Table 2 Maternal and paternal chromosome assignment to the male genome assembly based on alignment to the maternal female genome assembly12.

From: A haplotype-phased male genome sequence of the stinging nettle, Urtica dioica ssp. dioica

Chromosome

Proportion of MH1 aligning with

Proportion of MH2 aligning with

Male haplotypes

FH1

FH2

FH1

FH2

Maternal haplotype

Paternal haplotype

1

1.2%

98.4%

0.6%

0.2%

MH1

MH2

2

2.6%

97.4%

0.0%

0.2%

MH1

MH2

3

0.0%

0.0%

87.3%

4.8%

MH2

MH1

4

46.4%

23.1%

1.6%

0.3%

MH1

MH2

5

0.0%

0.1%

84.8%

19.2%

MH2

MH1

6

0.0%

0.0%

99.6%

2.1%

MH2

MH1

7

86.2%

1.3%

0.1%

0.0%

MH1

MH2

8

99.5%

0.5%

0.3%

0.3%

MH1

MH2

9

29.9%

63.6%

0.2%

0.9%

MH1

MH2

10

34.1%

13.6%

1.0%

0.0%

MH1

MH2

11

7.5%

93.1%

0.2%

0.2%

MH1

MH2

12

11.6%

72.0%

0.0%

0.1%

MH1

MH2

13

0.8%

47.8%

0.0%

0.0%

MH1

MH2

  1. Maternally-inherited chromosomes were identified based on visual inspection of the pairwise alignment plot coloured by the percent nucleotide identity (Fig. 4, Supplementary Fig. 4), where FH1 and FH2 were used as reference. Higher alignment rates between of a male chromosome haplotype with its female counterpart was considered as evidence of maternal inheritance. To calculate the proportion of a male haplotype (MH1/MH2) in perfect alignment with the female haplotypes (FH1/FH2), we used >99.7% alignment blocks and calculated the (total length of alignment/total chromosome length × 100%) for each chromosome pair.
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