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Table 3 Completeness of the v2 and v3 annotations ofL. perenne

From: Chromosome-scale assembly and annotation of the perennial ryegrass genome

Completeness categories

Gene models

 

v2

v3

 

Nr. of hits

% of total

Nr. of hits

% of total

(A) BUSCO completeness (n=1440)

Complete BUSCOs (C)

1340

93.1

1391

96.6

Complete and single copy BUSCOs (S)

1291

89.7

1331

92.4

Complete and duplicated BUSCOs (D)

49

3.4

60

4.2

Fragmented BUSCOs (F)

44

3.1

27

1.9

Missing BUSCOs (M)

56

3.8

22

1.5

(B) coreGF completeness (n=7076)

Represented gene families

6762

95.6

6851

96.8

Missing gene families

314

4.4

225

3.2

coreGF completeness score

0.938

 

0.956

 

(C) BLAST to reference proteomes

Barley MIPS HC proteins (26159 sequences)

23524

89.9

23977

91.7

Barley Morex_V2 HC proteins (32787 sequences)

27637

84.3

28233

86.1

B. distachyon v1.0 proteins (31029 sequences)

26330

84.9

26815

86.4

  1. (A): Completeness scores assessed by BUSCO (v3.0.2 [23]) using the embryophyta_odb9 reference set (1440 single-copy orthologs)
  2. (B): Core Gene Families (coreGFs) completeness scores using the monocot reference set of PLAZA v4 (7076 coreGFs from five species, [25]). The representation across all individual coreGFs is summarized in a global weighted coreGF score
  3. (C): Transcript nucleotide sequences were searched by BLASTx against reference protein sequences. Top hits at an e-value threshold of e-4 with least 70% subject coverage were considered as significant matches