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
GSM1651990	39,552,743	8,740,563	GEO	0	flower	A17	wt	A	1	flower (mixed stages) -- control conditions
SRR943041	2,274,660	618,240	SRA	0	root	A17	wt	AA	1	root -- infected with Ralstonia solanacearum GMI1000
SRR943042	2,617,063	443,741	SRA	0	root	A17	wt	AB	1	root -- control conditions
SRR943043	10,458,956	2,452,463	SRA	0	root	A17	wt	AC	1	root (10-days-old plants) -- infected with Verticillium albo-atrum V31.2
SRR943046	14,233,111	2,018,980	SRA	0	leaf	A17	wt	AD	1	leaf -- control conditions
SRR943049	14,935,215	7,283,207	SRA	0	root	A17	wt	AE	1	root (5-days-old plants) -- treated with Myc-LCO factor
SRR943050	17,203,749	4,977,630	SRA	0	root	A17	wt	AE	1	root (5-days-old plants) -- treated with Myc-LCO factor
SRR943051	16,361,768	4,660,472	SRA	0	root	A17	wt	AE	1	root (5-days-old plants) -- treated with Myc-LCO factor
SRR943052	11,111,155	4,820,750	SRA	0	root	A17	wt	AF	1	root (5-days-old plants) -- treated with Nod factor
SRR943053	16,111,290	5,053,869	SRA	0	root	A17	wt	AF	1	root (5-days-old plants) -- treated with Nod factor
SRR943054	15,493,635	6,910,979	SRA	0	root	A17	wt	AF	1	root (5-days-old plants) -- treated with Nod factor
SRR943055	14,379,313	6,915,250	SRA	0	root	A17	wt	AG	1	root (5-days-old plants) -- treated with Myc/Nod factor
SRR943056	17,893,597	4,946,681	SRA	0	root	A17	wt	AG	1	root (5-days-old plants) -- treated with Myc/Nod factor
SRR943057	16,868,331	4,700,717	SRA	0	root	A17	wt	AG	1	root (5-days-old plants) -- treated with Myc/Nod factor
GSM1651991	23,167,990	9,832,735	GEO	0	nodule	A17	wt	B	1	nodule (14-days-old plants) -- collected 14-days after inoculation with Sinorhizobium meliloti strain 2011
GSM1651992	16,738,234	5,515,077	GEO	0	root	A17	wt	C	1	denodule root (28-days-old plants) -- control conditions
GSM1651993	15,174,893	9,817,685	GEO	0	nodule	A17	wt	D	1	nodule (14-days-old plants) -- collected 16-days after inoculation with Sinorhizobium meliloti strain 2011
GSM1651994	7,947,118	3,267,140	GEO	0	root	A17	wt	E	1	denodule root (30-days-old plants) -- control conditions
GSM721574	5,516,208	904,026	GEO	0	shoot	A17	wt	F	1	shoot (4-5-weeks-old plants) -- control conditions
GSM721575	5,765,351	740,614	GEO	0	shoot	A17	wt	G	1	shoot (4-5-weeks-old plants) -- drought stress
SRR088874	4,957,411	1,133,865	SRA	0	mycorrhizal root	A17	wt	H	1	mycorrhizal root (seedling stage) -- collected 3 weeks after inoculation with Glomus intraradices
SRR088875	5,663,026	1,197,776	SRA	0	root	A17	wt	I	1	root (seedling stage) -- collected 3 weeks after control conditions growth
SRR1954869	26,506,387	5,133,668	SRA	0	leaf	A17	wt	J	1	leaf (2-months-olds plants) -- control conditions
SRR1954870	16,690,323	8,090,235	SRA	0	root	A17	wt	K	1	root (3-weeks-old plants) -- control conditions
SRR1954871	20,825,715	5,941,127	SRA	0	seedling	A17	wt	L	1	seedling (2-days-old plants) -- control conditions
SRR1954872	28,715,651	7,949,287	SRA	0	hairy root	A17	wt	M	1	hairy root (miRNA overexpression control with empty vector) -- control conditions
SRR1954873	20,929,198	6,242,004	SRA	0	hairy root	A17	wt	M	1	hairy root (miRNA overexpression control with empty vector) -- control conditions
SRR1954884	31,021,910	7,448,207	SRA	0	hairy root	A17	wt	N	1	hairy root (target mimics control with empty vector) -- control conditions
SRR1954885	32,156,491	8,865,729	SRA	0	hairy root	A17	wt	N	1	hairy root (target mimics control with empty vector) -- control conditions
SRR522482	9,420,949	1,889,041	SRA	0	root	A17	wt	O	1	root (4-days-old plants) -- control conditions
SRR522483	10,914,054	1,551,103	SRA	0	root	A17	wt	O	1	root (4-days-old plants) -- control conditions
SRR701982	13,578,444	3,418,597	SRA	0	nodule	A17	wt	P	1	nodule (22-days-old plants) -- collected 10-days after inoculation with Sinorhizobium meliloti 2011
SRR701983	10,177,913	3,776,823	SRA	0	nodule	A17	wt	P	1	nodule (22-days-old plants) -- collected 10-days after inoculation with Sinorhizobium meliloti 2011
SRR701984	9,181,045	3,477,990	SRA	0	nodule	A17	wt	P	1	nodule (22-days-old plants) -- collected 10-days after inoculation with Sinorhizobium meliloti 2011
SRR804912	20,125,482	3,234,229	SRA	0	callus	A17	wt	Q	1	callus (10-days-old leaf explant non root forming callus) -- treated with NAA/BAP
SRR804913	19,923,172	2,636,676	SRA	0	callus	A17	wt	R	1	callus (10-days-old leaf explant root forming callus) -- treated with NAA
SRR804914	15,595,903	1,921,698	SRA	0	root	A17	wt	S	1	root (3-days-old seedling -- non-meristematic cells in elongation zone) -- control conditions
SRR804915	21,755,483	2,950,453	SRA	0	root	A17	wt	T	1	root (3-days-old seedling -- meristematic cells in tip) -- control conditions
SRX327823	5,820,682	1,166,001	SRA	0	root	A17	wt	U	1	root (tip) -- control conditions
SRR943044	18,735,314	2,531,010	SRA	0	root	A17	wt	U	1	root (tip) -- control conditions
SRR943047	8,217,513	1,555,287	SRA	0	root	A17	wt	U	1	root (tip) -- control conditions
SRR943036	3,187,922	505,276	SRA	0	root	A17	wt	V	1	root (tip) -- salt stress
SRR943045	15,872,611	1,668,187	SRA	0	root	A17	wt	V	1	root (tip) -- salt stress
SRR943048	11,782,566	2,247,351	SRA	0	root	A17	wt	V	1	root (tip) -- salt stress
SRR943037	3,525,710	616,303	SRA	0	nodulated root	A17	sunn-sickle	W	1	nodulated root (5-days-old plants) -- collected 5 days after inoculation with Sinorhizobium meliloti Sm2011
SRR943038	2,752,258	682,119	SRA	0	root	A17	sunn-sickle	X	1	root (5-days-old plants) -- collected 5 days after control conditions growth
SRR943039	2,976,846	825,564	SRA	0	mycorrhizal root	A17	wt	Y	1	mycorrhizal root (7-weeks-old plants) -- inoculated with Rhizophagus irregularis
SRR943040	2,721,422	1,008,954	SRA	0	root	A17	wt	Z	1	root (7-weeks-old plants) -- control conditions

	miRBase21-BestBlastHit	Jagadeeswaran_et_al_2009	ShortStack
MIRNA	143	0	108
nearMIRNA	24	0	60
siRNA20	0	0	23
siRNA21	97	1	1,355
siRNA22	23	0	644
siRNA23	3	0	14
siRNA24	454	0	109,003
OtherRNA	23	0	5,941
NotExpressed	186	0	0

Data from Lunardon et al. (2020)

Genome and annotations summary

Medicago truncatula (Barrel Medic) genome build 4.0 (mtr-b4.0)

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Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (48)