Table 4 Assembly metrics with comparison to other cyprinid genomes.

From: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Attribute

C. carassius (w)

C. carassius (f)

C. gibelio

C. auratus

Cyprinus carpio

Sequencing

74x PacBio CLR Illumina HiSeq, HiC

43x PacBio HiFi, Arima2 Hi-C

45x PacBio HiFi, OmniC Illumina reads

71x PacBio CLR

185x PacBio CLR, Oxford Nanopore, Illumina HiSeq

Assembly

Flye, MaSuRCA-POLCA, AllHiC, Arima pipeline, Juicebox

Hifiasm, purge_dups, YaHS

Hifiasm unitigger, 3D-dna

Canu

wtdbg, quickmerge

MitoAnnotator

MitoHiFi

n/a

cloning

cloning

Total lengtha

1,654,898

1,684,296

1,583,352

1,820,629

1,671,603

Ungapped length

1,654,776

1,684,071

1,582,055

1,820,404

1,663519

GC content (%)

38.27

38.31

37.63

37.48

37.09

BUSCOs (%)b:

99.6

99.3

99.5

99.3

98.6

Protein-coding genes

45,667

41,837

43,901

53,065

43,531

Chromosomes

50

50

50

59

50

Scaffolds

261c

238

51c

6,213

1,975

Scaffold N50

31,733

32,664

30,678

22,763

29,545

Scaffold N90

26,847

27,139

26,107

87

20,764

Scaffold auN

33,279

33,770

33,145

18,403

29,423

Scaffold L50

23

23

22

32

24

Scaffold L90

45

45

44

1,508

49

Ns per 100 kbp

4

10

82

12

474

Longest scaffold

51,097

53,934

55,533

37,185

48,440

Contigs

941

1,070

2,648

8,460

14,642

Contig N50

15,168

3,822

5,134

821

1,574

Contig N90

2,094

1,005

885

74

121

Contig auN

14,386

4,570

6,406

1,399

2,876

Contig L50

40

135

91

513

226

Contig L90

149

462

343

3,543

1,764

  1. aAll lengths in kbp. bThese BUSCO scores for complete orthologs are either calculated as part of the BRAKER3 pipeline (wild-type crucian carp, C. carassius (w)) or sourced from NCBI genome information (all others). They differ slightly from scores obtained in Blobtool snail plot (Figs. 2c, 5a), which are likely estimated from the genome rather than the predicted proteins. cIncluding the scaffold identified as MT.
Back to article page