Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

Sun, Yao; Kurisaki, Masaki; Hashiguchi, Yasuyuki; Kumazawa, Yoshinori

doi:10.1186/s12864-017-4080-0

Table 1 RNA-Seq data analyzed in this study

From: Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

Higher taxa	Family	Species	organ	SRA Accession No.	read length (bp)^a	RNA-Seq total reads^b	mtDNA-derived reads	polyA reads^c	Accession No. of reference mtDNA^d
Squamata Lacertilia	Lacertidae	Takydromus tachydromoides	liver	DRR072216	101	53,655,734	3,627,027	8795	LC101816
	Scincidae	Scincella lateralis	liver	SRR629642	100	91,047,166	5,473,971	3035	KU646826
	Eublepharidae	Eublepharis macularius	liver	SRR629643	100	70,002,306	4,146,912	2889	AB738955
	Shinisauridae	Shinisaurus crocodilurus	liver	DRR034612	151	19,549,612	1,374,172	1280	AB080274
	Agamidae	Pogona vitticeps	liver	SRR629641	100	87,625,132	8,515,182	6198	AB166795
	Agamidae	Phrynocephalus przewalskii	mixed tissue	SRR1298770	100	111,576,922	8,671,591	2155	NC_022719
	Iguanidae	Sceloporus undulatus	liver	SRR629640	100	71,604,846	4,067,660	3333	AB079242
Squamata Serpentes	Viperidae	Agkistrodon piscivorus	liver	SRR629645	100	75,023,884	8,161,006	3236	DQ523161
	Colubridae	Pantherophis guttatus	mixed tissue	ERR216308	100	27,504,812	999,617	700	AM236349
	Xenopeltidae	Xenopeltis unicolor	liver	SRR629647	100	89,792,506	5,340,226	2728	AB179620
Testudines	Chelydridae	Chelydra serpentina	liver	SRR629521	100	67,455,518	2,811,802	1026	EF122793
	Emydidae	Terrapene carolina	liver	SRR629650	100	88,575,286	6,905,832	4410	-
	Kinosternidae	Sternotherus odoratus	liver	SRR629648	100	95,375,174	2,977,994	1985	NC_017607
	Pelomeducidae	Pelusios castaneus	liver	SRR629649	100	90,326,648	8,875,110	4853	KC692463
Crocodylia	Alligatoridae	Alligator mississippiensis	liver	SRR629636	100	72,260,274	3,303,351	4719	Y13113
Aves	Phasianidae	Gallus gallus	liver	ERR348573	100	110,458,976	20,095,817	1182	X52392
	Upupidae	Upupa epops	retina and cochlea	SRR3203224	126	90,142,570	4,448,201	1550	KT356220
	Falconidae	Falco tinnunculus	retina and cochlea	SRR3203231	126	100,655,654	6,448,806	1403	NC_011307
	Accipitridae	Aegypius monachus	retina and cochlea	SRR3203236	126	95,683,290	5,999,094	1818	KF682364
Mammalia	Hominidae	Homo sapiens	brain	SRR611068	101	80,651,654	8,716,424	49,201	NC_012920
	Muridae	Mus musculus	heart and kidney	SRR3655009	151	34,241,696	4,141,929	770	NC_005089
	Elephantidae	Elephas maximus	blood	SRR2911072	100	70,104,696	2,570,995	1531	DQ316068
	Bovidae	Bos taurus	liver	SRR3168807	100*	48,278,779	2,277,754	5086	AF492351
Amphibia	Pipidae	Xenopus tropicalis	brain	SRR1189558	101	31,605,646	1,092,532	706	NC_006839

^aMost are paired-end reads, but a value with an asterisk indicates single-end reads
^bNumber of paired-end (except for B. taurus) RNA-Seq reads
^cSum of numbers of independent polyA-containing reads for all major polyadenylation sites (forward and reverse paired-end reads derived from a common cDNA fragment were merged for the independent counting)
^dAn accession number for T. tachydromoides relates to the mtDNA sequence determined for the RNA-sequenced individual. Accession numbers for the other species correspond to the mtDNA sequences of a conspecific or congeneric individual obtained from the DDBJ/ENA/GenBank database, which was used to infer the mtDNA sequence of the RNA-sequenced individual. An unpublished mtDNA sequence (Yamada, C., unpublished data) was referred to for T. carolina

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ISSN: 1471-2164

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