Table 1. Quality and composition of Lepidoptera genomes.

Feature	Pra	Pse	Pgl	Ppo	Pxu	Dpl	Hme	Mci	Cce	Lac	Mse	Bmo	Pxy
Genome size (Mb)	246	406	375	227	244	249	274	390	729	298	419	481	394
Genome size without gap (Mb)	243	347	361	218	238	242	270	361	689	290	400	432	387
Heterozygosity (%)	1.5	1.2	2.3	n.a.	n.a.	0.55	n.a.	n.a.	1.2	1.5	n.a.	n.a.	˜2
Scaffold N50 (kb)	617	257	231	3672	6199	716	194	119	233	525	664	3999	734
CEGMA (%)	99.6	99.3	99.6	99.3	99.6	99.6	98.2	98.9	100	99.3	99.8	99.6	98.7
CEGMA coverage by single scaffold (%)	88.7	87.4	86.9	85.8	88.8	87.4	86.5	79.2	85.3	86.8	86.4	86.8	84.1
Cytoplasmic Ribosomal Proteins (%)	98.9	98.9	98.9	98.9	97.8	98.9	94.6	94.6	98.9	98.9	98.9	98.9	93.5
De novo assembled transcripts (%)	99	97	98	n.a.	n.a.	96	n.a.	97	97	98	n.a.	98	83
GC content (%)	32.7	39.0	35.4	34.0	33.8	31.6	32.8	32.6	37.1	34.4	35.3	37.7	38.3
Repeat (%)	22.7	17.2	22.0	n.a.	n.a.	16.3	24.9	28.0	34.0	15.5	24.9	44.1	34.0
Exon (%)	7.9	6.20	5.07	5.11	8.59	8.40	6.38	6.36	3.11	6.96	5.34	4.03	6.35
Intron (%)	33.3	25.5	25.6	24.8	45.5	28.1	25.4	30.7	24.0	31.6	38.3	15.9	30.7
Number of proteins (thousands)	13.2	16.5	15.7	15.7	13.1	15.1	12.8	16.7	16.5	17.4	15.6	14.3	18.1
Number of universal ortholog lost	48	35	33	235	71	18	225	356	35	82	120	236	808
Number of species specific genes	27	101	32	9	240	69	52	59	101	87	165	98	399

n.a. Data not available

Pra: Pieris rapae; Lac: Lerema accius; Cce: Calycopis cecrops; Pgl: Pterourus glaucus; Dpl: Danaus plexippus; Hme: Heliconius melpomene; Mci: Melitaea cinxia; Bmo: Bombyx mori; Pxy: Plutella xylostella; Mse: Manduca sexta; Ppo: Papilio polytes; Pse: Phoebis sennae; Pxu: Papilio xuthus.

Heterozygosity: Calculated as the percent of heterozygous positions detected by the Genome Analysis Toolkit (GATK) for Pgl, Lac, Cce, Pra and Pse; or taken from information in the literature for Dpl ²⁰; or estimated based on the histogram of K-mer frequencies for Pxy ^{18, 41}.