Lunardon et al. 2020

Version v2 of Citrus sinensis cv. Valencia from The Citrus sinensis Annotation Project

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
GSM712528	2,520,313	620,885	GEO	0	leaf	unknown	wt	A	1	leaf (young -- fully expanded) -- control conditions
GSM712529	2,017,205	707,219	GEO	0	flower	unknown	wt	B	1	flower (fully open) -- control conditions
SRR039884	3,233,338	1,113,131	SRA	0	fruit pulp	Anliu	wt	C	1	fruit pulp (170 days after flowering) -- control conditions
SRR039885	4,586,147	2,234,739	SRA	0	fruit pulp	Hong Anliu	wt	D	1	fruit pulp (170 days after flowering) -- control conditions
SRR1044049	20,388,217	2,657,918	SRA	0	callus	Valencia	wt	E	1	callus (nonembryogenic) -- control conditions
SRR1044050	21,327,176	2,854,644	SRA	0	callus	Valencia	wt	F	1	callus (embryogenic) -- control conditions
SRR1044051	20,537,513	3,410,761	SRA	0	callus	Valencia	wt	G	1	callus (embryogenic -- mix of calli exposed to somatic embryo induction for 1 -- 2 -- 3 -- 4 weeks) -- control conditions
SRR1259268	19,202,971	2,749,327	SRA	0	root	Xuegan	wt	H	1	root (15-weeks-old plants irrigated with 0 microM H3BO3 for 15 weeks; about 5-mm-long root apex) -- boron-deficiency stress
SRR1259269	19,104,573	3,235,635	SRA	0	root	Xuegan	wt	I	1	root (15-weeks-old plants irrigated with 10 microM H3BO3 for 15 weeks; about5-mm-long root apex) -- control conditions
SRR2166946	15,081,791	2,837,025	SRA	0	leaf	Xuegan	wt	J	1	leaf (15-weeks-old plants irrigated with 0 microM H3BO3 for 15 weeks; fully-expanded leaf) -- boron-deficiency stress
SRR2166947	14,912,125	2,794,084	SRA	0	leaf	Xuegan	wt	K	1	leaf (15-weeks-old plants irrigated with 10 microM H3BO3 for 15 weeks; fully-expanded leaf) -- control conditions
SRR2848261	8,527,712	1,574,327	SRA	0	leaf	Xuegan	wt	L	1	leaf (11-weeks-old plants cultured with 400microM H3BO3 for 15 weeks; fully expanded leaf -- excised at one third the height of the plant) -- boron toxicity stress
SRR2848262	11,384,206	2,177,308	SRA	0	leaf	Xuegan	wt	M	1	leaf (11-weeks-old plants cultured with 10microM H3BO3 for 15 weeks; fully expanded leaf -- excised at one third the height of the plant) -- control conditions
SRR2977531	17,699,534	2,515,387	SRA	0	leaf	Xuegan	wt	N	1	leaf (15-weeks-old plants irrigated with 0 mM MgSO4 for 16 weeks; fully-expanded -- about 7-weeks-old leaf) -- magnesium-deficiency stress
SRR2977532	19,054,186	3,102,367	SRA	0	leaf	Xuegan	wt	O	1	leaf (15-weeks-old plants irrigated with 1 mM MgSO4 for 16 weeks; fully-expanded -- about 7-weeks-old leaf) -- control conditions
SRR3457416	17,428,347	2,922,729	SRA	0	root	Xuegan	wt	P	1	root (15-weeks-old plants -- cultivated in Mg-deficiency conditions for 16 weeks -- fully expanded root) -- magnesium-deficiency stress
SRR3457417	18,422,206	3,306,847	SRA	0	root	Xuegan	wt	Q	1	root (31-weeks-old plants -- fully expanded root) -- control conditions
SRR3774375	23,128,798	10,818,424	SRA	0	fruit pulp	Fengwan' navel	wt	R	1	fruit pulp (170 days after flowering) -- control conditions
SRR3774376	21,349,592	10,369,319	SRA	0	fruit pulp	Fengwan' navel	wt	R	1	fruit pulp (170 days after flowering) -- control conditions
SRR3774377	18,861,279	11,762,620	SRA	0	fruit pulp	Fengjie 72-1' navel	wt	S	1	fruit pulp (170 days after flowering) -- control conditions
SRR3774378	13,576,213	9,700,361	SRA	0	fruit pulp	Fengjie 72-1' navel	wt	S	1	fruit pulp (170 days after flowering) -- control conditions
SRR847765	11,588,991	3,900,594	SRA	0	leaf	Anliu	wt	T	1	leaf (young and mature stages) -- control conditions
SRR847766	9,683,709	4,767,057	SRA	0	flower	Anliu	wt	U	1	flower (early flower bud -- flower bud and mature flower) -- control conditions

	ShortStack	miRBase22-BestBlastHit	Liu_et_al_2014
MIRNA	92	94	0
nearMIRNA	56	14	0
siRNA20	58	1	0
siRNA21	1,980	18	1
siRNA22	437	9	0
siRNA23	131	3	0
siRNA24	67,227	10	0
OtherRNA	2,197	18	0
NotExpressed	0	1	0

Data from Lunardon et al. (2020)

Genome and annotations summary

Citrus sinensis (Sweet Orange) genome build 2 (csi-b2)

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Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (23)