Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana)

Usha, S.; Jyothi, M. N.; Suchithra, B.; Dixit, Rekha; Vijay, Durg; Babu, R. Nagesh

doi:10.1007/s12539-015-0130-y

Cited by 6 publications

(2 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Because of the functional importance of miRNAs in the field of molecular biology, significant research has been conducted in this area, leading to the development of many tools (Chou et al., 2016; Backes et al., 2017) for the in silico identification of miRNA and their target genes. Based on the characteristics of miRNA conserved across different species, novel miRNAs have been successfully identified from EST sequences using computational methods in Pinctada martensii (Zheng et al., 2016) and Eleusine coracana (Usha et al., 2017).…”

Section: Introductionmentioning

confidence: 99%

Improved annotation of Lutzomyia longipalpis genome using bioinformatics analysis

Yang

2019

PeerJ

View full text Add to dashboard Cite

Lutzomyia longipalpis, a sand fly, is a vector-spreading pathogenic protozoan in the New World. MicroRNA (miRNA) is evolutionarily-conserved non-coding RNA, which plays critical roles in various biological processes. To date, the functions of most proteins in L. longipalpis are unknown, and few studies have addressed the roles of miRNAs in this species. In the present study, we re-annotated the protein-coding genes and identified several miRNAs using a set of comparative genomics tools. A large number of L. longipalpis proteins were found to be homologous with those in the mosquito genome, indicating that they may have experienced similar selective pressures. Among these proteins, a set of 19 putative salivary proteins were identified, which could be used for studying the transmission of Leishmania. Twenty-one novel miRNAs were characterized, including two miRNAs, miR-4113-5p and miR-5101, which are unique to L. longipalpis. Many of the targets of these two genes were found to be involved in ATP hydrolysis-coupled proton transport, suggesting that they may have important roles in the physiology of energy production. Topology analysis of the miRNA-gene network indicated that miR-9388-5p and miR-3871-5p regulate several critical genes in response to disease development. In conclusion, our work provides a basis for improving the genome annotation of L. longipalpis, and opens a new door to understanding the molecular regulatory mechanisms in this species.

show abstract

Section: Introductionmentioning

confidence: 99%

Improved annotation of Lutzomyia longipalpis genome using bioinformatics analysis

Yang

2019

PeerJ

View full text Add to dashboard Cite

show abstract

“…Till date, miRNAs have been identified in variety of species using computational approach such as silkworm, where 16 novel miRNAs were identified using homology search of Genomic survey sequence (GSS) [9], 8 potential novel miRNAs were identified in Festuca arundinacea using ESTs and GSS [10], 6 miRNAs that regulate twenty potential targets were predicted in mulberry [11], in Soybean 521 novel miRNA genes belonging to 58 families were identified [12]. Three conserved miRNAs belonging to miR166 and miR1310 were identified in Finger millet using ESTs [13]. Niger (Guizotia abyssinica (L. f.) Cass, Compositae) is a dicotyledonous herb and oilseed crop cultivated in Ethiopia and India.…”

Section: Introductionmentioning

confidence: 99%

Computational identification of miRNAs and their targets from Niger (Guizotia abyssinica)

2017

J App Biol Biotech

View full text Add to dashboard Cite

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. In this study we used homology-based analysis with available expressed sequence tag (EST) of Niger (Guizotia abyssinica) to predict conserved miRNAs. Two potent miRNAs targeting 49 genes were identified. The newly identified miRNAs belongs to miR2592 and miR396 family. Targets recognized were F-box proteins, leucine zipper, DEAD box RNA helicase, disease resistant proteins. Gene annotations revealed miRNAs were involved in growth and development and Encyclopaedia of Genes and Genomes (KEGG) pathway analyses showed miRNAs were involved in metabolic pathways.

show abstract

In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L.

Kohnehrouz

Bastami

Nayeri

2017

Interdiscip Sci Comput Life Sci

View full text Add to dashboard Cite

microRNAs (miRNAs) are a newly discovered class of non-coding small RNAs roughly 22 nucleotides long. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation, apoptosis and stress responses. The identification of miRNAs and their targets is an important need to understand their roles in the development and physiology of sweet onion (Allium cepa). In this research, several computational approaches were combined to make concise prediction of the potential miRNAs and their targets. We used previously known miRNAs from other plant species against Expressed Sequence Tags (EST) database to search for the potential miRNAs. As a result, nine potential miRNAs were identified in eight ESTs of A. cepa, belonging to eight families. We could further BLAST the mRNA database and found total 154 number of the potential targets in A. cepa based on these potential miRNAs. According to the mRNA target information provided by NCBI, most of the target mRNAs appeared to be involved in plant growth, signal transduction, development, and stress responses. Gene ontology (GO) analysis implicated these targets in 32 biological processes such as protein ubiquitination, plant hormone signalling pathways and heme biosynthesis.

show abstract

Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana)

Cited by 6 publications

References 37 publications

Improved annotation of Lutzomyia longipalpis genome using bioinformatics analysis

Improved annotation of Lutzomyia longipalpis genome using bioinformatics analysis

Computational identification of miRNAs and their targets from Niger (Guizotia abyssinica)

In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L.

Contact Info

Product

Resources

About