Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs

Li, Song; Mead, Edward A; Liang, Shaohui; Tu, Zhijian

doi:10.1186/1471-2164-10-581

Table 1 Sequence, location, and expression of miRNAs in Aedes aegypti.

From: Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs

Name ^{1, 2}	mirBase Name	Sequence ³	Contig ⁴	Start ⁴	End ⁴	Strand	Embryo ⁵	Gut_SF ⁵	Gut_BF ⁵
aae-miR-M1-1	aae-miR-2943-1	TTAAGTAGGCACTTGCAGGCAAA	CONTIG_15246	25749	25829	+	28	0	0
aae-miR-M1-2	aae-miR-2943-2	TTAAGTAGGCACTTGCAGGCAAA	CONTIG_15246	25911	25981	+	28	0	0
aae-miR-M2	aae-miR-2942	TATTCGAGACTTCACGAGTTAAT	CONTIG_11944	151669	151750	+	0	0	7
aae-miR-M3	aae-miR-2945	TGACTAGAGGCAGACTCGTTTA	CONTIG_2929	123975	124056	+	33	0	6
aae-miR-M3*	aae-miR-2945*	AGCGGGTCCGTTTCTAGTGTCATG	CONTIG_2929	123975	124056	+	3	0	0
aae-miR-M4a	aae-miR-2944a	GAAGGAACTTCTGCTGTGATCTGA	CONTIG_18252	93868	93929	+	91	2	0
aae-miR-M4a*	aae-miR-2944a*	TATCACAGTAGTTGTACTTTAA	CONTIG_18252	93868	93929	+	3	0	0
aae-miR-M4b	aae-miR-2944b	GAAGGAACTCCCGGTGTGATATA	CONTIG_18252	93731	93792	+	62	0	0
aae-miR-M4b*	aae-miR-2944b*	TATCACAGCAGTAGTTACCTGA	CONTIG_18252	93731	93792	+	24	0	0
aae-miR-N1-1	aae-miR-2941-2	TAGTACGGCTAGAACTCCACGGA	CONTIG_16241	318005	318105	-	288	1	1
aae-miR-N1-2	aae-miR-2941-1	TAGTACGGCTAGAACTCCACGGA	CONTIG_16241	317700	317799	-	288	1	1
aae-miR-N2	aae-miR-2946	TAGTACGGAAAAGATATGGGGA	CONTIG_16241	318135	318222	-	5	0	0
aae-miR-1174	aae-miR-1174	TCAGATCTACTTAATACCCAT	CONTIG_7232	17531	17665	+
aae-miR-1175	aae-miR-1175	TGAGATTCTACTTCTCCGACTTAA	CONTIG_7232	17737	17816	+	0	0	1
aae-miR-1175*	aae-miR-1175*	TAAGTGGAGTAGTGGTCTCATCGCT	CONTIG_7232	17737	17816	+	0	2	59
aae-miR-1890	aae-miR-1890	TGAAATCTTTGATTAGGTCT GG	CONTIG_10435	60786	60931	+	1	0	0
aae-miR-1891-1	aae-miR-1891-1	TGAGGAGTTAATTTGCGTGTTT	CONTIG_10244	3984	4069	-	2	0	0
aae-miR-1891-2	aae-miR-1891-2	TGAGGAGTTAATTTGCGTGTTT	CONTIG_18287	4656	4741	+	2	0	0
aae-miR-1889	aae-miR-1889	CACGTTACAGATTGGGGTTTCC	CONTIG_4323	23786	23921	-	0	0	3
aae-bantam	aae-bantam	TGAGATCATTTTGAAAGCTGATT	CONTIG_3301	208288	208426	-	1	2	2
aae-let-7	aae-let-7	TGAGGTAGTTGGTTGTATAGT	CONTIG_2929	321614	321684	+	0	0	5
aae-miR-1	aae-miR-1	TGGAATGTAAAGAAGTATGGAG	CONTIG_25061	66256	66338	+	1	0	1
aae-miR-10	aae-miR-10	ACCCTGTAGATCCGAATTTGTT	CONTIG_17639	8749	8833	+	1	0	0
aae-miR-100	aae-miR-100	AACCCGTAGATCCGAACTTGTG	CONTIG_2929	307441	307568	+
aae-miR-1000-1	aae-miR-1000-1	ATATTGTCCTGTCACAGCAGT	CONTIG_35246	172	265	-
aae-miR-1000-2	aae-miR-1000-2	ATATTGTCCTGTCACAGCAGT	CONTIG_9774	12985	13078	+
aae-miR-11	aae-miR-11	CATCACAGTCTGAGTTCTTGCTT	CONTIG_23911	46399	46488	+	1861	42	436
aae-miR-11*	aae-miR-11*	CGAGAACTCCGGCTGTGACCTGTG	CONTIG_23911	46399	46488	+	4	0	2
aae-miR-12	aae-miR-12	TGAGTATTACATCAGGTACTGGT	CONTIG_4323	23386	23503	-
aae-miR-124	aae-miR-124	TAAGGCACGCGGTGAATGCCAAG	CONTIG_531	21343	21423	-	3	0	0
aae-miR-125	aae-miR-125	TCCCTGAGACCCTAACTTGTGA C	CONTIG_2929	321885	321975	+	0	0	3
aae-miR-133	aae-miR-133	TTGGTCCCCTTCAACCAGCTGT	CONTIG_24522	50243	50347	-
aae-miR-137-1	aae-miR-137-1	TTATTGCTTGAGAATACACGTA	CONTIG_7773	15414	15486	-
aae-miR-137-2	aae-miR-137-2	TTATTGCTTGAGAATACACGTA	CONTIG_29705	92457	92529	+
aae-miR-13b	aae-miR-13	TATCACAGCCATTTTGACGAGTT	CONTIG_12793	17619	17710	-	168	2	42
aae-miR-14	aae-miR-14	TCAGTCTTTTTCTCTCTCCTAT	CONTIG_12112	693	785	-	1	1	6
aae-miR-184	aae-miR-184	TGGACGGAGAACTGATAAGGGC	CONTIG_19030	3452	3535	-	957	76	1307
aae-miR-190	aae-miR-190	AGATATGTTTGATATTCTTGGTTG	CONTIG_10108	2092	2180	-	83	2	43
aae-miR-193	aae-miR-193	TACTGGCCTACTAAGTCCCAAC	CONTIG_19568	51035	51158	+
aae-miR-2a	aae-miR-2a	TATCACAGCCAGCTTTGATGAGCT	CONTIG_12793	16130	16216	-	1217	80	249
aae-miR-210	aae-miR-210	TTGTGCGTGTGACAACGGCTAT	CONTIG_19443	85221	85292	-	3	12	12
aae-miR-219	aae-miR-219	TGATTGTCCAAACGCAATTCTTG	CONTIG_15776	56993	57078	+
aae-miR-2b	aae-miR-2b	TATCACAGCCAGCTTTGAAGAGCG	CONTIG_12793	17471	17562	-	758	74	147
aae-miR-2c	aae-miR-2c	TATCACAGCCAGCTTTGATGAGC	CONTIG_12793	17971	18048	-	1218	80	249
aae-miR-252	aae-miR-252	CTAAGTACTAGTGCCGCAGGAGA	CONTIG_3685	79002	79177	-	38	0	1
aae-miR-252*	aae-miR-252*	CCTGCTGCCCAAGTGCTTATCGAA	CONTIG_3685	79002	79177	-	5	0	0
aae-miR-263	aae-miR-263a	AATGGCACTGGAAGAATTCACGGG	CONTIG_27430	4746	4821	-	53	1	1
aae-miR-263*	aae-miR-263a*	CGTGTTCTGGCAGTGGCATCCC	CONTIG_27430	4746	4821	-	6	0	0
aae-miR-263b	aae-miR-263b	CTTGGCACTGGGAGAATTCACAG	CONTIG_1908	33267	33357	+	6	0	0
aae-miR-263b*	aae-miR-263b*	TGGATCTTTTCGTGCCATCGT	CONTIG_1908	33267	33357	+	1	0	0
aae-miR-275	aae-miR-275	TCAGGTACCTGAAGTAGCGCGCG	CONTIG_1651	96625	96720	+	0	0	5
aae-miR-275*	aae-miR-275*	CGCGCTAAGCAGGAACCGAGACT	CONTIG_1651	96625	96720	+	1	0	6
aae-miR-276-1	aae-miR-276-1	TAGGAACTTCATACCGTGCTCT	CONTIG_417	10988	11177	-
aae-miR-276-2	aae-miR-276-2	TAGGAACTTCATACCGTGCTCT	CONTIG_7617	38953	39087	+
aae-miR-277	aae-miR-277	TAAATGCACTATCTGGTACGACA	CONTIG_12646	3556	3644	+
aae-miR-278	aae-miR-278	TCGGTGGGACTTTCGTCCGTTT	CONTIG_1172	33037	33128	+	6	0	2
aae-miR-279	aae-miR-279	TGACTAGATCCACACTCATTAA	CONTIG_17556	116934	117006	-	26	0	2
aae-miR-281	aae-miR-281	CTGTCATGGAATTGCTCTCTTTA	CONTIG_27100	34036	34204	+	1	16	50
aae-miR-281*	aae-miR-281*	AAAGAGAGCTATCCGTCGACAGTA	CONTIG_27100	34036	34204	+	164	5686	4806
aae-miR-282-1	aae-miR-282-1	AATCTAGCCTCTCCTAGGCTTTGTCTG	CONTIG_15805	19414	19548	+
aae-miR-282-1*	aae-miR-282-1*	ACATAGCCTGACAGAGGTTAGG	CONTIG_15805	19414	19548	+	2	0	0
aae-miR-282-2	aae-miR-282-2	AATCTAGCCTCTCCTAGGCTTTGTCTG	CONTIG_15982	5479	5613	-
aae-miR-282-2*	aae-miR-282-2*	ACATAGCCTGACAGAGGTTAGG	CONTIG_15982	5479	5613	-	2	0	0
aae-miR-283	aae-miR-283	CAATATCAGCTGGTAATTCTGG G	CONTIG_4323	32334	32426	-	6	1	131
aae-miR-285	aae-miR-285	TAGCACCATTCGAAATCAGT	CONTIG_1634	212427	212492	-	0	1	0
aae-miR-286a-1	aae-miR-286b-1	TGACTAGACCGAACACTCGTATCC	CONTIG_21241	18407	18503	+	8	0	0
aae-miR-286a-2	aae-miR-286b-2	TGACTAGACCGAACACTCGTATCC	CONTIG_8291	17656	17752	+	8	0	0
aae-miR-286b	aae-miR-286a	TGACTAGACCGAACACTCGCGTC CT	CONTIG_18252	93413	93509	+	10	0	0
aae-miR-305	aae-miR-305	ATTGTACTTCATCAGGTGCTCTGG	CONTIG_1651	105677	105766	+	0	0	2
aae-miR-305*	aae-miR-305*	CGGCACATGTTGGAGTACACTTAA	CONTIG_1651	105677	105766	+	0	0	7
aae-miR-306	aae-miR-306	TCAGGTACTGAGTGACTCTCAG	CONTIG_24640	55004	55128	+	119	0	27
aae-miR-307	aae-miR-307	TCACAACCTCCTTGAGTGAGCGA	CONTIG_1157	147943	148043	-	1	0	0
aae-miR-308	aae-miR-308	AATCACAGGAGTATACTGTGAG	CONTIG_6324	6462	6528	+
aae-miR-308*	aae-miR-308*	CGCGGTATATTCTTGTGGCTTGA	CONTIG_6324	6462	6528	+	2	0	0
aae-miR-31	aae-miR-31	TGGCAAGATGTTGGCATAGCTGAAA	CONTIG_21960	98153	98301	-	1	0	3
aae-miR-315	aae-miR-315	TTTTGATTGTTGCTCAGAAAGCC	CONTIG_21501	12498	12562	+	27	1	0
aae-miR-315*	aae-miR-315*	CTTTCGAGCAGTAATCAAAGTc	CONTIG_21501	12498	12562	+	5	0	0
aae-miR-316	aae-miR-316	TGTCTTTTTCCGCTTACTGCCG	CONTIG_13460	10738	10828	-	0	0	1
aae-miR-317-1	aae-miR-317-1	TGAACACAGCTGGTGGTATCTCAGT	CONTIG_12640	88437	88524	+	36	38	737
aae-miR-317-2	aae-miR-317-2	TGAACACAGCTGGTGGTATCTCAGT	CONTIG_8451	9550	9637	-	36	38	737
aae-miR-3a-1	aae-miR-309a-1	TCACTGGGCAAAGTTTGTCGCA	CONTIG_21241	18967	19043	+	6	0	0
aae-miR-3a-2	aae-miR-309a-2	TCACTGGGCAAAGTTTGTCGCA	CONTIG_8291	18216	18292	+	6	0	0
aae-miR-3b	aaw-miR-309b	TCACTGGGCATAGTTTGTCGCA	CONTIG_18252	94047	94117	+	3	0	0
aae-miR-3b*	aae-miR-309b*	CGTCAAACTCCGTTCAGTTGGTG	CONTIG_18252	94047	94117	+	1	0	0
aae-miR-33	aae-miR-33	GTGCATTGTAGTTGCATTGCA	CONTIG_18815	108787	108866	+
aae-miR-34	aae-miR-34	TGGCAGTGTGGTTAGCTGGTTGTG	CONTIG_12646	4278	4400	+	44	55	639
aae-miR-375	aae-miR-375	TTTGTTCGTTTGGCTCGAGTTA	CONTIG_14081	238834	238944	-	1	0	0
aae-miR-7	aae-miR-7	TGGAAGACTAGTGATTTTGTTGTT	CONTIG_31115	46028	46112	+	14	0	0
aae-miR-71	aae-miR-71	AGAAAGACATGGGTAGTGAGATA	CONTIG_12793	18215	18396	-	39	2	7
aae-miR-71*	aae-miR-71*	TCTCACTACCTTGTCTTTCATG	CONTIG_12793	18215	18396	-	6	0	0
aae-miR-79	aae-miR-79	ATAAAGCTAGATTACCAAAGCAT	CONTIG_24640	55215	55284	+	2	0	0
aae-miR-8	aae-miR-8	TAATACTGTCAGGTAAAGATGTC	CONTIG_16942	34594	34660	+	32	1	38
aae-miR-8*	aae-miR-8*	CATCTTACCGGGCAGCATTAGA	CONTIG_16942	34594	34660	+	7	2	4
aae-miR-87	aae-miR-87	GGTGAGCAAATTTTCAGGTGT	CONTIG_15587	30157	30251	+
aae-miR-927	aae-miR-927	TTTAGAATTCCTACGCTTTACC	CONTIG_1795	170460	170534	+
aae-miR-929-1	aae-miR-929-1	ATTGACTCTAGTAGGGAGTCC	CONTIG_12461	76647	76734	-
aae-miR-929-2	aae-miR-929-2	ATTGACTCTAGTAGGGAGTCC	CONTIG_34315	3294	3381	+
aae-miR-92a	aae-miR-92a	TATTGCACTTGTCCCGGCCTAT	CONTIG_6821	67755	67832	+	74	0	5
aae-miR-92a*	aae-miR-92a*	CGGTACGGACAGGGGCAACATT	CONTIG_6821	67755	67832	+	6	0	0
aae-miR-92b	aae-miR-92b	AATTGCACTTGTCCCGGCCTGC	CONTIG_6824	4049	4131	+	74	0	5
aae-miR-92b*	aae-miR-92b*	AGGTCGTGACTTGTGCCCGTTTG	CONTIG_6824	4049	4131	+	12	0	0
aae-miR-932	aae-miR-932	TCAATTCCGTAGTGCATTGCAG	CONTIG_28378	72232	72319	-
aae-miR-957	aae-miR-957	TGAAACCGTCCAAAACTGAGGC	CONTIG_591	147619	147787	+
aae-miR-965	aae-miR-965	TAAGCGTATAGCTTTTCCC	CONTIG_3410	87378	87524	+
aae-miR-970	aae-miR-970	TCATAAGACACACGCGGCTAT	CONTIG_11324	29252	29338	+	1	0	3
aae-miR-981	aae-miR-981	TTCGTTGTCGACGAAACCTGCA	CONTIG_7302	184768	184853	-
aae-miR-988	aae-miR-988	CCCCTTGTTGCAAACCTCACGC	CONTIG_17684	77966	78086	-	3	0	1
aae-miR-988*	aae-miR-988*	GTGTGCTTTGTGACAATGAGA	CONTIG_17684	77966	78086	-	2	0	2
aae-miR-989	aae-miR-989	TGTGATGTGACGTAGTGGTAC	CONTIG_6774	51048	51137	-	2	33	3
aae-miR-993	aae-miR-993	GAAGCTCGTTTCTATAGAGGTATCT	CONTIG_28305	82579	82660	+
aae-miR-996	aae-miR-996	TGACTAGATTACATGCTCGTCT	CONTIG_17556	112174	112267	-
aae-miR-998	aae-miR-998	TAGCACCATGAGATTCAGCTC	CONTIG_23911	46676	46764	+	164	6	42
aae-miR-999	aae-miR-999	TGTTAACTGTAAGACTGTGTCT	CONTIG_6027	163128	163269	+
aae-miR-9a-1	aae-miR-9a-1	TCTTTGGTTATCTAGCTGTATGA	CONTIG_19539	116871	116951	+	16	1	2
aae-miR-9a-2	aae-miR-9a-2	TCTTTGGTTATCTAGCTGTATGA	CONTIG_19541	4061	4141	+	16	1	2
aae-miR-9b	aae-miR-9b	TCTTTGGTGATTTTAGCTGTATGC	CONTIG_24640	55513	55604	+	134	0	69
aae-miR-9c	aae-miR-9c	TCTAAAGCTTTAGTACCAGAGGTC	CONTIG_24640	28160	28257	+	5	0	0
aae-miR-iab-4-1	aae-miR-iab-4-1	CGGTATACCTTCAGTATACGTAAC	CONTIG_17255	44653	44726	-
aae-miR-iab-4-2	aae-miR-iab-4-2	CGGTATACCTTCAGTATACGTAAC	CONTIG_23219	23581	23654	+

Notes:
1. The first block (miR-M1-1 through miR-N2) are novel miRNAs that are discovered in this study. We have not detected homology to any known miRNAs or genomic sequences outside of mosquito species. The second block (miR-1174 through miR-1889) contains miRNAs that are homologous to previously reported "mosquito-specific" miRNAs. The third block, comprised of the remaining miRNAs, contains miRNAs that have homologues outside of mosquitoes.
2. Naming in this column is temporary. Mirbase assigned names are shown in column 2, which was received after the acceptance of the manuscript. "-1", and "-2" suffixes refer to different hairpins that produce the same mature miRNA. "a", and "b" suffixes refer to different hairpins that produce similar but not identical miRNAs.
3. Underlined sequences are cases where there are extra bases at the 5' or 3' ends and they are the majority in at least six small RNA sequences. Italicized sequences are cases where such sequences are detected but they are either not the majority or there are less than six 454 sequence hits. As poly-As are added to the small RNAs, adenine(s) at the 3' end cannot be confirmed by this sequencing approach.
4. The contig, start, and end positions refer to the locations of the pre-miRNA hairpins.
5. The last three columns are the number of sequence hits in small RNA libraries obtained by 454 sequencing. The total small RNA reads are 55, 000, 33, 000, and 42, 000 in embryos, sugar-fed midguts (Gut_SF), and blood-fed midguts (Gut_BF), respectively. The total number of hits for all Ae. aegypti miRNAs are 8369, 6260, and 9922 in embryos, sugar-fed midguts (Gut_SF), and blood-fed midguts (Gut_BF), respectively. There are a few cases where we did not distinguish the hits from nearly identical miRNAs.

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ISSN: 1471-2164

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