Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

Brown, Steven D; Nagaraju, Shilpa; Utturkar, Sagar; De Tissera, Sashini; Segovia, Simón; Mitchell, Wayne; Land, Miriam L; Dassanayake, Asela; Köpke, Michael

doi:10.1186/1754-6834-7-40

Biotechnology for Biofuels and Bioproducts

Table 3 Regions of low sequence-coverage

From: Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

Locus tag	Start^a	End^a	Product description	Pacbio coverage (×^b)	454 Coverage (×)	Illumina coverage (×)	454 Hybrid contig coverage^c	Draft assembly contig coverage
CAETHG_0145	156117	156914	Methionine synthase	87	26	62	Complete	Partial
CAETHG_0152	161167	161292	Hypothetical protein	94	16	55	Complete	Partial
CAETHG_0153	161313	161963	Dihydropteroate synthase DHPS	93	22	46	Complete	Partial
CAETHG_0433	472649	474331	Transcriptional regulator, PucR family	110	25	57	Complete	Partial
CAETHG_0601	661798	663339	Citrate lyase, alpha subunit	109	25	64	Partial	Partial
CAETHG_0602	663332	664234	Citrate lyase, beta subunit	111	29	65	None	None
CAETHG_0603	664234	664530	Citrate lyase acyl carrier protein	107	29	63	None	None
CAETHG_0604	664553	665587	Citrate lyase ligase	109	23	63	None	Partial
CAETHG_0605	665628	666806	Malic protein NAD-binding protein	101	27	69	None	None
Intergenic	827340	827520	NA	106	30	53	None	None
CAETHG_0774	832108	833028	SufBD protein	109	23	65	Complete	Partial
CAETHG_0814	873533	874333	Hypothetical protein	106	23	69	Complete	None
CAETHG_0815	874375	874953	Hypothetical protein	102	23	55	Complete	None
rRNA	885055	887942	23s_rRNA	87	77	147	None	None
rRNA	888206	889703	16s_rRNA	102	56	165	None	None
CAETHG_0871	940541	941353	3-dehydroquinate dehydratase	109	27	59	Complete	Partial
CAETHG_1038	1116305	1121431	Cell wall binding repeat 2-containing protein	127	27	69	Partial	None
CAETHG_1052	1136476	1138017	Citrate lyase, alpha subunit	107	22	53	Partial	None
CAETHG_1053	1138010	1138912	Citrate lyase, beta subunit	106	29	75	Complete	None
CAETHG_1054	1138912	1139208	Citrate lyase acyl carrier protein	109	37	70	Complete	None
CAETHG_1055	1139370	1140533	Malic protein NAD-binding protein	107	27	51	Partial	Partial
Intergenic	1148600	1148780	NA	131	16	63	Complete	None
CAETHG_1100	1186843	1187643	Hypothetical protein	118	23	68	Complete	None
CAETHG_1101	1187685	1188263	Hypothetical protein	105	28	59	Complete	None
CAETHG_1630	1752229	1753149	SufBD protein	118	26	79	Complete	Partial
CAETHG_1634	1755642	1756505	modD protein	115	22	69	Complete	Partial
CAETHG_1708	1841018	1841572	Lumazine-binding	132	23	66	Complete	Complete
CAETHG_1816	1956238	1956534	Microcompartments protein	138	35	76	Complete	Partial
CAETHG_1817	1956609	1956899	Microcompartments protein	139	19	81	Complete	None
CAETHG_1818	1956948	1957598	Propanediol utilization protein	144	24	74	Complete	None
CAETHG_1819	1957600	1959153	Acetaldehyde dehydrogenase (acetylating)	153	25	67	Complete	None
CAETHG_1826	1963196	1964038	Ethanolamine utilization protein EutJ family protein	161	34	73	Complete	Partial
CAETHG_1827	1964020	1964790	Hypothetical protein	162	22	68	Complete	Partial
CAETHG_1949	2079078	2080271	Hypothetical protein	161	30	79	Complete	Partial
CAETHG_1963	2095013	2096206	Hypothetical protein	128	36	97	Complete	Partial
tRNA	2113813	2113886	tRNA_Met	128	15	61	None	Complete
rRNA	2114155	2117042	23s_rRNA	122	81	161	None	None
rRNA	2117334	2118831	16s_rRNA	118	66	128	None	None
tRNA	2135117	2135189	tRNA_Met	132	22	64	Complete	None
tRNA	2135201	2135286	tRNA_Leu	133	16	59	Complete	None
tRNA	2135301	2135374	tRNA_Met	133	17	57	Complete	None
tRNA	2135394	2136466	tRNA_Met	139	35	74	Complete	None
tRNA	2135478	2135563	tRNA_Leu	140	30	62	Complete	None
CAETHG_2076	2220169	2221506	Sigma54 specific transcriptional regulator, Fis family	122	32	85	Partial	Partial
CAETHG_2077	2221658	2221885	Transcriptional regulator, Fis family	126	21	92	Partial	None
CAETHG_2078	2222014	2222994	Putative sigma54 specific transcriptional regulator	135	30	77	Partial	Partial
rRNA	2271738	2273235	16s_rRNA	165	10	26	None	None
rRNA	2273527	2276414	23s_rRNA	158	10	26	None	None
tRNA	2276744	2276817	tRNA_Met	153	28	70	None	Complete
rRNA	2355334	2356831	16s_rRNA	145	11	24	None	None
rRNA	2357123	2360010	23s_rRNA	136	13	23	None	None
tRNA	2360340	2360412	tRNA_Lys	122	15	65	Complete	Partial
rRNA	2372238	2373735	16s_rRNA	128	13	21	None	None
rRNA	2374027	2376914	23s_rRNA	126	14	19	None	None
rRNA	2392702	2394199	16s_rRNA	134	12	20	None	None
rRNA	2394596	2397483	23s_rRNA	142	11	21	None	None
CAETHG_2238	2397706	2397882	Hypothetical protein	138	23	57	Partial	Complete
CAETHG_2268	2424703	2425503	Integrase catalytic region	115	26	61	Complete	None
CAETHG_2269	2425545	2426123	Hypothetical protein	124	26	56	Complete	None
Intergenic	2666300	2666515	NA	145	25	69	Complete	None
Intergenic	2710650	2710840	NA	124	36	71	Complete	None
CAETHG_2526	2714747	2715550	Hypothetical protein	133	28	74	Complete	Partial
Intergenic	2769840	2769880	NA	124	23	67	Complete	None
CAETHG_2620	2822788	2823741	Transposase IS66	124	30	59	Partial	Complete
CAETHG_2621	2823723	2824328	Transposase IS66	127	30	52	Partial	Partial
rRNA	2935186	2936683	16s_rRNA	127	14	27	None	None
tRNA	2936973	2937045	tRNA_Ala	125	19	51	None	None
tRNA	2937053	2937126	tRNA_Ile	125	26	58	None	None
rRNA	2937443	2940330	23s_rRNA	117	14	28	None	None
rRNA	2966992	2968489	16s_rRNA	126	11	20	None	None
tRNA	2968779	2968851	tRNA_Ala	132	20	50	None	None
tRNA	2968859	2968932	tRNA_Ile	131	23	70	None	None
rRNA	2969222	2972109	23s_rRNA	128	10	19	None	None
CAETHG_2843	3078642	3079445	Dihydropteroate synthase DHPS	152	30	66	Complete	Partial
CAETHG_2844	3079499	3080131	Hypothetical protein	148	32	71	Complete	Partial
CAETHG_2848	3085939	3086742	Dihydropteroate synthase DHPS	146	27	66	Complete	Partial
CAETHG_2849	3086796	3087428	Hypothetical protein	139	31	75	Complete	Partial
CAETHG_3037	3301321	3302088	MCP methyltransferase, CheR-type	149	23	65	Complete	Partial
CAETHG_3075	3342748	3343524	Transposase IS66	112	39	74	Complete	Partial
CAETHG_3281	3537107	3537880	Hypothetical protein	109	27	55	Complete	Partial
CAETHG_3282	3537862	3538704	Ethanolamine utilization protein	107	30	62	Complete	None
CAETHG_3283	3538721	3539026	Microcompartments protein	103	20	65	Complete	None
CAETHG_3284	3539020	3539286	Ethanolamine utilization protein EutN/carboxysome structural protein Ccml	106	25	55	Complete	None
CAETHG_3285	3539304	3539975	Ethanolamine utilization EutQ family protein	110	29	63	Complete	None
CAETHG_3286	3540008	3540784	Microcompartments protein	106	30	61	Complete	None
CAETHG_3287	3540833	3542350	Acetaldehyde dehydrogenase (acetylating)	111	27	61	Complete	Partial
Intergenic	3848150	3848350	NA	126	34	39	Complete	None
rRNA	3872016	3873511	16s_rRNA	98	10	18	None	None
rRNA	3873937	3876824	23s_rRNA	107	14	21	None	None
CAETHG_4028	4315106	4316413	VanW family protein	98	24	66	Complete	Partial
CAETHG_4029	4316730	4319132	Collagen triple helix repeat-containing protein	94	13	38	Complete	Partial
CAETHG_4035	4325792	4326292	VanW family protein	78	21	54	Complete	Partial

^aThe genomic regions which were not assembled in 454/Draft assembly are listed above; ^bthe ‘x’ coverage defines the raw-read coverage averaged over given coordinates; ^c‘Complete/partial’ contig coverage defines whether the region was completely/partially assembled while ‘None’ defines that this region is missing in the respective assembly. Missing regions in either 454/Draft assembly are shown in bold.

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ISSN: 2731-3654

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