







































Highlights in Bioscience;


 

Highlights in BioScience      
ISSN: 2682-4043                                                       
 

 

 
Highlights in BioScience                              DOI: 10.36462/H.BioSci.20191                              May 2019 | Volume2 
http://highlightsin.org/index.php/bioscience/                                 

Page 1 of 7 

 

 

 

 

 

 

 

 

 

 

 

 

 
Citation: Awan  Z., Ali A.and Iqbal A. 

(2019). Plant Molecular Biology 

Databases. Highlights in BioScience, 

Volume 2.Article ID 20191, 

dio:10.36462/ H.BioSci.20191 

 

 

 

 

Received: March  3, 2019 

 

Accepted: April  25, 2019 

 

Published: May 5, 2019 

 

 

Copyright:© 2019 Awan et al. This is 

an open access article distributed under 

the terms of the Creative Commons 

Attribution License, which permits 

unrestricted use, distribution, and 

reproduction in any medium, provided 

the original author and source are 

credited. 

 

 

Data Availability Statement: All 

relevant data are within the paper 

 

 

Funding: The authors have no support 

or funding to report. 

 

 

 

 

 

Plant Molecular Biology Databases 

Zubair Awan
1
, Aqib Ali

2 
and Abbas Iqbal

2 

 

1
Agriculture University, Peshawar, Pakistan. 

2
Institute of Biotechnology, Agriculture University, Pakistan. 

 

 

Abstract 

 

Many of plant biological database comprise data from study fields 

including metabolomics, proteomics, genomics, microarray gene 

expression, and phylogenetic. Information in biological databases 

involves the role of genes, composition, chromosomal location, 

clinical impacts of mutations, and similarity of biological sequences 

and characteristics. We are here targeting to review and rank some 

of plant databases according to their use and feature. Hoping that 

scientists could use this study to pick, combine and correlate 

distinct databases, based on their study needs and objective 

specifications. 

 

Keywords: plant biological database, bioinformatics, software, phylogenetic, 

metabolomics, proteomics, genomics.  

 

 

 

Introduction 

Many of plant databases were constructed from some biological fields 

including metabolomics, proteomics, genomics, microarray gene expression, and 

phylogenetic(1). With bioinformatics tools the number of plant database were 

growing (2), so here we described many of plant database such as RicyerDB,    

PlantRGDB, Functional trait databases, ERISdb, HaloDom, PlantProm DB, 

CTDB, CmMDb, CicArMiSatDB, eHALOPH, MSDB, Kazusa Marker DataBase 

, PMDBase, SnoRNA database , OGDD, PlantRNA, PRGdb, PineElm SSRdb , 

SBMDb, SpinachDB, SisatBase, Sinbase, Ricebase, ReprOlive, and Planteome 

database 

 

RicyerDB 

The Rice Yield-related Database (RicyerDB) was developed to complement 

associated influence rice research (Oryza sativa L.) yield in various aspects by 

manually curating associated databases and literature and information on 

genomics and proteomics that can be helpful for a detailed knowledge of rice 

biology. RicyerDB offers a more useful resource for researching, browsing and  

Review Article                                                                             Open Access   



 
 

                                                                                                                                             Plant Molecular Biology Databases 

 

 

 
Highlights in BioScience                              DOI: 10.36462/H.BioSci.20191                              May 2019 | Volume2 
http://highlightsin.org/index.php/bioscience/                                 

Page 2 of 7 

analyzing genes related to yield efficiently. You can readily 

query and download the entire information collection through 

the webpage. Furthermore, RicyerDB also built a network of 

communication between protein and protein with biological 

assessment. The intermingled rice database opens a fresh 

path for scientists to obtain rice gene data in terms of its 

impacts on rice breeding traits. At http://server.malab.cn/ 

Ricyer/index.html, the web server is publicly accessible (3). 

 

PlantRGDB 

PlantRGDB (Plant Retrocopied Gene DataBase) was 

built as the first plant retrocopy database to provide a 

supposedly full unified catalog of plant genomic retrocopies. 

Free access to the database is http://aegilops.wheat.ucdavis 

.edu/plantrgdb. It included 49 species of plants and 38,997 

retrocopies along with data on classification. PlantRGDB 

offers a user-friendly internet interface to search, browse and 

download the data base retrocopies. PlantRGDB also 

provides graphical viewer-integrated sequence data to display 

each retrocopy's composition. Report the retrocopy 

characteristics of each species using a browse feature. 

Furthermore, helpful instruments such as sophisticated search 

and BLAST are accessible to more conveniently search the 

database (4). 

 

Functional trait databases 

Tavşanoğlu and Pausas (5) depicted a functional 

database of traits that emerged as key instruments for a broad 

spectrum of ecological studies worldwide. Their database of 

functional characteristics for Mediterranean Basin vascular 

plant species. The database contains 25,764 personal 

documents of 44 characteristics from 2,457 plant taxa 

dispersed in 119 taxonomic families. Trait information were 

acquired from an extensive survey of literature, along with 

some field and experimental findings. All documents are 

fully mentioned and include geographic coordinates in many 

instances. The database is organized to include various 

concentrations of character data precision for each input. 

BROT 2.0 should promote the testing of plant functional 

ecology hypotheses within the Mediterranean Basin and 

compare this region with other ecosystems around the world. 

The BROT2.0 is offline database as well as its trait 

definitions can be used in other areas of the globe as a model 

to create comparable trait databases. 

 

ERISdb 

Kabza et al. (6) conducted a large-scale assessment of 

splice sites in eight species of plants using new algorithms 

and tools. Theanalyzes included orthological splice sites, 

polypyrimidine sections, and branch locations being 

identified. They also recognized putative intronic and 

exoniccis-regulatory motifs, U12 introns and splice sites in 5 

plant species in 45 microRNA genes. In the form of 

expressed sequence tag and RNA-Seq information, they also 

provide experimental proof for plant splice sites. All 

information is deposited in a novel ERISdb database and is 

freely available at http://lemur.amu.edu.pl/share/ERISdb/. 

 

HaloDom 

Loukas et al. (7) documented from scientific literature 

more than 1000 halophilic species. Of these, 21.9% 

correspond to archaea, 50.1% to bacteria and 27.9% in 

eukaryotes. Their documents comprise fundamental data such 

as the salinity discovered by a specific organism, its 

taxonomy and genomic data through NCBI and other 

connections. You can access the internet database called 

"HaloDom" at http://www.halodom.bio.auth.gr. 

 

PlantProm 

Shahmuradov et al. (8) obtained a plant promoter 

repository, is an annotated, non-redundant set of RNA 

polymerase II proximal promoter sequences with 

experimentally determined transcription start site(s), TSS, 

from different plant species. PlantProm DB includes 305 

records from monocot, dicot and other crops, including 71, 

220 and 14 promoters. It offers TSS, promoter type ranking 

of promoters and Nucleotide Frequency Matrices (NFM) 

DNA sequence of promoter areas for promoter components: 

TATA-box, CCAAT-box and TSS-motif (Inr).Analysis of 

TSS motifs disclosed that their structure is distinct in dicots 

and monocots, as well as in promoters without TATA and 

TATA. The database acts as a instructional base for the 

development of forecast programs for plant promoters. You 

can find PlantProm DB at http://mendel.cs.rhul.ac.uk/. 

 

CTDB 

Verma et al. (9) designed an incorporated Chickpea 

Transcriptome Database (CTDB) that offers a extensive 

internet interface for visualizing and easily retrieving 

chickpea transcriptome information. The database includes 

numerous resources for searching for similarities, searching 

for functional annotations, and assessment of relative gene 

expression. The database contains a catalog of transcription 

factor relatives and their chickpea expression profiles. In 

order to study the expression profiles of chickpea transcripts 

in major tissues/organs and various stages of flower 

development, the gene expression data were integrated. To 

enable relative genomic research between distinct legumes 

http://server.malab.cn/%20Ricyer/index.html
http://server.malab.cn/%20Ricyer/index.html
http://lemur.amu.edu.pl/share/ERISdb/
http://www.halodom.bio.auth.gr/
http://mendel.cs.rhul.ac.uk/


 
 

                                                                                                                                             Plant Molecular Biology Databases 

 

 

 
Highlights in BioScience                              DOI: 10.36462/H.BioSci.20191                              May 2019 | Volume2 
http://highlightsin.org/index.php/bioscience/                                 

Page 3 of 7 

and Arabidopsis, utilities such as similarity search, orthology 

recognition and relative gene expression have also been 

introduced in the database. In addition, the CTDB is a tool 

for finding functional molecular markers (microsatellites and 

single nucleotide polymorphisms) between distinct kinds of 

chickpea. The CTDB can be found at http://nipgr.res.in/ctdb. 

html. 

 

CmMDb 

The first entire genome based microsatellite DNA 

marker repository of Cucumis melo L was created by Bhawna 

et al. (10). And a extensive internet resource that helps to 

identify varieties and map the Cucurbitaceae family 

physically.  Microsatellite repository of The Melo Cucumis 

L. includes 39,072 SSR markers along with repeat motif, 

sequence length, motif sequence, marker ID, motif type and 

chromosomal location. The database features a new 

automated plant primer design tool to satisfy the 

requirements of wet laboratory scientists. At http://65.181. 

125.102/cmmdb2/index.html, CmMDb is readily accessible. 

 

CicArMiSatDB 

Doddamani et al. (11) reported a user-friendly relational 

database called the Chickpea Microsatellite Database to 

support genetic research and apps for reproduction. This 

database offers comprehensive data about SSRs as well as 

their genome characteristics. SSRs were categorized and 

rendered available via a internet interface that was easy to 

use. At http://cicarmisatdb.icrisat.org, CicArMiSatDB the 

database is readily accessible. 

 

eHALOPH 

A database of salt-tolerant plant-halophytes was built by 

Santos et al. (12). Data of plant species tolerant of salt levels 

of about 80 mM or more sodium chloride have been 

gathered, together with information on plant species, life 

form, ecotypes, highest tolerated salinity, existence or lack of 

salt glands, photosynthetic pathways, antioxidants, secondary 

metabolites, compatible solutes, habitat, financial use and 

whether germination, microbial articles are available.The 

eHALOPH database may be used to analyze tolerance-

related traits and to inform selection of species that may be 

used for saline farming, bioremediation or environmental 

recovery and rehabilitation of decayed wetlands or other 

regions. The database available at http://www.sussex.ac.uk/ 

affiliates/halophytes/. 

 

MSDB 

A MSDB (Microsatellite Database) of > 650 million 

SSRs from 6,893 species such as  archaea, fungi, bacteria, 

plants and animals was founded by Avvaru et al. (13). This 

database is the most comprehensive tool for various species 

accessing and analyzing SSR information. In addition to 

researching information in a customizable tabular format, the 

interactive plotting scheme allows users to display and 

compare various species information concurrently. Using the 

Django framework and MySQL, MSDB is created. It can be 

found at http://tdb.ccmb.res.in/msdb. 

 

Kazusa Marker DataBase 

A database was developed by Shirasawa et al. (14), the 

Kazusa Marker DataBase. This database involves DNA 

marker data such as SSR and SNP markers, genetic 

association maps, and physical maps. This database also 

provides keyword searches for markers, sequence 

information used to develop markers, and experimental 

environments. There are mainly 10 specific crop species:  

pepper, tomato, strawberry, soybean, radish, peanut, red 

clover, white clover, and eucalyptus. This DataBase is a 

helpful instrument for fundamental and advanced sciences 

like genomics, genetics, and crop molecular breeding. 

Database link http://marker.kazusa.or.jp. 

 

PMDBase 

A database, PMDBase, was established by Yu et al. 

(15), which integrates large quantities of microsatellite DNAs 

out of genome-sequenced species of plants and involves a 

web service for microsatellite DNAs. PMDBase recognized 

26 230 099 microsatellite DNAs covering 110 species of 

plants. For each microsatellite DNA, up to three 

combinations of primers were provided. For 81 species, the 

microsatellite DNA genomic characteristics were provided 

with the respective genes or transcripts from various 

databases. Microsatellite DNAs could be studied with a user-

friendly internet interface and tailored software by browsing 

and locating modules. In addition, they constructed 

MISAweb and embedded Primer3web to help users 

recognise microsatellite DNAs of their own online molecular 

sequences and construct corresponding primers. All 

microsatellite DNA datasets can be easily downloaded. 

PMDBase will be updated with the latest genome data on a 

regular basis and can be accessed via the http://www.sesame-

bioinfo.org/PMDBase  

 

http://nipgr.res.in/ctdb.%20html
http://nipgr.res.in/ctdb.%20html
http://cicarmisatdb.icrisat.org/
http://www.sussex.ac.uk/%20affiliates/halophytes/
http://www.sussex.ac.uk/%20affiliates/halophytes/
http://tdb.ccmb.res.in/msdb
http://marker.kazusa.or.jp/
http://www.sesame-bioinfo.org/PMDBase
http://www.sesame-bioinfo.org/PMDBase


 
 

                                                                                                                                             Plant Molecular Biology Databases 

 

 

 
Highlights in BioScience                              DOI: 10.36462/H.BioSci.20191                              May 2019 | Volume2 
http://highlightsin.org/index.php/bioscience/                                 

Page 4 of 7 

Plant snoRNA database 

The Plant SnoRNA database (16) offers data from 

Arabidopsis and eighteen other plant species on small 

nucleolar RNAs. Information involves genes, information on 

transcription, target alteration sites for methylation and 

pseudouridylation, primary gene association, and number of 

versions of genes. The Arabidopsis data is split by target 

locations in rRNA, snRNAor unidentified, into box C / D and 

box H / ACA snoRNAs, and within all of these groups. For 

many snoRNA genes, alignments of orthological genes and 

gene variations from various plant species are accessible. It 

accessible via http://www.scri.sari.ac.uk/plant_snoRNA/. 

 

OGDD 

An Olive Genetic Diversity Database (OGDD) (17) is 

therefore provided http://www.bioinfo-cbs.org/ogdd/. It is a 

worldwide olive tree as well as oil genetic, morphological 

and chemical database with a dual function. In reality, it 

offers users with extra morphological and chemical data for 

each recognized cultivar in addition to being a reference 

system produced to identify unknown olive or virgin olive oil 

cultivars depending on their microsatellite allele size. Using a 

number of effective query interfaces and evaluation 

instruments, OGDD is currently intended to allow users to 

readily collect and visualize biologically significant data. 

 

PlantRNA 

Database of PlantRNA (18) http://plantrna.ibmp.cnrs.fr/   

compiles gene sequences of RNA (tRNA) transformation 

from completely annotated nuclear, plastidial as well as 

mitochondrial genomes. For highest performance and 

certainty, the array of annotated tRNA gene sequences was 

manually selected. This database's novelty lies in the 

incorporation of biological data appropriate to all the tRNAs 

stored in the library. This involves 30- and 50-flank 

sequences, transcription initiation region, A and B box 

sequences, and tRNA intron sequences, aminoacyl-tRNA 

synthetases, poly(T) transcription termination extends, and 

tRNA maturation and alteration enzymes. The present 

annotation includes the full genomes of 11 species: 5 

flowering plants ( Oryza sativa, Arabidopsis thaliana,  

Medicago truncatula, Populus trichocarpa, and 

Brachypodium distachyon), 2 red fungi (Ostreococcus tauri 

and Chlamydomonas rein-hardtii),  1 purple fungus 

(Ectocarpus siliculosus),1 glauco-phyte (Cyanophora 

paradoxa)  and 1 pennate diatom. 

 

PRGdb 

The Plant Resistance Genes database (19) http://prgdb. 

org has been modernized with a new software, new sections, 

new instruments and fresh genetic improvement information, 

enabling convenient entry not only to the plant science 

society but also to breeders who want to enhance resistance 

to plant disease. The home page provides an overview of 

easy-to-read search boxes for streamlining data queries and 

showing directly plant species for which candidate or cloned 

gene data were collected. For each host plant species, bulk 

information files and curated gene annotations are produced 

accessible. In order to show shared features with other genes, 

the fresh Gene Model view provides comprehensive data on 

each cloned resistance gene structure. PRGdb provides 153 

genes of reference resistance and Pathogen Receptor Genes 

(PRGs) annotated applicant 177072. Compared to the earlier 

publication, the amount of putative genes from 76 sequenced 

Viridiplantae and algae genomes has been improved from 

106 to 177 K. 

 

PineElm_SSRdb 

A total of 359511 SSRs were recognized in pineapple 

(chromosome sequence 356385, chloroplast sequence 45, 

mitochondrial sequence 249, and EST sequence 2832) (20). 

The database contains the list of EST-SSR tags and their 

information. Conclusions: PineElm SSRdb is a non-

commercial academic database accessible at http://app. 

bioelm.com/ with a mapping instrument that can create 

circular maps of the chosen target collection. For breeders, 

scientists and graduates operating on Ananas spp, this 

repository will be of enormous use. And others operating on 

cross-species marker transferability, diversity research, 

mapping and fingerprinting of genetic material. 

 

SBMDb 

Iquebal et al. (21) Using the Primer3 core, integrated at 

the backend in SBMDb, embedded markers and correlating 

location information of the selected chromosome, location / 

interval and primers could be produced. They as well 

reported 2027 polymorphic markers in a panel of five 

genotypes depending on e-PCR identification. These 

indicators can be used in variety enhancement program for 

DUS screening of variety recognition and MAS / GAS. The 

current database provides a broad source of probable markers 

for the development and implementation of fresh molecular 

breeding methods needed to boost the industrial use of this 

plant, particularly for sugar, health care goods, medications 

and color coloring. URL of the database: http://webapp. 

cabgrid.res.in/sbmdb/. 

http://www.scri.sari.ac.uk/plant_snoRNA/
http://www.bioinfo-cbs.org/ogdd/
http://plantrna.ibmp.cnrs.fr/


 
 

                                                                                                                                             Plant Molecular Biology Databases 

 

 

 
Highlights in BioScience                              DOI: 10.36462/H.BioSci.20191                              May 2019 | Volume2 
http://highlightsin.org/index.php/bioscience/                                 

Page 5 of 7 

SpinachDB 

Yang et al. (22) has been created to effectively record, 

annotate, mine and evaluate the datasets of genomics and 

genetics. All 21702 spinach genes have also been annotated. 

A total of 1,5741 spinach genes have been cataloged into 

4,351 families, including a significant number of 

transcription factors being identified. To build a high-density 

genetic map, 11 grown and wild spinach cultivars recognized 

a total of 131592 SSRs and 1125743 prospective SNPs 

situated in 548801 loci of spinach dna. The SpinachDB page 

includes seven primary parts, including the homepage; the 

GBrowse map integrating genes, genome, SNP and SSR 

marker data; the Blast alignment service; the search tool for 

gene family classification; the search tool for orthological 

and concurrent gene pairs; and the download and helpful 

contact data. In addition to the related data mining and 

assessment instruments, SpinachDB will be continuously 

extended to include freshly created solid genomics and 

genetic data sets. URL of your database: http://222.73.98.124 

/spinachdb. 

 

SisatBase 

Dossa et al. (23) recognized 138,194 genome-wide 

SSRs, 76.5% of which have been physically linked to the 13 

pseudo-chromosomes. Within these SSRs, up to three 

primers combinations were provided for 101,930 SSRs and 

used together with two freshly sequenced sesame accessions 

to amplify the reference genome in silico. A total of 79,957 

SSRs (78%) were polymorphic among the three genomes 

indicating their successful use in various breeding 

implementations assisted by genomics. Of 48 sesame 

accessions from various growing areas of Africa, 23 of these 

polymorphic SSRs were chosen and evaluated to have high 

polymorphic potential., In addition, SisatBase has established 

a user-friendly internet database that offers free access to 

SSR information as well as an embedded functional analysis 

tool. All in all, the SSR and SisatBase reference would serve 

as useful resources for genetic evaluation, genomic studies, 

and advancement of sesame breeding, particularly in 

developing countries. URL of the database: http://www. 

sesame-bioinfo.org/SisatBase/. 

 

Sinbase 

Sinbase was intended by Wang et al. (24), a internet-

based database with extensive genomic, genetic and relative 

genomic data on sesame. Sinbase involves pseudo-molecular 

chromosomal sequences of constructed sesame, transposable 

elements (372,167), protein-coding genes (27,148), and non-

coding RNAs (1,748). With multiple plant genomes as well 

as for Arabidopsis thaliana, Glycine max, Vitis vinifera, and 

Solanum lycopersicum, Sinbase offers distinctive and useful 

data on colinear areas. Sinbase also offers helpful search and 

data mining instruments, including a quest for keywords and 

local BLAST service. Is available free of charge at http:// 

ocri-genomics.org/Sinbase/. 

 

Ricebase 

Edwards et al. (25) created a Ricebase database and an 

integrative genomics database for rice (Oryza sativa) with a 

focus on merging datasets in a manner that retains important 

connections between previous and present genetic research. 

Ricebase involves information on DNA sequence, gene 

annotations, and data on nucleotide variety and statistics on 

molecular fragment size markers. Rice study has benefited 

from early acceptance and comprehensive use of easy 

sequence repetition (SSR) markers; however, most of the rice 

SSR models were created prior to the most recent rice 

pseudo-molecule assembly. The interpretation of recent 

studies using SNPs in the light of the literature quoting SSRs 

needs a common coordination scheme. SSR markers and 

laboraratoly tested amplicons sizes are provided in a web-

based relationship database and are accessible as a map 

placed in a genome browser with connections between the 

browser and the database. The merged capacities of Ricebase 

connect genetic markers, genome background, alleles 

throughout rice germplasm and possibly user-curated 

phenotypic interpretations as a community tool for genetic 

exploration and breeding in rice. It is publicly available at 

http://ricebase.org. 

 

ReprOlive 

Claros (26) provided an olive tree reproductive 

transcriptome database containing samples of pollen and 

pistil at separate phases of development, as well as leaf and 

root as a control of vegetative tissues. It was created from 

2,077,309 pure reads to 1,549 Sanger sequences. Using a 

predefined workflow centered on open-source instruments, 

sections were pre-processed, compiled, mapped, and 

annotated with expression information, GO terms, 

descriptions, InterPro tags, KEGG pathways, EC numbers, 

ORFs, and SSRs. Tentative transcripts (TTs) have also been 

annotated with the respective orthologists in the Arabidopsis 

thaliana of the TAIR and RefSeq records to allow the 

inclusion of LinkedData. The result is a reproductive 

transcriptome of 72,846 contigs with an median duration of 

686 bp, of which 63,965 (87.8 per cent) included at least one 

functional annotation, and 55,356 (75.9 per cent) had an 

orthologist. ReprOlive offers these outcomes with free access 

and download capacity. Retrieval processes for sequence as 

http://ricebase.org/


 
 

                                                                                                                                             Plant Molecular Biology Databases 

 

 

 
Highlights in BioScience                              DOI: 10.36462/H.BioSci.20191                              May 2019 | Volume2 
http://highlightsin.org/index.php/bioscience/                                 

Page 6 of 7 

well as transcript annotations are given. Graphical location of 

annotated enzymes in KEGG processes is also feasible. It 

freely available at http://reprolive.eez.csic.es. 

 

Planteome database 

The Planteome initiative (27) http://www.planteome.org   

offers a suite of reference and species-specific ontologies for 

crops and annotations of genes as well as phenotypes. 

Ontologies act as popular norms for the semantic integration 

of a wide and increasing body of plant phenomics, genomics, 

and genetic data. Reference ontologies involve Plant 

Ontology, Plant Treatment Ontology and Plant Experimental 

Conditions Ontology created by the Planteome initiative, 

along with Gene Chemical Entities in Biological Interest, 

Ontology, Attribute Ontology, Phenotype, and others.The 

initiative also offers access to species-specific Crop 

Ontologies created by multiple plant breeding and study 

groups around the globe. It also offers incorporated 

information on plant characteristics, phenotypes, and gene 

function and activity from 95 plant taxa, annotated with 

reference ontological terms. 

. 

 

 

Referances 

 

1.  Mokhtar MM, Adawy SS, El-Assal SE-DS, Hussein 

EHA. Genic and Intergenic SSR Database Generation, 

SNPs Determination and Pathway Annotations, in Date 

Palm (Phoenix dactylifera L.). PLoS One. Public 

Library of Science; 2016;11(7):e0159268.  

2. Adawy SS, Mokhtar MM, Alsamman AM, Sakr MM. 

Development of annotated EST-SSR database in olive 

(Olea europaea). Int J Sci Res. 2015;4(9):1063–73.  

3. Jiang J, Xing F, Zeng X, Zou Q. RicyerDB : A Database 

For Collecting Rice Yield-related Genes with 

Biological Analysis. Int J Biol Sci. 2018;14(8):965–70.  

4. Wang Y. PlantRGDB : A Database of Plant Retrocopied 

Genes Special Online Collection – Database Paper. 

Plant Cell Physiol. 2018;58(January 2017):1–7.  

5. Tavşanoğlu Ç, Pausas JG. Data Descriptor : A 

functional trait database for Mediterranean Basin 

plants. Sci DATA. 2018;5:1–18.  

6. Kabza M, Pokrzywa R, Gudys A. ERISdb : A Database 

of Plant Splice Sites and Splicing Signals. Plant Cell 

Physiol. 2018;54(January):1–8.  

7. Loukas A, Kappas I, Abatzopoulos TJ. HaloDom : a 

new database of halophiles across all life domains. J 

Biol Res. 2018;25(2):1–8.  

8. Shahmuradov IA, Gammerman AJ, Hancock JM, 

Bramley PM, Solovyev V V. PlantProm : a database of 

plant promoter sequences. Nucleic Acids Res. 

2018;31(1):114–7.  

9. Verma M, Kumar V, Patel RK, Garg R, Jain M. CTDB: 

An integrated chickpea transcriptome database for 

functional and applied genomics. PLoS One. 

2015;10(8):1–10.  

10.  Bhawna, Chaduvula PK, Bonthala VS, Manjusha V, 

Siddiq EA, Polumetla AK, et al. CmMDb: A versatile 

database for Cucumis melo microsatellite markers and 

other horticulture crop research. PLoS One. 

2015;10(4):1–11.  

11.  Doddamani D, Katta MA, Khan AW, Agarwal G, Shah 

TM, Varshney RK. CicArMiSatDB: the chickpea 

microsatellite database. BMC Bioinformatics [Internet]. 

2014;15(1):212. 

12.  Santos J, Al-azzawi M, Aronson J, Flowers TJ, 

Coimbra U De. eHALOPH a Database of Salt-Tolerant 

Plants : Helping put Halophytes to Work Special 

Online Collection – Database Paper. Plant Cell Physiol. 

2018;57(October 2015):1–10.  

13.  Avvaru AK, Saxena S, Sowpati DT, Mishra RK. 

MSDB: A Comprehensive Database of Simple 

Sequence Repeats. Genome Biol Evol. 

2017;9(6):1797–802.  

14.  Shirasawa K, Isobe S, Tabata S, Hirakawa H. Kazusa 

Marker DataBase: a database for genomics, genetics, 

and molecular breeding in plants. Breed Sci [Internet]. 

2014;64(3):264–71 

15.  Yu J, Dossa K, Wang L, Zhang Y, Wei X, Liao B, et 

al. PMDBase: A database for studying microsatellite 

DNA and marker development in plants. Nucleic Acids 

Res. 2017;45(D1):D1046–53.  

16.  Brown JWS, Echeverria M, Qu L, Lowe TM, 

Kastenmayer JP, Bachellerie J, et al. Plant snoRNA 

database. Nucleic Acids Res. 2003;31(1):432–5.  

17.  Ben Ayed R, Ben Hassen H, Ennouri K, Ben Marzoug 

R, Rebai A. OGDD (Olive Genetic Diversity 

http://reprolive.eez.csic.es/
http://www.planteome.org/


 
 

                                                                                                                                             Plant Molecular Biology Databases 

 

 

 
Highlights in BioScience                              DOI: 10.36462/H.BioSci.20191                              May 2019 | Volume2 
http://highlightsin.org/index.php/bioscience/                                 

Page 7 of 7 

Database): A microsatellite markers’ genotypes 

database of worldwide olive trees for cultivar 

identification and virgin olive oil traceability. Database. 

2016;2016:1–9.  

18.  Daujat M, Duche A, Gobert A, Salinas T, Michaud M, 

Gutmann B, et al. PlantRNA , a database for tRNAs of 

photosynthetic eukaryotes. Nucleic Acids Res. 

2012;41(October 2012):273–9.  

19.  Osuna-cruz CM, Paytuvi-gallart A, Donato A Di, 

Sundesha V, Andolfo G, Cigliano RA, et al. PRGdb 3 . 

0 : a comprehensive platform for prediction and 

analysis of plant disease resistance genes. Nucleic 

Acids Res. Oxford University Press; 

2018;46(November 2017):1197–201.  

20.  Chaudhary S, Mishra BK, Vivek T, Magadum S, Yasin 

JK. PineElm_SSRdb: a microsatellite marker database 

identified from genomic, chloroplast, mitochondrial and 

EST sequences of pineapple (Ananas comosus (L.) 

Merrill). Hereditas. Hereditas; 2016;153(1):16.  

21.  Iquebal MA, Jaiswal S, Angadi UB, Sablok G, Arora 

V, Kumar S, et al. SBMDb: First whole genome 

putative microsatellite DNA marker database of 

sugarbeet for bioenergy and industrial applications. 

Database. 2015;2015(1):1–10.  

22.  Yang XD, Tan HW, Zhu WM. SpinachDB: A Well-

Characterized Genomic Database for Gene Family 

Classification and SNP Information of Spinach. PLoS 

One. 2016;11(5):e0152706.  

23.  Dossa K, Yu J, Liao B, Cisse N, Zhang X. 

Development of Highly Informative Genome-Wide 

Single Sequence Repeat Markers for Breeding 

Applications in Sesame and Construction of a Web 

Resource : SisatBase. Front Plant Sci. 

2017;8(August):1–10.  

24.  Wang L, Yu J, Li D, Zhang X, E-mail C. Sinbase : An 

Integrated Database to Study Genomics , Genetics and 

Comparative Genomics in Sesamum indicum Special 

Online Collection – Database Paper. Plant Cell Physiol. 

2018;56.  

25.  Edwards JD, Baldo AM, Mueller LA. Ricebase: a 

breeding and genetics platform for rice, integrating 

individual molecular markers, pedigrees and whole-

genome-based data. Database. Oxford University Press; 

2016;2016.  

26.  Claros MG. ReprOlive : a database with linked data for 

the olive tree ( Olea europaea L .) reproductive 

transcriptome. Front Plant Sci. 2015;6(August):1–14.  

27.  Cooper L, Meier A, Elser JL, Mungall C, Sinn BT, 

Cavaliere D, et al. The Planteome database : an 

integrated resource for reference ontologies , plant 

genomics and phenomics. Nucleic Acids Res. 

2018;46(November 2017):1168–80.  

 

 

 

 

 

 


