Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

Nunes, Cristiano C; Gowda, Malali; Sailsbery, Joshua; Xue, Minfeng; Chen, Feng; Brown, Douglas E; Oh, YeonYee; Mitchell, Thomas K; Dean, Ralph A

doi:10.1186/1471-2164-12-288

BMC Genomics

Table 2 Distribution of mycelia small RNAs with perfect map to nuclear and mitochondria genomes.

From: Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

	Alignment^a			Read Count^b			Prorated^c			Features^d
	Total	Sense	Antisense	Total	Sense	Antisense	Total	Sense	Antisense	Mapped	Total	Coverage
Genome	386741	211969	158036	32518	28592	6657	31985	26267	3569	3448	14880	23%
Genes	41318	23046	20923	8459	6213	5095	4226	2522	1704	1156	11043	10%
Introns	5396	3577	1821	1890	1848	263	209	191	17	121	19651	1%
Exons	36860	20202	19302	8270	5702	5075	4017	2331	1686	1200	30705	4%
5' UTR^e	11416	5020	6505	4907	3147	3204	2103	971	1132	223	11241	2%
EST Supp.	3337	1715	1729	1151	502	844	691	100	590	83	2558	3%
Unsupp.	8079	3306	4777	3955	2760	2496	1412	870	542	151	8683	2%
CDS	4111	2959	1154	2463	2170	422	887	800	87	720	30486	2%
EST Supp.	2607	1636	973	1177	930	354	686	628	58	561	18154	3%
Unsupp.	1504	1324	182	1406	1302	136	201	172	29	159	12332	1%
3' UTR	23571	13686	12378	4347	3253	3342	1027	560	467	342	11076	3%
EST Supp.	3609	1882	1777	662	603	315	218	170	48	156	2551	6%
Unsupp.	19962	11805	10602	3921	2870	3243	810	390	419	198	8525	2%
tRNA^f	30934	25184	5752	5555	5468	89	4018	3983	35	338	341	99%
5' Leader	2020	1975	47	1494	1452	44	375	375	0	112	341	33%
Mature	19615	19336	281	4243	4241	4	3137	3134	2	338	341	99%
3' Term	12937	7510	5429	1841	1799	44	506	474	32	209	341	61%
rRNA	67781	67765	18	19559	19550	11	18197	18188	9	48	48	100%
5.8 S	1630	1630	1	950	950	1	950	950	0	3	3	100%
8 S	36761	36761	1	1141	1141	1	804	804	0	41	41	100%
18 S	5185	5183	4	5185	5183	4	4242	4240	2	2	2	100%
28 S	24205	24192	15	12283	12277	8	12201	12194	7	2	2	100%
snRNA	162	162	1	129	129	1	90	90	0	8	14	57%
Transposable Elements	248528	113951	134620	3369	1522	1883	3305	1484	1821	1898	3448	55%
Intergenic	35342	-	-	4175	-	-	2150	-	-	-	-	-
Mitochondria	1448	1423	13	1445	1422	13	912	886	10	36	37	97%
Genes	961	950	13	961	950	13	216	206	10	15	15	100%
CDS	17	17	1	17	17	1	16	16	0	7	16	44%
tRNA	1074	1074	1	1073	1073	1	464	464	0	18	20	90%
Mature	346	346	1	345	345	1	107	107	0	18	20	90%
rRNA	314	314	1	314	314	1	216	216	0	2	2	100%
Intergenic	18	-	-	18	-	-	16	-	-	-	-	-

^a Alignment refers to the summation of small RNA alignments to any genomic feature.
^b Read Count represents the summation of distinct reads mapping to a given feature. Noteworthy the values for each genome feature are generally less than the sum of its sub-features due to the small RNAs mapping to multiple features (See "Material and Methods" for more details).
^c Prorated apportions the weight of any small RNA between alignments and features.
^d Features represent the proportion of genomic features mapped by small RNAs where mapped indicates the number of members for each genomic feature mapped by small RNAs among the total possible.
^e Values indicate number of small RNAs that mapped to sub-features within gene models that are supported by ESTs (EST Supp.) or have no EST supporting evidence (Unsupp.)
^f tRNA entries include pseudo-tRNAs.

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ISSN: 1471-2164

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