Plant Circular RNA Database

Release 2

In the second version, apart from the five organisms (Arabidopsis thaliana, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Zea mays), circRNA information from another three organisms, including Gossypium hirsutum, Glycine max and Triticum aestivum, have been added based on the published papers. Totally, the number of circRNA entries collected by PlantcircBase has been increased to 89,997. Detail statistics were shown in tables as following.

Table 2.1 The number of circRNAs in PlantcircBase (Release 2)

Organisms	Number of circRNAs		Full-length sequence of circRNAs		Acting as miRNA sponge*	Networks of circRNA-miRNA-mRNA*	Tissues	References
Organisms	Total	BS valided*	Total	FL valided*	Acting as miRNA sponge*	Networks of circRNA-miRNA-mRNA*	Tissues	References
Oryza sativa	12,037	10	0	0	405	251	Roots, shoots	Ye et al., 2015
	2,354	30	0	0	73	49	Leaves	Lu et al., 2015
	2,824	0	2,824	61	14	10	Roots	Ye et al., 2016
	26,160	37	0	9	585	343	Leaves, anthers, pistils, seeds, shoots, roots	Chu et al., 2017
Arabidopsis thaliana	6	6	0	0	0	0	Roots	Wang et al., 2014
	6,012	0	0	0	292	237	Leaves	Ye et al., 2015
	165	0	0	0	5	4	Siliques, seeds	Lu et al., 2015
	974	6	0	0	21	17	NA	Sun et al., 2016
	30,534	13	0	0	2,411	2,206	Inflorescences, roots, leaves, aerial	Chu et al., 2017
	2,165	19	0	0	46	35	Seedlings	Pan et al., 2017
	5,861	10	0	0	173	141	Whole plants	Chen et al., 2017
	168	4	0	0	7	6	Leaves	Liu et al., 2017
	164	4	0	0	3	2	Leaves	Dou et al., 2017
Zea mays	496	0	0	0	1	1	Shoots	Lu et al., 2015
Zea mays	2,771	37	0	0	39	36	Seedling leaves	Chen et al., 2017
Hordeum vulgare	47	16	0	0	0	0	Leaves and seeds	Darbani et al. 2016
Solanum lycopersicum	854	0	0	0	6	5	Fruit	Zuo et al. 2016
Solanum lycopersicum	783	2	0	0	10	7	Fruit	Tan et al., 2017
Triticum aestivum	88	16	0	0	7	5	Seedling leaves	Wang et al. 2016
Glycine max	5,372	7	0	0	61	56	Leaves, roots, stems	Zhao et al. 2016
Gossypium hirsutum	499	7	0	0	7	0	Leaves, ovules	Zhao et al. 2016

* miRNA sponges were predicted using eTM_finder (Ye et al., 2014);
  miRNA targets were predicted using psRNATarget (Dai and Zhao, 2011) (http://plantgrn.noble.org/psRNATarget/);
  BS valided means the back-splicing site has of circRNA been experimentally valided by Sanger sequencing;
  FL valided means the full-length of circRNA has been experimentally valided by Sanger sequencing.

Table 2.2 Summary of circRNA entries in PlantcircBase (Release 2)

Organisms	Total circRNAs	Back-splicing site validated	Full length sequence validated	Acting as miRNA sponge	Networks of circRNA-miRNA-mRNA
Oryza sativa	40,314	137	70	901	539
Arabidopsis thaliana	38,938	61	0	2,641	2,392
Zea mays	3,267	37	0	40	37
Hordeum vulgare	47	16	0	0	0
Solanum lycopersicum	1,472	2	0	15	12
Triticum aestivum	88	16	0	7	5
Glycine max	5,372	7	0	61	56
Gossypium hirsutum	499	7	0	7	0

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