Table 1 List of Diptera (n = 42) and Out group Lepidoptera (n = 2) used in this study for comparative mitogenomics and phylogenetic analysis (A = Ancestral mitogenome arrangement).

From: Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Sl no.	Accession no	Family	Organisms	Mito genome (bp)/AT%	CR (bp)/AT%	rRNA (bp)/AT%	tRNA (bp)/AT%	PCG size (bp)/AT%	Mito genome pattern	Common name	Economic importance	Lifestyle/food habit	References
1	NC_019632	Calliphoridae	Chrysomya bezziana	15,236	392	2116	1469	11,151	A + trnI + duplication CR	Old World screwworm	Causes Myiasis in animal and human	Obligate ectoparasite/necrophagous	^4,6,59
1	NC_019632	Calliphoridae	Chrysomya bezziana	75.89	87.75	79.63	76.31	74.53	A + trnI + duplication CR	Old World screwworm	Causes Myiasis in animal and human	Obligate ectoparasite/necrophagous	^4,6,59
2	NC_026996	Calliphoridae	Aldrichina grahami	14,903	89	2107	1475	11,118	A	Blow fly	Forensic insect, transmit human and animal pathogens	Necrophagous	^60,61,62
2	NC_026996	Calliphoridae	Aldrichina grahami	76.75	92.13	80.06	76.47	75.91	A	Blow fly	Forensic insect, transmit human and animal pathogens	Necrophagous	^60,61,62
3	NC_025338	Calliphoridae	Chrysomya pinguis	15,838	988	2114	1478	11,151	A + trnI	Blowfly	Forensically Important	Ectoparasite/necrophagous	^10,11,12
3	NC_025338	Calliphoridae	Chrysomya pinguis	76.06	88.25	79.75	75.98	74.11	A + trnI	Blowfly	Forensically Important	Ectoparasite/necrophagous	^10,11,12
4	NC_019631	Calliphoridae	Chrysomya albiceps	15,491	657	2113	1472	11,151	A + trnI + duplication CR	Hairy maggot blowfly	Cause secondary myiases	Necrophagous	^13,44
4	NC_019631	Calliphoridae	Chrysomya albiceps	77.26	85.69	80.40	76.22	76.16	A + trnI + duplication CR	Hairy maggot blowfly	Cause secondary myiases	Necrophagous	^13,44
5	NC_019636	Calliphoridae	Protophormia terraenovae	15,170	356	2112	1472	11,151	A	Northern blowfly	Myiasis pest of livestock	Ectoparasite/necrophagous	^4,14
5	NC_019636	Calliphoridae	Protophormia terraenovae	75.87	90.73	80.06	76.01	74.44	A	Northern blowfly	Myiasis pest of livestock	Ectoparasite/necrophagous	^4,14
6	NC_019635	Calliphoridae	Chrysomya saffranea	15,839	994	2114	1472	11,151	A + trnI + duplication CR	Steelblue blowfly	Forensic insect and causes myiasis in human beings and animals	Necrophagous	^4,15
6	NC_019635	Calliphoridae	Chrysomya saffranea	76.45	88.12	79.84	76.08	74.63	A + trnI + duplication CR	Steelblue blowfly		Necrophagous	^4,15
7	NC_019638	Calliphoridae	Hemipyrellia ligurriens	15,938	1119	2115	1473	11,157	A	Blowfly	Forensic insect, myiasis in goat, buffalo and bull, vector of pathogens	Parasite/necrophagous	^4,16,17
7	NC_019638	Calliphoridae	Hemipyrellia ligurriens	77.35	89.72	80.14	76.98	75.50	A	Blowfly		Parasite/necrophagous	^4,16,17
8	NC_019637	Calliphoridae	Lucilia porphyrina	15,877	1047	2115	1470	11,157	A	Porphyrina blow fly/Oriental blow fly	Forensic insect, myiasis in livestock, human	Ectoparasite/human or animal corpses/necrophagous	^4,11,18,19
8	NC_019637	Calliphoridae	Lucilia porphyrina	76.26	88.92	79.57	76.46	74.26	A	Porphyrina blow fly/Oriental blow fly	Forensic insect, myiasis in livestock, human	Ectoparasite/human or animal corpses/necrophagous	^4,11,18,19
9	NC_019634	Calliphoridae	Chrysomya rufifacies	15,412	574	2114	1473	11,151	A + trnI + duplication CR	Hairy maggot blowfly	Forensic insect, myiasis in livestock	Necrophagous	⁴
9	NC_019634	Calliphoridae	Chrysomya rufifacies	77.20	84.84	80.22	76.57	76.18	A + trnI + duplication CR	Hairy maggot blowfly	Forensic insect, myiasis in livestock	Necrophagous	⁴
10	NC_019633	Calliphoridae	Chrysomya megacephala	15,273	428	2114	1472	11,151	A + trnI + duplication CR	Oriental latrine fly	Forensic insect, myiasis in livestock	Necrophagous	²⁰
10	NC_019633	Calliphoridae	Chrysomya megacephala	75.98	87.14	79.70	75.88	74.66	A + trnI + duplication CR	Oriental latrine fly	Forensic insect, myiasis in livestock	Necrophagous	²⁰
11	NC_002660	Calliphoridae	Cochliomyia hominivorax	16,022	1175	2110	1470	11,157	CR A	New World screw-worm fly	Forensic insect, myiasis in mammals	Necrophagous	⁶³
11	NC_002660	Calliphoridae	Cochliomyia hominivorax	76.90	90.80	79.81	76.59	74.72	CR A	New World screw-worm fly	Forensic insect, myiasis in mammals	Necrophagous	⁶³
12	NC_002697	Calliphoridae	Chrysomya putoria	15,837	1008	2114	1471	11,154	A + trnI + duplication CR	Tropical African latrine blowfly	Forensic insect, myiasis in mammals	Necrophagous	²¹
12	NC_002697	Calliphoridae	Chrysomya putoria	76.70	88.59	79.99	76.13	74.91	A + trnI + duplication CR	Tropical African latrine blowfly	Forensic insect, myiasis in mammals	Necrophagous	²¹
13	NC_031381	Calliphoridae	Chrysomya phaonis	15,831	992	2112	1472	11,151	A + trnI	Blow flies	Medical and forensic importance	Necrophagous	²²
13	NC_031381	Calliphoridae	Chrysomya phaonis	76.09	88.10	79.59	75.81	74.23	A + trnI	Blow flies	Medical and forensic importance	Necrophagous	²²
14	NC_029486	Calliphoridae	Lucilia coeruleiviridis	14,989	168	2110	1471	11,145	A + Partial CR	Green bottle fly	Forensic insect, myiasis in pig and other mammals	Ectoparasite/necrophagous	^19,23
14	NC_029486	Calliphoridae	Lucilia coeruleiviridis	76.02	87.5	80	76.88	74.87	A + Partial CR	Green bottle fly	Forensic insect, myiasis in pig and other mammals	Ectoparasite/necrophagous	^19,23
15	NC_029215	Calliphoridae	Calliphora chinghaiensis	15,269	441	2113	1463	11,190	Translocation of trnS1	Blue bottle flies	Forensic importance	Necrophagous	^24,25
15	NC_029215	Calliphoridae	Calliphora chinghaiensis	76.75	84.35	80.59	76.82	75.55	Translocation of trnS1	Blue bottle flies	Forensic importance	Necrophagous	^24,25
16	NC_028411	Calliphoridae	Calliphora vomitoria	16,134	1319	2110	1471	11,151	A	Blue bottle fly	Forensic importance and causes myiasis	Necrophagous	^26,27,64
16	NC_028411	Calliphoridae	Calliphora vomitoria	77.55	90.29	80.33	76.41	75.54	A	Blue bottle fly	Forensic importance and causes myiasis	Necrophagous	^26,27,64
17	NC_028412	Calliphoridae	Chrysomya nigripes	15,832	966	2115	1476	11,154	A + trnI + duplication CR	Blowfly	Forensic importance	Necrophagous	^22,65
17	NC_028412	Calliphoridae	Chrysomya nigripes	76.92	88.09	80.14	76.01	75.24	A + trnI + duplication CR	Blowfly	Forensic importance	Necrophagous	^22,65
18	NC_028056	Calliphoridae	Lucilia illustris	15,954	1094	2153	1469	11,100	CR A	Green bottle fly	Forensic importance and myiasis in pet Animals	Ectoparasite/necrophagous	^19,66
18	NC_028056	Calliphoridae	Lucilia illustris	77.42	90.85	79.74	76.85	75.60	CR A	Green bottle fly	Forensic importance and myiasis in pet Animals	Ectoparasite/necrophagous	^19,66
19	NC_028057	Calliphoridae	Lucilia Caesar	15,954	1117	2152	1469	11,121	CR A	Common greenbottle	Forensic importance and facultative wound myiasis	Ectoparasite/necrophagous	^19,67,68
19	NC_028057	Calliphoridae	Lucilia Caesar	77.30	90.59	79.73	76.78	75.39	CR A	Common greenbottle	Forensic importance and facultative wound myiasis	Ectoparasite/necrophagous	^19,67,68
20	NC_013932	Oestridae	Hypoderma lineatum	16,354	1493	2101	1453	11,136	A	Common cattle grub/warble fly	Causes Myiasis in ruminants	Ectoparasite/sarcophagous/carnivore	^69,70,71,72
20	NC_013932	Oestridae	Hypoderma lineatum	77.85	87.54	80.48	77.70	75.85	A	Common cattle grub/warble fly	Causes Myiasis in ruminants	Ectoparasite/sarcophagous/carnivore	^69,70,71,72
21	NC_006378	Oestridae	Dermatobia hominis	16,360	1545	2112	1458	11,157	Insertion of trnV between trnK-trnD	Human botfly/tropical warble fly	Causes Myiasis in human, cattle, dogs and forensically importance	Endoparasites of birds and mammals/carnivore	^70,73,74,75
21	NC_006378	Oestridae	Dermatobia hominis	77.81	91.39	81.43	77.09	75.23	Insertion of trnV between trnK-trnD	Human botfly/tropical warble fly		Endoparasites of birds and mammals/carnivore	^70,73,74,75
22	NC_029812	Oestridae	Gasterophilus pecorum	15,750	1001	2048	1461	11,103	A	Horse botfly	Gastrointestinal myiasis in equines and forensic science	Obligate intestinal parasites/carnivore	^69,76
22	NC_029812	Oestridae	Gasterophilus pecorum	70.73	80.81	74.31	75.56	68.46	A	Horse botfly	Gastrointestinal myiasis in equines and forensic science	Obligate intestinal parasites/carnivore	^69,76
23	NC_029834	Oestridae	Gasterophilus intestinalis	15,660	875	2107	1470	11,103	CR A	Horse botfly	Gastric myiasis in horse, donkey	Obligate internal parasites /carnivore	^77,78,79
23	NC_029834	Oestridae	Gasterophilus intestinalis	70.16	80.8	73.84	74.69	67.88	CR A	Horse botfly	Gastric myiasis in horse, donkey	Obligate internal parasites /carnivore	^77,78,79
24	NC_026196	Sarcophagidae	Ravinia pernix	15,778	1750	2114	1470	11,154	A		Forensic importance, potential for myiasis	Endo-parasitoid/saprophagous	^3,60
24	NC_026196	Sarcophagidae	Ravinia pernix	77.17	84.34	80.36	76.32	75.46	A		Forensic importance, potential for myiasis	Endo-parasitoid/saprophagous	^3,60
25	NC_026112	Sarcophagidae	Sarcophaga melanura	15,190	360	2108	1475	11,154	A	Flesh fly	Forensic importance, causes myiasis	Ectoparasite/saprophagous	^61,62,80,81
25	NC_026112	Sarcophagidae	Sarcophaga melanura	75.64	90.27	80.07	76.61	74.04	A	Flesh fly	Forensic importance, causes myiasis	Ectoparasite/saprophagous	^61,62,80,81
26	NC_025944	Sarcophagidae	Sarcophaga Africa	15,144	338	2111	1469	11,151	A	Flesh fly	Intestinal myiasis and forensic science	Ectoparasite/saprophagous	^81,82,83
26	NC_025944	Sarcophagidae	Sarcophaga Africa	75.74	89.34	79.91	76.31	74.32	A	Flesh fly	Intestinal myiasis and forensic science	Ectoparasite/saprophagous	^81,82,83
27	NC_025574	Sarcophagidae	Sarcophaga portschinskyi	14,929	118	2109	1468	11,139	A	Flesh fly	Forensic importance	Ectoparasite/saprophagous	^81,84
27	NC_025574	Sarcophagidae	Sarcophaga portschinskyi	76.18	89.83	80.41	76.08	75.12	A	Flesh fly	Forensic importance	Ectoparasite/saprophagous	^81,84
28	NC_025573	Sarcophagidae	Sarcophaga similis	15,158	354	2107	1461	11,139	A	Flesh fly	Responsible for myiasis and forensic importance	Ectoparasite/saprophagous	^81,85,86,87
28	NC_025573	Sarcophagidae	Sarcophaga similis	76.36	87.57	80.25	76.11	75.21	A	Flesh fly	Responsible for myiasis and forensic importance	Ectoparasite/saprophagous	^81,85,86,87
29	NC_023532	Sarcophagidae	Sarcophaga peregrine	14,922	123	2108	1470	11,139	A	Flesh fly	Responsible for myiasis and forensic importance	Ectoparasite/saprophagous	^81,88,89
29	NC_023532	Sarcophagidae	Sarcophaga peregrine	74.97	87.80	79.83	76.12	73.61	A	Flesh fly	Responsible for myiasis and forensic importance	Ectoparasite/saprophagous	^81,88,89
30	NC_017605	Sarcophagidae	Sarcophaga impatiens	15,169	359	2113	1469	11,154	A	Flesh fly	Forensic importance Carrion breeding	Ectoparasite/saprophagous	^81,90
30	NC_017605	Sarcophagidae	Sarcophaga impatiens	74.76	88.30	79.46	76.37	73.08	A	Flesh fly	Forensic importance Carrion breeding	Ectoparasite/saprophagous	^81,90
31	NC_026667	Sarcophagidae	Sarcophaga crassipalpis	15,420	613	2109	1484	11,153	A	Flesh fly	Forensic importance responsible of myiasis	Ectoparasite/saprophagous	^81,91,92
31	NC_026667	Sarcophagidae	Sarcophaga crassipalpis	76.22	89.39	80.03	76.21	74.65	A	Flesh fly	Forensic importance responsible of myiasis	Ectoparasite/saprophagous	^81,91,92
32	NC_028413	Sarcophagidae	Sarcophaga albiceps	14,935	125	2111	1470	11,139	A	Flesh fly	Forensically important	Ectoparasite/saprophagous	^81,93
32	NC_028413	Sarcophagidae	Sarcophaga albiceps	75.86	90.4	79.77	75.78	74.84	A	Flesh fly	Forensically important	Ectoparasite/saprophagous	^81,93
33	Current Study	Tachinidae	*Blepharipa* sp.	15,080	168	2143	1466	11,166	A	Uzi Fly	Endoparasite of muga silkworm	Endoparasite/parasitoid	This Study
33	Current Study	Tachinidae	*Blepharipa* sp.	78.41	92.60	82.54	78.24	77.27	A	Uzi Fly	Endoparasite of muga silkworm	Endoparasite/parasitoid	This Study
34	NC_019640	Tachinidae	Rutilia goerlingiana	15,331	568	2101	1451	11,131	A	Tachinid flies	Insect endoparasite	Endoparasite/parasitoid	⁴
34	NC_019640	Tachinidae	Rutilia goerlingiana	77.70	91.07	81.81	77.18	76.11	A	Tachinid flies	Insect endoparasite	Endoparasite/parasitoid	⁴
35	NC_018118^a	Tachinidae	Elodia flavipalpis	14,932	105	2120	1463	11,154	A	Tachinid flies	Natural enemies of the leaf-roller moths	Endoparasite/parasitoid	³²
35	NC_018118^a	Tachinidae	Elodia flavipalpis	79.96	92.38	83.49	79.76	79.09	A	Tachinid flies	Natural enemies of the leaf-roller moths	Endoparasite/parasitoid	³²
36	NC_014704^a	Tachinidae	Exorista sorbillans	14,960	105	2117	1471	11,136	A	Uzi Fly	Endoparasite of mulberry silkworm	Endoparasite/parasitoid	⁴²
36	NC_014704^a	Tachinidae	Exorista sorbillans	78.44	98.09	81.76	76.75	77.64	A	Uzi Fly	Endoparasite of mulberry silkworm	Endoparasite/parasitoid	⁴²
37	NC_016713	Agromyzidae	Liriomyza bryoniae	16,183	1354	2111	1468	11,169	A	Tomato leaf miner	Pest species of Tomato and other vegetables (Cucurbitaceae and Solanaceae,)	Ectoparasite /polyphagous/herbivore	^94,95,96
37	NC_016713	Agromyzidae	Liriomyza bryoniae	79.26	95.49	82.42	78.54	76.66	A	Tomato leaf miner		Ectoparasite /polyphagous/herbivore	^94,95,96
38	NC_015926	Agromyzidae	Liriomyza sativae	15,551	741	2111	1465	11,160	A	Vegetable leafminer	Pest species vegetables	Ectoparasite /polyphagous/herbivore	^95,97
38	NC_015926	Agromyzidae	Liriomyza sativae	77.53	92.98	82.18	76.99	75.59	A	Vegetable leafminer	Pest species vegetables	Ectoparasite /polyphagous/herbivore	^95,97
39	NC_014402	Tephritidae	Bactrocera minax	16,043	1140	2115	1466	11,151	A	Oriental citrus fly	Pest of citrus and related genera of Rutaceae	Phytophagous/herbivore	^98,99
39	NC_014402	Tephritidae	Bactrocera minax	67.28	77.63	73.71	72.30	64.21	A	Oriental citrus fly	Pest of citrus and related genera of Rutaceae	Phytophagous/herbivore	^98,99
40	NC_029468	Tephritidae	Bactrocera umbrosa	15,898	944	2120	1465	11,157	A	Oriental fruit fly	Pest of Moraceae family	Phytophagous/herbivore	^99,100
40	NC_029468	Tephritidae	Bactrocera umbrosa	70.48	86.22	77.02	74.12	67.19	A	Oriental fruit fly	Pest of Moraceae family	Phytophagous/herbivore	^99,100
41	NC_015079	Culicidae	Culex pipiens pipiens	14,856	0	2118	1475	11,187	Inversion (trnA-trnR = > trnR-trnA)	Culex Mosquito	Vector of multiple diseases (West Nile virus)	Free living/multivoltine	¹⁰¹
41	NC_015079	Culicidae	Culex pipiens pipiens	77.63	0	82.24	78.98	76.46	Inversion (trnA-trnR = > trnR-trnA)	Culex Mosquito	Vector of multiple diseases (West Nile virus)	Free living/multivoltine	¹⁰¹
42	NC_027502	Culicidae	Anopheles culicifacies	15,330	498	2113	1474	11,199	Inversion (trnA-trnR = > trnR-trnA)	Anopheles Mosquito	Vector of multiple diseases	Free living/multivoltine	¹⁰²
42	NC_027502	Culicidae	Anopheles culicifacies	78.44	92.57	82.06	78.56	77.04	Inversion (trnA-trnR = > trnR-trnA)	Anopheles Mosquito	Vector of multiple diseases	Free living/multivoltine	¹⁰²
43	NC 002355	Lepidoptera (Order)	Bombyx mori	15,643	499	2158	1468	11,142	trnM-trnI-trnQ	Mulberry Silkworm	Economically beneficial in silk and textile	Phytophagous/herbivore	¹⁰³
43	NC 002355	Lepidoptera (Order)	Bombyx mori	81.32	95.39	84.80	81.40	79.50	trnM-trnI-trnQ	Mulberry Silkworm	Economically beneficial in silk and textile	Phytophagous/herbivore	¹⁰³
44	KU379695	Lepidoptera (Order)	Antheraea assamensis	15,272	328	2123	1465	11,175	trnM-trnI-trnQ	Muga Silkworm	Economically beneficial in silk and textile	Phytophagous/herbivore	¹⁰⁴
44	KU379695	Lepidoptera (Order)	Antheraea assamensis	80.18	91.15	84.26	80.75	78.75	trnM-trnI-trnQ	Muga Silkworm	Economically beneficial in silk and textile	Phytophagous/herbivore	¹⁰⁴

^aMitogenomes were used for manual curation of Blepharipa sp.

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Table 1 List of Diptera (n = 42) and Out group Lepidoptera (n = 2) used in this study for comparative mitogenomics and phylogenetic analysis (A = Ancestral mitogenome arrangement).

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