Table 1.

Summary of assembly metrics of the 32 genomes sequenced in this work.

Strain	Location	Contigs	Genome size	N50 (Mb)	BUSCO complete	BUSCO duplicate	QV	c.CUSCO	sc.CUSCO	Completeness (ISO1 aligned bases)	Euchromatic size (Mb)
AKA-017a,b	Akka, Finland	164	142.7	18.9	98.7%	0.50%	51.04	82.35%	94.12%	96.30%	100.1
AKA-018c	Akka, Finland	162	136.7	2.3	98.4%	0.70%	37.63	72.94%	92.94%	93.50%	100.9
COR-014a,b	Cortes de Baza, Spain	161	138.1	7.7	98.3%	0.50%	43.62	72.94%	96.47%	96.70%	100.4
COR-018c	Cortes de Baza, Spain	402	143.5	0.9	98.0%	1.00%	38.47	55.29%	96.47%	94.30%	103.3
COR-023c	Cortes de Baza, Spain	620	139.5	0.6	97.8%	0.80%	37.42	35.29%	92.94%	93.60%	101.5
COR-025c	Cortes de Baza, Spain	377	143.4	0.7	98.1%	1.00%	37.83	57.65%	92.94%	94.00%	102.7
GIM-012c	Gimenells, Spain	383	140	1.2	98.4%	0.80%	40.56	45.88%	87.06%	94.10%	101.2
GIM-024a,b,c	Gimenells, Spain	316	142.3	6.8	99.0%	0.50%	50.77	77.65%	94.12%	95.20%	100.2
JUT-008c	Jutland, Denmark	330	148.5	9.6	98.4%	0.50%	49.52	80.00%	96.47%	93.60%	101.5
JUT-011a,b	Jutland, Denmark	184	138.4	4	98.7%	0.50%	44.94	70.59%	98.82%	96.50%	100.8
KIE-094a,b	Kiev, Ucrania	343	143.8	3.8	98.7%	0.80%	48.78	75.29%	96.47%	96.20%	101.9
LUN-004a,b	Lund, Sweden	314	138.1	2	98.7%	0.60%	44.24	62.35%	96.47%	96.30%	101.1
LUN-007c	Lund, Sweden	360	142.4	1.1	98.0%	0.60%	39.91	52.94%	95.29%	94.10%	102.1
MUN-008c	Munich, Germany	250	142.2	1.1	97.5%	0.90%	37.76	68.24%	94.12%	94.10%	101.7
MUN-009	Munich, Germany	385	149.3	5.6	97.9%	0.50%	45.97	71.76%	95.29%	94.10%	102.1
MUN-013c	Munich, Germany	406	138.4	1	98.2%	0.50%	39.28	49.41%	90.59%	93.80%	101.9
MUN-015	Munich, Germany	251	140	1.2	98.0%	1.00%	38.19	65.88%	92.94%	93.90%	101.8
MUN-016a	Munich, Germany	217	142	7.8	98.50%	0.60%	NA	77.65%	92.94%	96.60%	100.7
MUN-020c	Munich, Germany	324	138.1	1.3	97.10%	1.10%	40.93	48.24%	82.35%	93.80%	101.2
RAL-059c	Raleigh, USA	688	143.5	0.8	98.10%	0.90%	43.25	51.76%	94.12%	93.20%	101.7
RAL-091c	Raleigh, USA	887	145.1	0.5	97.50%	1.00%	44.04	57.65%	92.94%	92.80%	103.9
RAL-176c	Raleigh, USA	1185	151.3	0.4	97.10%	0.80%	46.62	43.53%	88.24%	92.70%	102.9
RAL-177a,b,c	Raleigh, USA	188	141.9	14.6	97.40%	0.40%	46.70	84.71%	96.47%	95.70%	100.7
RAL-375a,b,c	Raleigh, USA	179	141.2	13.5	96.10%	0.40%	44.86	82.35%	96.47%	96.10%	100.7
RAL-426c	Raleigh, USA	500	137	0.7	97.60%	0.50%	38.04	51.76%	90.59%	93.50%	102.0
RAL-737c	Raleigh, USA	469	147.8	1.5	97.40%	0.50%	42.11	70.59%	95.29%	93.20%	102.1
RAL-855c	Raleigh, USA	332	144.4	3.9	97.00%	0.40%	41.78	78.82%	97.65%	93.40%	102.2
SLA-001a,b	Slankamen, Serbia	432	143.7	0.8	97.90%	0.80%	38.45	58.82%	97.65%	96.60%	103.0
STO-022a,b	Stockholm, Sweden	153	142.4	3.1	98.10%	0.70%	36.00	71.76%	96.47%	96.90%	102.5
TEN-015a,b	Tenerife, Spain	329	140.5	1.1	97.90%	1.00%	40.30	61.18%	94.12%	96.20%	102.0
TOM-007	Tomelloso, Spain	222	139.5	3.2	98.20%	0.70%	NA	57.65%	92.94%	96.90%	101.0
TOM-008a,c	Tomelloso, Spain	219	136.6	1.9	98.10%	0.80%	41.75	61.18%	85.88%	94.10%	101.3
ISO1-Sold	Reference Genome	518	147.8	3.4	96.00%	0.50%	42.92	77.65%	91.76%	97.57%	101.9

Genomes were sequenced using ONT except MUN-016 and TOM-007 that were sequenced using PacBio.

Additional information on the strains can be found in Supplementary Data 1 and on the sequencing in Supplementary Tables S2 and S3. Besides contig-CUSCO scores (c.CUSCO) scaffold-CUSCO scores (sc.CUSCO) are also given (the later values are higher as expected if the piRNA flanking regions are present in the assembled genomes).

^aThe 13 strains used in the construction of the de novo MCTE library.

^bThe 11 strains used in the comparison of TE annotations using REPET, TIDAL and TEMP.

^cThe 20 strains used in the cis-eQTL analysis.

^dGenome assembled using long-read sequencing data of the D. melanogaster reference genome provided in Solares et al.¹⁸.