,239 (31.3%)

719 (6.8%)

Number of multi-CDS exon genes (% of no. of gene type)

13,255 (86.6%)

681 (87.1%)

2,714 (68.7%)

9,860 (93.2%)

Intron analysis

Number of introns (% of total OGSv3.2 introns)

66,212 (100%)

3,585 (5.4%)

4,333 (6.5%)

58,294 (88%)

Number of introns validated by EST intron coordinates (% of introns of gene type)

54,514 (82.3%)

2,573 (71.8%)

1,930 (44.5%)

50,011 (85.8%)

Peptide analysis

Number of genes with a peptide match (% of no. of gene type)

3,631 (23.7%)

132 (16.9%)

82 (2.1%)

3,417 (32.3%)

Protein analysis

No. of genes with overlap to at least one protein alignment (% of no. of gene type)

6,778 (44.3%)

270 (34.5%)

186 (4.7%)

6,322 (59.8%)

No. of genes with overlap to a Dmel protein alignment (% of no. of gene type)

1,205 (7.9%)

38 (4.9%)

13 (0.3%)

1,154 (10.9%)

Total spliced and un-spliced expressed sequence support

No. of genes with overlap to at least one transcript alignment from any of the ten libraries (% of no. of gene type)

13,517 (88.3%)

704 (90.0%)

2,771 (70.1%)

10,042 (94.9%)

Spliced expressed sequence analysis

No. of genes with overlap to at least one spliced transcript alignment from each of the ten libraries (% of no. of gene type)

1,062 (6.9%)

32 (4.1%)

15 (0.4%)

1,015 (9.6%)

No. of genes with overlap to at least one spliced transcript alignment from any of the ten libraries (% of no. of gene type)

12,172 (79.5%)

622 (79.5%)

2,110 (53.4%)

9,440 (89.2%)

No. of genes without overlap to any spliced transcript alignments in any of the ten libraries (% of no. of gene type)

3,142 (20.5%)

160 (20.5%)

1,843 (46.6%)

1,139 (10.8%)

Genes broadly expressed across four tissues (% of no. of gene type)

2,326 (15.2%)

60 (7.7%)

95 (2.4%)

2,171 (20.5%)

Genes narrowly expressed in only a single tissue (% of no. of gene type)

3,346 (21.8%)

234 (29.9%)

1,139 (28.8%)

1,973 (18.7%)

No. of genes without overlap to any spliced transcript alignments in any of the four tissues (% of no. of gene type)

3,632 (23.7%)

192 (24.6%)

1,985 (50.2%)

1,455 (13.8%)

Analysis of alignments to other bee genomes

No. of genes that align to Aflo_1.0 (% of no. of gene type)

13,491 (88.1%)

566 (72.4%)

2,584 (65.4%)

10,341 (97.8%)

No. of genes that align to Bter_1.0 (% of no. of gene type)

12,262 (80.1%)

527 (67.4%)

1,566 (39.6%)

10,169 (96.1%)

Evidence-supported genes

No. of genes with overlap to at least one form of biological evidence (% of no. of gene type)

14,084 (92.0%)

713 (91.2%)

2,930 (74.1%)

10,441 (98.7%)

No. of genes that align to Aflo_1.0 and/or Bter_1.0 and/or overlap at least one form of biological evidence (% of no. of gene type)

14,836 (96.9%)

734 (93.9%)

3,555 (89.9%)

10,547 (99.7%)

GC analysis

Number of genes on GC compositional domains >10 kb (% of OGSv3.2 total)

15,224 (99.4%)

777 (5.1%)

3,923 (25.8%)

10,524 (69.1%)

Avg. GC content of compositional domain gene resides in

29.60%

26.40%

32.00%

28.90%

ENC analysis

Effective number of codons

44.95

41.97

45.69

44.9

  1. Genes were mapped to Amel_2.0 assembly with stringent mapping criteria of 80% gene coverage and 95% identity. Biological evidence includes transcript overlap (spliced or un-spliced), peptide hit, protein homolog alignment overlap, or InterPro domain presence.