Lunardon et al. 2020

Version 3.0 genome build from Phytozome 10 along with plastid and mitochondrial genomes

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
SRR1013389	23,133,032	1,649,617	SRA	0	protonemata	Gransden 2004	dcl3-10	dcl3-10		dcl3-10 protonemata (Gransden 2004)
SRR1013390	12,454,093	834,155	SRA	0	protonemata	Gransden 2004	dcl3-10	dcl3-10		dcl3-10 protonemata (Gransden 2004)
SRR1013387	11,715,543	1,076,738	SRA	0	protonemata	Gransden 2004	dcl3-5	dcl3-5		dcl3-5 protonemata (Gransden 2004)
SRR1013388	13,020,339	1,419,049	SRA	0	protonemata	Gransden 2004	dcl3-5	dcl3-5		dcl3-5 protonemata (Gransden 2004)
SRR1013391	8,497,917	763,234	SRA	0	protonemata	Gransden 2004	dcl4-1	dcl4-1		dcl4-1 protonemata (Gransden 2004)
SRR1013392	16,523,999	1,469,279	SRA	0	protonemata	Gransden 2004	dcl4-1	dcl4-1		dcl4-1 protonemata (Gransden 2004)
SRR1013395_SRR1013399	40,935,165	3,984,185	SRA	0	protonemata	Gransden 2009	mdcl-107	mdcl-107		mdcl-107 protonemata (Gransden 2009)
SRR1013396_SRR1013400	26,192,173	2,250,284	SRA	0	protonemata	Gransden 2009	mdcl-107	mdcl-107		mdcl-107 protonemata (Gransden 2009)
SRR1013393_SRR1013397	26,715,900	2,454,159	SRA	0	protonemata	Gransden 2009	mdcl-77	mdcl-77		mdcl-77 protonemata (Gransden 2009)
SRR1013394_SRR1013398	24,979,344	2,251,650	SRA	0	protonemata	Gransden 2009	mdcl-77	mdcl-77		mdcl-77 protonemata (Gransden 2009)
SRR1013409	14,272,671	1,792,434	SRA	0	protonemata	Gransden 2004	nrpd1-12	nrpd1-12		nrpd1_12 protonemata (Gransden 2004)
SRR1013410	16,195,300	1,241,154	SRA	0	protonemata	Gransden 2004	nrpd1-12	nrpd1-12		nrpd1_12 protonemata (Gransden 2004)
SRR1013401_SRR1013405	30,210,997	3,362,485	SRA	0	protonemata	Gransden 2004	nrpe1b-128	nrpe1b-128		nrpe1b_128 protonemata (Gransden 2004)
SRR1013402_SRR1013406	27,604,771	2,930,989	SRA	0	protonemata	Gransden 2004	nrpe1b-128	nrpe1b-128		nrpe1b_128 protonemata (Gransden 2004)
SRR1013411_SRR1013413	22,793,767	1,725,836	SRA	0	protonemata	Gransden 2004	rdr2-1	rdr2-1		rdr2-1 protonemata (Gransden 2004)
SRR1013412_SRR1013414	31,045,259	2,224,908	SRA	0	protonemata	Gransden 2004	rdr2-1	rdr2-1		rdr2-1 protonemata (Gransden 2004)
SRR1013415	16,730,988	1,370,312	SRA	0	protonemata	Gransden 2004	rdr2-2	rdr2-2		rdr2-2 protonemata (Gransden 2004)
SRR1013416	18,625,807	1,620,341	SRA	0	protonemata	Gransden 2004	rdr2-2	rdr2-2		rdr2-2 protonemata (Gransden 2004)
SRR1013417	12,918,423	918,932	SRA	0	protonemata	Gransden 2004	rdr6-19	rdr6-19		rdr6-19 protonemata (Gransden 2004)
SRR1013418	11,173,292	1,497,997	SRA	0	protonemata	Gransden 2004	rdr6-19	rdr6-19		rdr6-19 protonemata (Gransden 2004)
SRR1013419	13,170,769	1,844,516	SRA	0	protonemata	Gransden 2004	rdr6-35	rdr6-35		rdr6-35 protonemata (Gransden 2004)
SRR1013420	15,107,056	1,665,913	SRA	0	protonemata	Gransden 2004	rdr6-35	rdr6-35		rdr6-35 protonemata (Gransden 2004)
SRR768442_SRR942518	30,266,912	2,713,281	SRA	0	protonemata	Gransden 2004	wild-type	wt04	4	wild-type protonemata (Gransden 2004)
SRR768443_SRR942519	31,991,519	3,067,711	SRA	0	protonemata	Gransden 2004	wild-type	wt04	4	wild-type protonemata (Gransden 2004)
SRR942522	11,102,464	1,272,028	SRA	0	protonemata	Gransden 2004	wild-type	wt04	4	wild-type protonemata (Gransden 2004)
SRR942523	13,557,852	1,887,975	SRA	0	protonemata	Gransden 2004	wild-type	wt04	4	wild-type protonemata (Gransden 2004)
SRR768444_SRR942520	20,203,817	2,289,859	SRA	0	protonemata	Gransden 2009	wild-type	wt09	4	wild-type protonemata (Gransden 2009)
SRR768445_SRR942521	25,472,325	1,997,869	SRA	0	protonemata	Gransden 2009	wild-type	wt09	4	wild-type protonemata (Gransden 2009)

	ShortStack	miRBase21	Cho_et_al_2008	Arif_et_al_2012	Coruh_et_al_2015
MIRNA	90	123	1	0	102
nearMIRNA	21	14	0	0	33
siRNA20	22	2	0	0	20
siRNA21	174	33	18	9	166
siRNA22	29	3	1	0	47
siRNA23	464	0	38	0	384
siRNA24	403	1	36	0	329
OtherRNA	9,581	45	47	0	183
NotExpressed	0	6	2	0	182

Data from Lunardon et al. (2020)

Genome and annotations summary

Physcomitrella patens (Spreading Earthmoss) genome build 3.0 (ppt-b3.0)

Go to genome browser

Download genome assembly FASTA file

BLAST search

Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (28)