Lunardon et al. 2020

Genome and annotations summary

Version v0.4 of Carica papaya cv. SunUp from Phytozome

Small RNA Loci

Click links below to show sub-sets of annotations

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

papaya_all_reference_set

46,974,712

10,030,230

none

mixed

refset1

merge of 5 libraries - reference set 1

Invidiual alignments (5)

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
GSM712525	3,705,338	959,441	GEO	0	leaf	SunUp	wt	A	1	leaf (1-2-weeks-old plants) -- control conditions
GSM712526	3,478,716	1,179,117	GEO	0	flower	AU9	wt	B	1	flower (from female plants -- 1-3-weeks after flowering) -- control conditions
GSM712527	3,004,374	1,500,892	GEO	0	leaf	AU9	wt	C	1	leaf (2-3-weeks-old male plants) -- infected with ringspot virus
SRR3538831	18,470,721	2,705,394	SRA	0	pistil	Zhonghuang	wt	D	1	pistil (1.5cm long -- non-functional rudimentary pistils from normal male flowers) -- control conditions
SRR3538833	18,315,563	3,685,386	SRA	0	pistil	Zhonghuang	wt	E	1	pistil (1.5cm long -- developed and functional pistils from male-to-hermaphrodite sex reversal flowers) -- sex change induced by low temperature

	ShortStack	miRBase21-BestBlastHit
MIRNA	31	46
nearMIRNA	30	14
siRNA20	15	0
siRNA21	1,668	4
siRNA22	50	0
siRNA23	16	1
siRNA24	26,059	11
OtherRNA	1,698	4
NotExpressed	0	7

Data from Lunardon et al. (2020)

Genome and annotations summary

Carica papaya (Papaya) genome build 0.4 (cpa-b0.4)

Go to genome browser

Download genome assembly FASTA file

BLAST search

Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (5)