Data from Lunardon et al. (2020)

Genome and annotations summary

Phaseolus vulgaris (Common Bean) genome build 1.0 (pvu-b1.0)

Version v1.0 of Phaseolus vulgaris cv. BAT93 from Phytozome

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Small RNA Loci

Click links below to show sub-sets of annotations

	Formey_et_al_2015	ShortStack
MIRNA	165	82
nearMIRNA	28	36
siRNA20	2	10
siRNA21	18	401
siRNA22	2	96
siRNA23	2	13
siRNA24	46	38,264
OtherRNA	24	2,892
NotExpressed	21	0

Small RNA-seq data

Reference Set

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
common_bean_all_reference_set	130,236,125	51,311,132	none	1	mixed	mixed	wt	refset1	1	merge of 15 libraries - reference set 1

Invidiual alignments (15)

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
GSM769289	2,331,097	1,410,017	GEO	0	root	Bat 93	wt	A	1	root (3-weeks-old plants) -- control conditions
GSM769290	2,171,949	844,838	GEO	0	flower	Bat 93	wt	B	1	flower (mix of -1 -- 0 -- +1 days from tripping) -- control conditions
ERR701178	7,888,685	5,792,200	SRA	0	callus	Negro Jamapa	wt	C	1	callus -- 6 days after inoculation of Agrobacterium rhizogenes in the stem of seedlings
ERR701618	27,438,102	10,835,279	SRA	0	leaf	Negro Jamapa	wt	D	1	leaf
SRR1946753	10,902,311	2,484,341	SRA	0	flower	Negro Jamapa	wt	E	1	flower bud (35-40-days-old plants) -- control conditions
SRR1946754	12,376,868	4,635,744	SRA	0	seedling	Pinto Villa	wt	F	1	seedling (1- 4-days-old plants) -- control conditions
SRR1946755	10,535,279	3,168,893	SRA	0	root	Negro Jamapa	wt	G	1	root (15-days-old plants) -- control conditions
SRR1946756	8,942,045	2,906,497	SRA	0	leaf	Pinto Villa	wt	H	1	leaf (10- and 20-days-old plants) -- control conditions
SRR1946757	4,418,192	2,288,205	SRA	0	nodule	Negro Jamapa	wt	I	1	nodule (2-days-old plants) -- collected 18 and 27 days after inoculation with Rhizobium tropici in the roots
SRR3479064	8,164,844	3,129,063	SRA	0	root hair	G19833	wt	J	1	root hair (3-days-old plants) -- induced for 6 h at 30 C in the dark with pure Rhizobium etli nodulation factors
SRR3479065	8,088,255	2,774,061	SRA	0	root hair	G19833	wt	J	1	root hair (3-days-old plants) -- induced for 6 h at 30 C in the dark with pure Rhizobium etli nodulation factors
SRR3479066	6,758,977	2,182,505	SRA	0	root hair	G19833	wt	J	1	root hair (3-days-old plants) -- induced for 6 h at 30 C in the dark with pure Rhizobium etli nodulation factors
SRR3479067	6,889,332	2,287,842	SRA	0	root hair	G19833	wt	K	1	root hair (3-days-old plants -- treated for 6 h at 30 C in the dark with mock solution) -- control conditions
SRR3479068	5,967,837	2,748,319	SRA	0	root hair	G19833	wt	K	1	root hair (3-days-old plants -- treated for 6 h at 30 C in the dark with mock solution) -- control conditions
SRR3479069	7,362,352	3,823,328	SRA	0	root hair	G19833	wt	K	1	root hair (3-days-old plants -- treated for 6 h at 30 C in the dark with mock solution) -- control conditions