Lunardon et al. 2020

accession	aligned reads	unaligned reads	source db	is refset? Alignments that are reference sets (value of 1) are mergers of other component libraries used to compile master small RNA annotations for a species.	tissue	ecotype / cultivar	genotype	replicate id Alignments that are biological replicates have the same replicate ids	refset id If set, the alignment is part of the indicated reference set	description
ERR493659	6,562,679	3,602,419	SRA	0	fruit	M82	wt	A	1	fruit (ripe) -- control conditions
SRR1061628	4,192,124	2,378,026	SRA	0	leaf	Pusa Ruby	wt	AA	1	leaf (4-6 leaf stage) -- mock infiltration
SRR1061629	4,148,179	1,206,808	SRA	0	leaf	Pusa Ruby	wt	AB	1	leaf (4-6 leaf stage) -- infiltrated with A. tumefaciens EHA105 harboring plasmid constructs with dimers of the Tomato leaf curl New Delhi virus ToLCNDV-A [HQ264185.1] and ToLCNDV-B [HQ2641856.1] genome components
SRR1258335	3,702,100	728,667	SRA	0	leaf	Micro-Tom	wt	AC	1	leaf (2-weeks-old plants -- upper systemic leaves) -- 20 days post inoculation with mock treatment
SRR1258336	3,772,176	1,213,951	SRA	0	leaf	Micro-Tom	wt	AD	1	leaf (2-weeks-old plants -- upper systemic leaves) -- 20 days post inoculation with Cucumber mosaic virus-Fny
SRR1344486	19,667,605	2,383,776	SRA	0	fruit pericarp	Ailsa Craig	wt	AE	1	fruit pericarp (37 days post-anthesis -- immature green) -- control conditions
SRR1344487	18,889,363	2,292,327	SRA	0	fruit pericarp	Ailsa Craig	wt	AE	1	fruit pericarp (37 days post-anthesis -- immature green) -- control conditions
SRR1344488	20,700,773	1,642,296	SRA	0	fruit pericarp	Ailsa Craig	wt	AF	1	fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions
SRR1344489	18,475,951	1,470,936	SRA	0	fruit pericarp	Ailsa Craig	wt	AF	1	fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions
SRR1344490	16,746,083	1,791,580	SRA	0	fruit pericarp	Ailsa Craig	wt	AG	1	fruit pericarp (51 days post-anthesis -- pink stage) -- control conditions
SRR1344491	19,059,238	2,082,276	SRA	0	fruit pericarp	Ailsa Craig	wt	AG	1	fruit pericarp (51 days post-anthesis -- pink stage) -- control conditions
SRR1344492	17,551,713	1,938,008	SRA	0	fruit pericarp	Ailsa Craig	wt	AH	1	fruit pericarp (56 days post-anthesis -- red ripe stage) -- control conditions
SRR1344493	14,182,318	1,564,258	SRA	0	fruit pericarp	Ailsa Craig	wt	AH	1	fruit pericarp (56 days post-anthesis -- red ripe stage) -- control conditions
SRR1344494	17,794,687	1,419,209	SRA	0	fruit pericarp	Ailsa Craig	rin	AI	1	fruit pericarp (37 days post-anthesis -- immature green) -- control conditions
SRR1344495	20,031,720	1,593,361	SRA	0	fruit pericarp	Ailsa Craig	rin	AI	1	fruit pericarp (37 days post-anthesis -- immature green) -- control conditions
SRR1344496	18,428,513	1,678,797	SRA	0	fruit pericarp	Ailsa Craig	rin	AJ	1	fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions
SRR1344497	19,055,486	1,908,180	SRA	0	fruit pericarp	Ailsa Craig	rin	AJ	1	fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions
SRR1344499	18,224,406	1,536,579	SRA	0	fruit pericarp	Ailsa Craig	rin	AK	1	fruit pericarp (56 days post-anthesis -- yellow ripe stage) -- control conditions
SRR1344500	17,123,670	1,449,018	SRA	0	fruit pericarp	Ailsa Craig	rin	AK	1	fruit pericarp (56 days post-anthesis -- yellow ripe stage) -- control conditions
SRR1344501	18,608,501	1,549,988	SRA	0	fruit pericarp	Ailsa Craig	rin	AL	1	fruit pericarp (51 days post-anthesis -- yellow stage) -- control conditions
SRR1344502	19,326,582	1,655,886	SRA	0	fruit pericarp	Ailsa Craig	rin	AL	1	fruit pericarp (51 days post-anthesis -- yellow stage) -- control conditions
SRR1609934	11,296,641	1,202,336	SRA	0	leaf	Micro-Tom	wt	AM	1	leaf (45-days-old plants -- young leaves) -- control conditions
SRR1795959	29,676,143	3,496,713	SRA	0	anther	Rutgers	wt	AN	1	anther (mix pre-meiotic -- meiotic and post-meiotic anthers) -- control conditions
SRR1795960	18,863,859	2,468,364	SRA	0	anther	Rutgers	7B-1	AO	1	anther (mix pre-meiotic -- meiotic and post-meiotic anthers but microsporogenesis in 7B-1 breaks down prior to the meiosis in microspore mother cells) -- control conditions
SRR1805790	29,048,176	2,102,891	SRA	0	seedling	Rutgers	wt	AP	1	seedling (2-weeks-old plants) -- mix of treatments: 10 microM ABA or 140 mM mannitol or 120 mM NaCl incubated for 0 -- 2 -- 4 -- 8 -- 12 -- and 24 h -- or cold treatment
SRR1805791	10,075,274	35,086,132	SRA	0	seedling	Rutgers	7B-1	AQ	1	seedling (2-weeks-old plants) -- mix of treatments: 10 microM ABA or 140 mM mannitol or 120 mM NaCl incubated for 0 -- 2 -- 4 -- 8 -- 12 -- and 24 h -- or cold treatment
SRR2039800	5,332,506	406,176	SRA	0	leaf	Rutgers	wt	AR	1	leaf -- 21-days post-inoculation with mock inoculation buffer
SRR2039801	5,378,772	551,162	SRA	0	leaf	Rutgers	wt	AS	1	leaf -- 21-days post-inoculation with Potato spindle tuber viroid mild
SRR2039802	4,662,974	944,613	SRA	0	leaf	Rutgers	wt	AT	1	leaf -- 21-days post-inoculation with Potato spindle tuber viroid intermediate
SRR2923817	17,085,067	1,324,551	SRA	0	leaf	Lukullus	wt	AU	1	leaf (4-weeks-old plants -- young leaf) -- control conditions
SRR2923834	19,659,667	1,531,113	SRA	0	leaf	Lukullus	wt	AU	1	leaf (4-weeks-old plants -- young leaf) -- control conditions
SRR2923841	20,837,839	1,381,062	SRA	0	leaf	Lukullus	sulf/+	AV	1	leaf (4-weeks-old plants -- young green leaf) -- control conditions
SRR2923842	19,234,220	1,423,059	SRA	0	leaf	Lukullus	sulf/+	AV	1	leaf (4-weeks-old plants -- young green leaf) -- control conditions
SRR2923843	21,342,680	1,484,233	SRA	0	leaf	Lukullus	sulf	AW	1	leaf (4-weeks-old plants -- young yellow leaf) -- control conditions
SRR2923844	14,818,417	969,933	SRA	0	leaf	Lukullus	sulf	AW	1	leaf (4-weeks-old plants -- young yellow leaf) -- control conditions
SRR2989577	5,420,877	303,831	SRA	0	leaf	Pusa Ruby	wt	AX	1	leaf -- 72 hours post infection with mock inoculation buffer
SRR2989578	7,877,445	365,923	SRA	0	leaf	Pusa Ruby	wt	AX	1	leaf -- 72 hours post infection with mock inoculation buffer
SRR2989579	7,006,090	1,103,632	SRA	0	leaf	Pusa Ruby	wt	AY	1	leaf -- 72 hours post infection with Alternaria
SRR2989580	3,063,723	315,288	SRA	0	leaf	Pusa Ruby	wt	AY	1	leaf -- 72 hours post infection with Alternaria
SRR350338	13,108,656	6,951,766	SRA	0	fruit	Ailsa Craig	wt	AZ	1	fruit (17 days post-anthesis immature and 52 days post-anthesis fully ripe) -- control conditions
ERR493660	7,622,120	2,978,992	SRA	0	fruit	M82	wt	B	1	fruit (ripe) -- control conditions
SRR350339	8,737,982	2,883,099	SRA	0	fruit	Ailsa Craig	wt	BA	1	fruit (39 days post-anthesis mature green 42 days post-anthesis breaker stage) -- control conditions
SRR4346447	33,902,656	3,272,000	SRA	0	root	Pusa ruby	wt	BB	1	root (5-weeks-old plants) -- control conditions
SRR4346448	26,139,517	4,492,871	SRA	0	root	Pusa ruby	wt	BC	1	root (5-weeks-old plants) -- +1-2-3 days in control conditions
SRR4346449	38,200,208	3,931,480	SRA	0	root	Pusa ruby	wt	BD	1	root (5-weeks-old plants) -- +1-2-3 days post infection with root-knot nematode Meloidogyne incognita
SRR4346450	23,890,199	3,393,750	SRA	0	root	Pusa ruby	wt	BE	1	root (5-weeks-old plants) -- +5-6-7 days in control conditions
SRR4346451	22,382,872	2,818,913	SRA	0	root	Pusa ruby	wt	BF	1	root (5-weeks-old plants) -- +5-6-7 days post infection with root-knot nematode Meloidogyne incognita
SRR4346452	38,261,724	4,451,570	SRA	0	root	Pusa ruby	wt	BG	1	root (5-weeks-old plants) -- +13-14-15 days in control conditions
SRR4346453	29,045,430	3,968,459	SRA	0	root	Pusa ruby	wt	BH	1	root (5-weeks-old plants) -- +13-14-15 days post infection with root-knot nematode Meloidogyne incognita
SRR4346454	30,951,125	4,496,602	SRA	0	root	Pusa ruby	wt	BI	1	root (5-weeks-old plants) -- +18-19-20 days in control conditions
SRR4346455	27,870,009	4,291,796	SRA	0	root	Pusa ruby	wt	BJ	1	root (5-weeks-old plants) -- +18-19-20 days post infection with root-knot nematode Meloidogyne incognita
SRR4346456	37,674,290	5,985,442	SRA	0	root	Pusa ruby	wt	BK	1	root (5-weeks-old plants) -- +26-27-28 days in control conditions
SRR4346457	49,690,172	9,710,050	SRA	0	root	Pusa ruby	wt	BL	1	root (5-weeks-old plants) -- +26-27-28 days post infection with root-knot nematode Meloidogyne incognita
SRR583817	3,052,266	320,058	SRA	0	shoot apex	M82	wt	BM	1	shoot apex (including 3 to 5 primordial leaves -- the first 2 leaves were removed) -- control conditions
SRR786979	3,407,981	5,094,727	SRA	0	leaf	MoneyMaker	wt	BN	1	leaf (6-weeks-old plants) -- control conditions
SRR786980	4,209,924	5,585,477	SRA	0	fruit	MoneyMaker	wt	BO	1	fruit -- control conditions
SRR786981	3,805,570	4,467,400	SRA	0	leaf	MoneyMaker	wt	BP	1	leaf (6-weeks-old plants) -- 24h post-inoculation with Botrytis cinerea
SRR786982	3,578,802	4,978,576	SRA	0	leaf	MoneyMaker	wt	BQ	1	leaf (6-weeks-old plants) -- 72h post-inoculation with Botrytis cinerea
SRR786983	4,375,582	6,270,086	SRA	0	fruit	MoneyMaker	wt	BR	1	fruit -- 24h post-inoculation with Botrytis cinerea
SRR786984	3,295,794	5,604,393	SRA	0	fruit	MoneyMaker	wt	BS	1	fruit -- 72h post-inoculation with Botrytis cinerea
SRR955375	14,871,429	1,199,809	SRA	0	leaf	Moneymaker	wt	BT	1	leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with control A. tumefaciens strain GV3101 containing pBinPLUS
SRR955376	14,358,897	1,839,531	SRA	0	leaf	Moneymaker	wt	BU	1	leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2]
SRR955377	10,209,452	1,909,559	SRA	0	leaf	Moneymaker	wt	BV	1	leaf (5-weeks-old plants -- 6-8 leaf stages) -- 30 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2]
SRR955378	14,644,169	1,408,592	SRA	0	leaf	FL505	wt	BW	1	leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with control A. tumefaciens strain GV3101 containing pBinPLUS
SRR955379	15,400,102	1,515,145	SRA	0	leaf	FL505	wt	BX	1	leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2]
SRR955380	8,838,237	1,336,894	SRA	0	leaf	FL505	wt	BY	1	leaf (5-weeks-old plants -- 6-8 leaf stages) -- 30 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2]
ERR493661	14,214,920	4,700,402	SRA	0	fruit	M82	wt	C	1	fruit (ripe) -- control conditions
ERR493662	9,777,330	2,845,003	SRA	0	fruit	M82	wt	D	1	fruit (ripe) -- control conditions
ERR493663	5,328,111	2,986,386	SRA	0	fruit	M82	wt	E	1	fruit (ripe) -- control conditions
ERR493664	7,948,331	1,069,121	SRA	0	fruit	M82	wt	F	1	fruit (ripe) -- control conditions
ERR493665	8,485,387	1,330,814	SRA	0	fruit	M82	wt	G	1	fruit (ripe) -- control conditions
ERR985504	3,562,284	487,790	SRA	0	pollen	Red Setter	wt	H	1	pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- control conditions
ERR985505	2,375,516	327,746	SRA	0	pollen	Red Setter	wt	H	1	pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- control conditions
ERR985506	2,508,926	334,058	SRA	0	pollen	Red Setter	wt	H	1	pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- control conditions
ERR985507	4,455,391	713,643	SRA	0	pollen	Red Setter	wt	I	1	pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- control conditions
ERR985508	4,130,060	633,746	SRA	0	pollen	Red Setter	wt	I	1	pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- control conditions
ERR985509	3,902,056	532,895	SRA	0	pollen	Red Setter	wt	I	1	pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- control conditions
ERR985510	4,508,717	591,569	SRA	0	pollen	Red Setter	wt	J	1	pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- control conditions
ERR985511	5,393,793	611,724	SRA	0	pollen	Red Setter	wt	J	1	pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- control conditions
ERR985512	6,059,255	610,645	SRA	0	pollen	Red Setter	wt	J	1	pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- control conditions
ERR985514	2,401,346	269,426	SRA	0	pollen	Red Setter	wt	K	1	pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- heat stress
ERR985515	4,116,337	462,338	SRA	0	pollen	Red Setter	wt	K	1	pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- heat stress
ERR985516	2,268,116	546,345	SRA	0	pollen	Red Setter	wt	L	1	pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- heat stress
ERR985517	2,027,464	414,355	SRA	0	pollen	Red Setter	wt	L	1	pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- heat stress
ERR985518	3,621,879	583,314	SRA	0	pollen	Red Setter	wt	L	1	pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- heat stress
ERR985519	3,495,240	419,771	SRA	0	pollen	Red Setter	wt	M	1	pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- heat stress
ERR985520	3,853,974	403,512	SRA	0	pollen	Red Setter	wt	M	1	pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- heat stress
ERR985521	3,828,118	391,165	SRA	0	pollen	Red Setter	wt	M	1	pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- heat stress
GSM803579	4,285,839	403,706	GEO	0	leaf	Heinz 1706	wt	N	1	leaf (3-weeks-old plants) -- control conditions
GSM803580	4,439,622	517,906	GEO	0	flower	Heinz 1706	wt	O	1	flower (pre-anthesis) -- control conditions
GSM803581	4,440,059	505,416	GEO	0	fruit	Heinz 1706	wt	P	1	fruit (breaker stage -- early ripening) -- control conditions
SRR039920	3,095,208	401,373	SRA	0	flower bud	Micro-Tom	wt	Q	1	flower bud (closed -- before flower blooming) -- control conditions
SRR039922	2,076,364	577,833	SRA	0	fruit	Micro-Tom	wt	R	1	fruit (1-3mm diameter) -- control conditions
SRR039924	2,589,066	691,753	SRA	0	fruit	Micro-Tom	wt	S	1	fruit (11-14mm diameter) -- control conditions
SRR039925	3,171,923	419,598	SRA	0	fruit	Micro-Tom	wt	T	1	fruit (mature green) -- control conditions
SRR039926	3,851,003	585,401	SRA	0	fruit	Micro-Tom	wt	U	1	fruit (breaker stage) -- control conditions
SRR039927	3,672,202	444,839	SRA	0	fruit	Micro-Tom	wt	V	1	fruit (3 days post breaker stage) -- control conditions
SRR039929	2,693,214	329,109	SRA	0	fruit	Micro-Tom	wt	W	1	fruit (7 days post breaker stage) -- control conditions
SRR065156	2,278,087	369,313	SRA	0	shoot	M82	wt	X	1	shoot (2-weeks-old plants) -- control conditions
SRR065157	4,923,482	574,253	SRA	0	shoot	M82	wt	X	1	shoot (2-weeks-old plants) -- control conditions
SRR1022870	5,736,556	783,184	SRA	0	shoot	M82	control transgene 35S:LhG4	Y	1	shoot (2-weeks-old plants) -- control conditions
SRR1022871	6,523,549	930,767	SRA	0	shoot	M82	control transgene 35S:LhG4	Y	1	shoot (2-weeks-old plants) -- control conditions
SRR1028350	13,613,597	1,887,855	SRA	0	shoot	M82	control transgene 35S:LhG4	Z	1	shoot (2-weeks-old plants) -- control conditions
SRR1028351	12,110,599	1,919,538	SRA	0	shoot	M82	control transgene 35S:LhG4	Z	1	shoot (2-weeks-old plants) -- control conditions

	ShortStack	miRBase21-BestBlastHit	Zuo_et_al_2013	Krasnikova_et_al_2009
MIRNA	80	50	0	0
nearMIRNA	93	2	0	0
siRNA20	79	1	0	0
siRNA21	1,676	12	1	1
siRNA22	3,343	1	0	0
siRNA23	3,638	1	0	0
siRNA24	134,003	6	0	0
OtherRNA	10,539	4	0	0
NotExpressed	0	0	0	0

Data from Lunardon et al. (2020)

Genome and annotations summary

Solanum lycopersicum (Tomato) genome build 2.5 (sly-b2.5)

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Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (104)