Genome-wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa

Parameswari Paul,Vignesh Dhandapani,Jana Jeevan Rameneni,Xiaonan Li,Ganesan Sivanandhan,Su Ryun Choi,Wenxing Pang,Subin Im,Yong Pyo Lim 한국원예학회 2016 한국원예학회 학술발표요지 Vol.2016 No.5

Genome wide identification and functional prediction of long non-coding RNAs in Brassica rapa

임용표,Parameswari Paul,Vignesh Dhandapani,최수련 한국유전학회 2016 Genes & Genomics Vol.38 No.6

Long non-coding RNAs (LncRNAs) are a large, diverse class of RNA molecules that has garnered attention for their potential to regulate gene expression and been identified in various organisms. Here we report the first prediction of lncRNAs in Brassica rapa (B. rapa) genome using computational method. We subjected the publicly available full length cDNA sequences and identified 2237 candidate lncRNAs, characterized their functions based on insilico methods. Housekeeping and small regulatory non-coding RNAs (ncRNAs) were removed from the pool. Although 14–15 % of the total sequences were predicted to be non-coding initially, on filtering only 4.6 % of the total sequences were predicted as lncRNAs carrying a large number of simple repeats. The lncRNAs had an average length of 497 bp and were mapped on each chromosome of B. rapa. They were classified to 4 groups based on their origin. Thirty six motifs involving transcription related activities, signaling mechanism and stress response were identified in the lncRNAs. Repeat elements and neighboring genes of the lncRNAs were analyzed since they were associated in function and regulating the expression of these long non-coding RNAs. We believe that this study would be an initial and reference for any further studies regarding long non-coding RNAs in B. rapa and other Brassica crops.

MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics

Vignesh, Dhandapani,Parameswari, Paul,Im, Su-Bin,Kim, Hae-Jin,Lim, Yong-Pyo Korea Genome Organization 2011 Genomics & informatics Vol.9 No.1

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics

Dhandapani Vignesh,Paul Parameswari,임수빈,김해진,임용표 한국유전체학회 2011 Genomics & informatics Vol.9 No.1

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA’s is a method in practice, computational identification of miRNA’s has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user’s interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk(Tool kit widgets) scripting languages. It is user friendly,portable offline software that works in all windows OS, sized to 3 MB.

Identification of potential microRNAs and their targets in Brassica rapa L.

Dhandapani, Vignesh,Ramchiary, Nirala,Paul, Parameswari,Kim, Joonki,Choi, Sun Hee,Lee, Jeongyeo,Hur, Yoonkang,Lim, Yong Pyo Springer-Verlag 2011 Molecules and cells Vol.32 No.1

Development of EST database and transcriptome analysis in the leaves of Brassica rapa using a newly developed pipeline

Vignesh Dhandapani,최수련,Parameswari Paul,김용권,Nirala Ramchiary,허윤강,임용표 한국유전학회 2012 Genes & Genomics Vol.34 No.6

Brassica rapa L. (AA, 2n = 20), an A genome diploid species of Brassica genus is of researchers interest recent days since enormous amount of data is available about the genome. Since EST analysis is a powerful tool in gene discovery we compared different existing methods and developed a new pipeline for EST computational analysis to analyze the available data. A total of 1,438 expressed sequence tags sizing from 83 to 2,023 base pairs were generated and subjected to various types of analysis. Cluster analysis of these ESTs identified 969unique sequences called unigenes, with 162 contigs and 807singlets. Similarity search produced 704 significant hits with E-value ≥ 10-5. The functions of the best hits were annotated by gene ontology (GO) analysis. Additionally, we classified 293 and 541 unigenes based on their functions, using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and protein structural domain databases, respectively. We also identified and categorized 171 microsatellites into di-, tri-, tetra-,and penta nucleotide repeats, and designed primers. Possible open reading frames (ORFs) were predicted for 960unigenes, by the comparison with a primary protein sequence database. In silico mapping of partial unigenes were done in bacterial artificial chromosome (BAC) sequences, downloaded from the Brassica genome project website. We determined 149single nucleotide polymorphisms (SNPs) and 3 indels from the coding region of 27 unigenes of B. rapa and similar Brassica napus ESTs clusters. All the generated EST sequences were submitted to the GenBank EST database (dbEST) as accessions from CO749247 to CO750425.

BrTraD : Database for Classification, Expression, and Functional Analysis of Genes in Brassica rapa

Seongmin Hong,Vignesh Dhandapani,Parameswari Paul,Devaraj Sangeeth Prasath,Su Ryun Choi,Man-sun Kim,Yong Pyo Lim 한국원예학회 2017 한국원예학회 학술발표요지 Vol.2017 No.5

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Vignesh Dhandapani,Nirala Ramchiary,Parameswari Paul,김준기,최선희,Jeongyeo Lee,Yoonkang Hur,임용표 한국분자세포생물학회 2011 Molecules and cells Vol.32 No.1

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA- mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20th position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualita-tively in different tissues of B. rapa.

Genome-wide identification, characterization, and comparative phylogeny analysis of MADS-box transcription factors in Brassica rapa

Jana Jeevan Rameneni,임용표,Vignesh Dhandapani,Parameswari Paul,임수빈,오만호,최수련 한국유전학회 2014 Genes & Genomics Vol.36 No.4

The involvement of MADS-box transcriptionfactors in the development of seeds, flowers, and fruit iswell known. Large numbers of MADS-box genes havebeen characterized and reported in major plants such asArabidopsis thaliana (107), Oryza sativa (75), Zea mays(75), and Cucumis sativus (43). However, there is littleinformation about MADS-box genes in the economicallyand morphologically important genus Brassica. Thus, weperformed a series of computational analyses on therecently published Brassica rapa genome and identified167 potential MADS-box genes. Chromosomal localizationof these genes revealed many duplicate genes and 10 tandemrepeats from B. rapa chromosomes, though none onA04, A08, and A10. Neighbor-joining phylogenetic analysiswas performed between B. rapa, A. thaliana, O. sativa,Z. mays, and C. sativus genes, and type-I and type-IIgroups were differentiated by their gene clades. Based ontheir phylogeny and functional characters, type-I group wasdivided into three clades and type-II group into 14 clades. Prediction and comparison of intron and exon patterns ofMADS-box genes authenticates the major differencebetween the groups. Semi-quantitative RT-PCR analysiswas carried out for 25 functionally categorized BrMADSboxgenes and comparatively studied among buds, sepals,petals, stamens, carpels, and siliques of the parental lineRcBr. The structural and functional annotation, as well asexpressional profiling of BrMADS in floral organs in thisstudy will be the basis of further functional validation andmolecular breeding of B. rapa crops.

Understanding Regulation of Clubroot Disease and Development of Molecular Markers for Accelerated Breeding

Su Ryun Choi,Sang Heon Oh,Parameswari Paul,Sushil Satish Chhapekar,Jana Jeevan Rameneni,Vignesh Dhandapani,Song Yeon Han,Chang Yeol Lee,Gyung Ja Choi,Yong Pyo Lim 한국원예학회 2021 한국원예학회 학술발표요지 Vol.2021 No.10

Clubroot (CR) caused by Plasmodiophora brassicae is a severe disease that decreases crop quality and productivity in cruciferous crops. Clubroot resistance linked quantitative trait loci and candidate genes have been identified during last two decades. However, disease lead crop damage continues to occur owing to differences in host variety and constant pathogen variation. Therefore, continued development of markers is required, and the underlying regulatory mechanisms such as the interrelationships between genes and the way in which genes are regulated need to be investigated. MicroRNAs (miRNAs) are attracting attention as regulators of gene expression, including during biotic stress responses. We try to understand how miRNAs regulate clubroot resistance-related genes in P. brassicae-infected Brassica rapa. Two Brassica miRNAs, Bra-miR1885a and Bra-miR1885b, were revealed to target TIR-NBS genes. In non-infected plants, both miRNAs were expressed at low levels to maintain the balance between plant development and basal immunity. However, their expression levels increased in P. brassicae-infected plants. Both miRNAs down regulated the expression of the TIR-NBS genes Bra019412 and Bra019410, which are located at a clubroot resistance-related quantitative trait locus. A qRT-PCR analysis revealed Bra019412 expression was negatively regulated by miR1885. A 5-prime rapid amplification of cDNA ends analysis confirmed the cleavage of Bra019412 by Bra-miR1885b. Thus, miR1885s potentially regulate CR resistance associated TIR-NBS gene expression during P. brassicae infections of B. rapa. Additionally, we have identified the candidate genes against ‘Banglim’ pathotype by fine-mapping with two inbred line 09CR500 and 09CR501. And we developed the novel gene-based markers based on ORF1, ORF2, ORF3 encoding TNL. And using diverse public available information, we have tested the marker availability with core collection population and improved. Those marker information will be useful in Brassica breeding programs such as marker-assisted selection and gene pyramiding to identify and develop resistant line and cultivars.