Comprehensive mitochondrial genome profile of New Zealand white rabbit (<i>Oryctolagus cuniculus</i>) using Nanopore sequencing technology

Lestari, D. A.; Sutopo, S.; Setiatin, E. T.; Mustofa, F.; Kurnianto, E.; Setiaji, A.

doi:10.1590/1519-6984.298644

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Original Article • Braz. J. Biol. 86 • 2026 • https://doi.org/10.1590/1519-6984.298644 linkcopy

Comprehensive mitochondrial genome profile of New Zealand white rabbit (Oryctolagus cuniculus) using Nanopore sequencing technology

Perfil abrangente do genoma mitocondrial do coelho branco da Nova Zelândia (Oryctolagus cuniculus) utilizando a tecnologia de sequenciamento Nanopore

Authorship SCIMAGO INSTITUTIONS RANKINGS

This study was aimed to discover, identify, and comprehensively explore the characteristics of the complete mitochondrial DNA genomes of the NZW rabbit (Oryctolagus cuniculus). This study utilized genomic DNA (gDNA) which was extracted from New Zealand White (NZW) rabbit’s liver tissue. The extracted gDNA was rigorously evaluated for both quality and quantity to ensure optimal suitability for mitochondrial DNA enrichment. The sequencing process was carried out using whole genome sequencing (WGS) analysis with Nanopore technology, employing the Oxford Nanopore Technologies GridION platform and bioinformatic tools. Data analysis was carried out using the MEGA11 software to uncover potential mutations, assess genetic diversity, genetic distance and visualize the phylogenetic relationships. The NZW rabbit mtDNA genome spans 17,374 bp, with adenine (31.5%) and thymine (28.3%) as the dominant nucleotides. Leucine is the most abundant amino acid (15.82%), while cysteine is the least abundant (0.61%). The s-rRNA and l-rRNA genes are 957 bp and 1,581 bp long, respectively. The 2,000 bp D-loop region contains two repetitive elements: a 20-bp sequence repeated 14 times and a 153-bp sequence repeated 5 times, which differs from that previously reported in other rabbit mtDNA genomes, thus becoming a specific characteristic and a novel finding of this study.

Keywords:
genome; MtDNA; NZW; Nanopore; rabbit

No	Organism Name	Genbank ID	Size	Reference
1	O. cuniculus (Indonesian Local)	-	17,469	(Setiaji et al., 2023)
2	O. cuniculus (Chuanbai Rex)	MN953621	17,174	(Wang et al., 2021)
3	O. cuniculus (New Zealand White)	MH985853	17,418	(Hu et al., 2018)
4	O. cuniculus (Yimeng Wool)	MN296708	16,740	(Yao et al., 2019)
5	O. cuniculus (Fujian Yellow)	MN518689.1	17,000	(Zhou et al., 2021)
6	O. cuniculus (Jiuyi Mountain)	PP357264.1	17,306	(Li and Guo, 2024)
7	L. capensis	GU937113.1	17,722	(Wang and Yang, 2010)
8	L. coreanus	KF040450.1	17,471	(Yu and Kwak, 2013)
9	L. europaeus	KY211025.1	16,680	(Arnason et al., 2002; Nilsson et al., 2003; Giannoulis et al., 2018)
10	L. granatensis	KJ397610.1	16,915	(Melo-Ferreira et al., 2014)
11	L. hainanus	JQ219662.1	16,646	(Wang et al., 2011)
12	L. sinensis	KM362831.1	17,438	(Ding et al., 2016a)
13	L. timidus	KR030072.1	17,749	(Fu, 2015)
14	L. tolai	MN539744.1	17,047	(Ding et al., 2016b; Shan et al., 2020)
15	L. yarkadensis	MN539747.1	16,808	(Shan, 2019; Huang et al., 2019)
16	B. idahoensis	OL436257	17,021	(Saha et al., 2022)

Gene 1	Position		Size (bp)	Nucleotide (%)				Amino Acid			Strand 2
Gene 1	Start	End	Size (bp)	T	C	A	G	Length	Start Codon	Stop Codon	Strand 2
Replication origin	1	11	11	33.3	25.0	41.7	-
ND3	12	285	273	32.2	23.4	31.1	13.2	90	ATC	TAG	H
trnR	275	342	67	35.8	10.4	40.3	13.4				H
ND4L	343	640	297	34.3	25.6	29.6	10.4	98	ATG	TAA	H
ND4	633	2008	1375	29.3	29.1	30.2	11.4	458	ATG	TAT	H
trnH	2011	2080	69	30.4	17.4	37.7	14.5				H
trnS	2080	2139	59	28.8	28.8	25.4	16.9				H
trnL	2139	2209	70	25.7	14.3	41.4	18.6				H
ND5	2209	4021	1812	30.6	27.1	30.8	11.5	603	ATT	TAG	H
ND6	4016	4541	525	40.4	6.5	19.8	33.3	174	ATG	AGG	L
trnE	4541	4609	68	36.8	14.7	30.9	17.6				L
CYTB	4612	5752	1140	28.9	30.4	28.0	12.7	379	ATG	AGG	H
trnT	5751	5817	66	28.8	19.7	28.8	22.7				H
trnP	5817	5883	66	28.8	15.2	21.2	34.8				L
D-loop	5884	7883	2000	27.0	28.5	31.8	12.8				H
trnF	7883	7952	69	21.7	23.2	37.7	17.4				H
s-rRNA	7952	8909	957	23.9	22.0	35.8	18.2				H
trnV	8909	8975	66	27.3	25.8	30.3	16.7				H
l-rRNA	8973	10554	1581	25.4	20.4	36.4	17.8				H
trnL	10554	10629	75	26.7	22.7	32.0	18.7				H
ND1	10631	11588	957	28.8	30.1	28.7	12.3	318	ATG	TAG	H
trnl	11586	11656	70	34.3	11.4	37.1	17.1				H
trnQ	11653	11725	72	31.9	13.9	25.0	29.2				L
trnM	11733	11802	69	27.5	24.6	29.0	18.8				H
ND2	11802	12846	1044	28.3	27.7	34.9	9.2	347	ATT	TAA	H
trnW	12853	12920	67	22.4	23.9	34.3	19.4				H
trnA	12922	12989	67	32.8	14.9	29.9	22.4				L
trnN	12989	13062	73	28.8	17.8	24.7	28.8				L
trnC	13095	13164	69	24.6	21.7	29.0	24.6				L
trnY	13164	13230	66	27.3	16.7	33.3	22.7				L
COX1	13237	14779	1542	31.0	25.3	26.4	17.3	513	ATG	TAG	H
trnS	14781	14850	69	33.3	17.4	21.7	27.5				L
trnD	14853	14922	69	39.1	14.5	36.2	10.1				H
COX2	14922	15606	684	28.7	26.6	30.4	14.3	227	ATG	TAG	H
trnK	15609	15678	69	26.1	18.8	31.9	23.2				H
ATP8	15679	15883	204	28.4	29.4	34.3	7.8	67	ATG	TAA	H
ATP6	15840	16521	681	29.7	29.5	29.5	11.3	226	ATG	TAA	H
COX3	16520	17324	804	29.1	28.5	27.2	15.2	267	ATG	TAG	H
trnG	17304	17374	70	30.3	22.9	32.9	14.3				H
Average				28.3	26.6	31.5	13.6

PGCs	Ala	Cys	Asp	Glu	Phe	Gly	His	Ile	Lys	Leu	Met	Asn	Pro	Gln	Arg	Ser	Thr	Val	Trp	Tyr
ND3	8.89	1.11	3.33	6.67	7.78	4.44	0.00	6.67	3.33	20.00	5.56	4.44	5.56	2.22	1.11	6.67	1.11	3.33	3.33	4.44
ND4L	8.16	3.06	1.02	2.04	7.14	4.08	2.04	7.14	0.00	23.47	8.16	5.10	2.04	2.04	1.02	7.14	5.10	7.14	0.00	4.08
ND4	6.55	0.66	1.09	1.75	3.93	3.71	2.18	9.39	2.62	20.31	6.55	4.15	4.59	2.18	2.18	9.17	9.83	3.06	2.84	3.28
ND5	7.46	0.66	1.82	1.82	7.46	4.48	1.99	10.61	3.32	14.76	5.47	5.80	4.15	3.15	1.33	8.29	9.12	3.65	1.99	2.65
ND6	3.45	0.57	2.87	5.17	7.47	15.52	0.00	6.32	1.15	10.34	8.62	1.15	1.72	0.00	1.15	8.05	3.45	16.09	2.30	4.60
CYTB	6.07	0.79	2.64	1.58	6.86	6.33	3.43	10.29	2.64	15.57	3.17	4.22	6.07	1.58	2.11	6.07	7.65	5.54	3.17	4.22
ND1	8.49	0.63	0.94	3.46	6.29	4.09	1.26	8.18	2.20	19.50	5.66	3.77	6.92	1.89	2.52	7.23	7.55	3.14	2.83	3.46
ND2	5.48	0.00	0.29	1.44	3.75	4.32	1.15	12.10	3.46	16.14	9.51	5.19	6.63	3.75	1.15	7.49	10.37	2.88	2.88	2.02
COX1	8.19	0.19	2.92	2.14	8.38	9.16	3.51	7.02	1.75	11.50	6.24	3.12	5.65	1.17	1.56	5.85	7.41	7.41	3.31	3.51
COX2	3.52	0.88	5.29	5.73	3.52	3.52	3.52	9.25	1.76	14.98	6.17	3.52	6.17	2.64	2.64	9.25	6.61	4.85	2.20	3.96
ATP8	2.99	1.49	1.49	2.99	5.97	0.00	2.99	5.97	7.46	13.43	5.97	1.49	10.45	4.48	0.00	8.96	11.94	2.99	4.48	4.48
ATP6	8.41	0.00	0.44	1.33	5.31	4.87	2.65	11.06	1.77	19.47	5.75	3.54	6.64	3.54	2.21	7.08	9.29	3.98	1.33	1.33
COX3	5.99	0.75	1.12	3.00	8.99	7.87	5.62	5.99	0.75	11.99	3.37	4.12	4.49	3.00	1.87	8.24	8.24	5.62	4.49	4.49
Average	6.72	0.61	1.88	2.52	6.37	5.79	2.50	9.03	2.39	15.82	6.00	4.11	5.34	2.36	1.75	7.59	8.10	5.04	2.73	3.34

Organism	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15
NZW (this study)1
FY2	0.0154
JM3	0.0321	0.0227
IL4	0.0026	0.0164	0.0340
CR5	0.0022	0.0156	0.0332	0.0032
YW6	0.0024	0.0124	0.0161	0.0034	0.0032
L._capensis	0.1993	0.1941	0.2053	0.2122	0.1912	0.1811
L._coreanus	0.1952	0.1925	0.2065	0.1963	0.1885	0.1788	0.0333
L._europaeus	0.1717	0.1754	0.1795	0.1723	0.1713	0.1708	0.0824	0.0774
L._granatensis	0.1787	0.1884	0.1910	0.1795	0.1785	0.1772	0.0340	0.0079	0.0771
L._hainanus	0.1728	0.1838	0.1857	0.1730	0.1741	0.1715	0.0860	0.0810	0.0717	0.0799
L._sinensis	0.1955	0.1923	0.2063	0.1957	0.1884	0.1790	0.0772	0.0735	0.0814	0.0701	0.0825
L._timidus	0.1953	0.1908	0.2052	0.2085	0.1874	0.1773	0.0321	0.0085	0.0766	0.0077	0.0813	0.0734
L._tolai	0.1836	0.1892	0.2017	0.1837	0.1847	0.1774	0.0326	0.0084	0.0749	0.0079	0.0801	0.0710	0.0073
L._yarkandensis	0.1766	0.1871	0.1887	0.1769	0.1770	0.1754	0.0712	0.0669	0.0801	0.0656	0.0829	0.0753	0.0664	0.0660
B._idahoensis	0.1931	0.2047	0.2113	0.1933	0.1920	0.1885	0.1909	0.1859	0.1834	0.1844	0.1786	0.1893	0.1854	0.1815	0.1856

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[TFN1] ¹
ND: NADH dehydrogenase; trnR: tRNA Arginine; trnH: tRNA Histidine; trnS: tRNA Serine; trnL: tRNA Leucine; trnE: tRNA Glutamic acid; CYTB: Cytochrome b; trnT: tRNA Threonine; trnT: tRNA Threonine; Dloop: Displacement loop; trnF: tRNA Phenylalanine; s-rRNA: short ribosomal RNA; trnV: tRNA Valine; l-rRNA: length ribosomal RNA; trnI: tRNA Isoleucine; trnQ: tRNA Glutamine; trnM: tRNA Methionone; trnW: tRNA Tryptophan; trnA: tRNA Alanine; trnN: tRNA Asparagine; trnC: tRNA Cystein; trnY: tRNA Tyrosine; COX: Cytochrome c oxidase; trnD: tRNA Aspartic acid; trnK: tRNA Lysine; ATP: Adenosine triphosphate; trnG: tRNA Glycine.

[TFN2] ²
L: light strand; H: heavy strand.