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. 2017 Mar 24;3(2):16. doi: 10.3390/ncrna3020016

Table 2.

An overview of the currently available databases for plant lncRNAs.

S.No. Name of the Database Publication Details and Reference No. Plant Species Number of Plant lncRNAs Description/Main Features Data Sources Link/URL
1. TAIR10 Lamesch et al., (2012)
Nucleic Acids Research
[91]		 Arabidopsis Information available about 33,602 genes of Arabidopsis

  • Arabidopsis gene structure and function annotation

  • Plant-specific

 AFGC cDNA arrays, the literature, and sequencing and function genomics projects https://www.arabidopsis.org/
2. PlantNATsDB Chen et al.
(2012)
Nucleic Acids Research
[92]		 Seventy plant species NATs (including both protein coding and non-coding transcripts): 2,146,803

  • A comprehensive database of NATs

  • Plant-specific

 Various data sources such as TAIR9, JGI Glyma1, JGI Cassava 1 http://bis.zju.edu.cn/pnatdb/
3. PLncDB Jin et al.
(2013)
Bioinformatics
[93]		 Arabidopsis thaliana >13,000 lncRNAs

  • A comprehensive genomic database of Arabidopsis lncRNAs

  • Plant-specific

 Data in the study by Liu et al., 2012 [63] http://chualab.rockefeller.edu/gbrowse2/homepage.html
4. NONCODE v4 Xie et al.
(2014)
Nucleic Acids Research
[94]		 A. thaliana 3853 lncRNA transcripts
and
2477 lncRNA genes

  • An integrated knowledge database with comprehensive collection and annotation of lncRNAs plus other ncRNAs

  • Not plant-specific

 The literature, specialized databases, and GenBank www.bioinfo.org/NONCODEv4/
5. PNRD Yi et al.
(2015)
Nucleic Acids Research
[95]		 Four plant species:
A. thaliana, Oryza sativa, Populus trichocarpa, and Zea mays. 		5573 lncRNAs

  • A comprehensive integrated web resource for lncRNAs and other ncRNAs

  • Plant-specific

 Integration of data from other databases and publications http://structuralbiology.cau.edu.cn/PNRD
6. lncRNAdb v2.0 Quek et al.
(2015)
Nucleic Acids Research
[36]		 A. thaliana and other plant species such as O. sativa, Medicago truncatula, Brassica rapa, Glycine max, etc. Seven lncRNA entries for A. thaliana
and
single-digit entries for other plant species

  • Reference database for functional lncRNAs, which have been experimentally validated.

  • Not plant-specific

 Manually curated from evidence supported by the literature http://www.lncrnadb.org/
7. PLNlncRbase Xuan et al.
(2015)
Gene
[96]		 Forty-three plant species 1187 lncRNAs

  • A resource for experimentally validated lncRNAs

  • Plant-specific

 Manually curated from evidence supported by the literature (over 200 studies) http://bioinformatics.ahau.edu.cn/PLNlncRbase
8. GreeNC Gallart et al.
(2016)
Nucleic Acids Research
[97]		 Thirty-seven plant species and 6 algae >120,000 (high-confidence) lncRNAs

  • A wiki-based information-rich database of lncRNAs

  • Plant-specific

 In silico identification based on data downloaded from Phytozome v10.3 http://greenc.sciencedesigners.com/
9. CANTATAdb Szczesśniak et al.
(2016)
Plant Cell Physiology
[98]		 10 plant species:
Amborella trichopoda, A. thaliana, Chlamydomonasreinhardtii, G. max, O. sativa, Physcomitrella patens, Selaginellamoellendorffii, Solanum tuberosum, Vitis vinifera, and Z. mays. 		45,117 lncRNAs

  • A database of lncRNAs with extended annotation like information about lncRNA-miRNA interactions

  • Plant-specific

 In silico identification based on publicly available RNA-Seq sample data http://cantata.amu.edu.pl/
10. DsTRD Shao et al. (2016)
PLoS ONE
[99]		 Salvia miltiorrhiza 27,687 lncRNAs

  • A transcriptional resource database specific for the medicinal plant danshen

 In silico identification using an in-house Perl script http://bi.sky.zstu.edu.cn/DsTRD/home.php
11. RNACentral The RNAcentral Consortium.
(2016)
Nucleic Acids Research
[100]		 Z. mays and A. thaliana ≈673 lncRNAs

  • A gateway for the users to access lncRNAs and other ncRNAs via single entry point

  • Not plant-specific

 40 expert databases http://rnacentral.org/
12. PLncRNAdb Ming Chen’s Lab
[101]		 Four plant species:
A. thaliana, Arabidospsis lyrata, P. trichocarpa, and Z. mays 		5000 lncRNAs

  • A database of lncRNAs with distinct annotation like information lncRNAs and various RBPs

  • Plant-specific

 In silico identification and the literature http://bis.zju.edu.cn/PlncRNADB/index.php

Abbreviations used in Table 2: AFGC, Arabidopsis Functional Genomics Consortium; JGI, Joint Genome Institue; lncRNA, long non-coding RNA; NAT, natural antisense transcript; ncRNA, non-coding RNA; RBP, RNA binding protein.