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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.