scholarly journals In Silico Investigation of Conserved miRNAs and Their Targets From the Expressed Sequence Tags in Neospora Caninum Genome

2021 ◽  
Vol 15 ◽  
pp. 117793222110467
Author(s):  
Moumita Das ◽  
Mahmudul Hasan ◽  
Sharmin Akter ◽  
Sawrab Roy ◽  
Binayok Sharma ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Developmental Stages ◽  
Neospora Caninum ◽  
Protozoan Parasite ◽  
Study Finding ◽  
Mature Mirnas ◽  
Etiologic Agent ◽  
Homology Search ◽  
Specific Gene ◽  
Expressed Sequence

Neospora caninum is a protozoan parasite, the etiologic agent of Neosporosis—a common cause of abortion in cattle worldwide. Herd level prevalence of Neosporosis could be as high as 90%. However, there is no approved treatment and vaccines available for Neosporosis. MicroRNA (miRNA) based prophylaxis and therapeutics could be options for Neosporosis in cattle and other animals. The current study aimed to investigate the genome of Neospora caninum to identify and characterize the conserved miRNAs through Expressed Sequence Tags (ESTs) dependent homology search. A total of 1,041 mature miRNAs of reference organisms were employed against 336 non-redundant ESTs available in the genome of Neospora caninum. The study predicted one putative miRNA “nca-miR-9388-5p” of 19 nucleotides with MFEI value -1.51 kcal/mol and (A + U) content% 72.94% corresponding with its pre-miRNA. A comprehensive search for specific gene targets was performed and discovered 16 potential genes associated with different protozoal physiological functions. Significantly, the gene “Protein phosphatase” was found responsible for the virulence of Neospora caninum. The other genes were accounted for gene expression, vesicular transport, cell signaling, cell proliferation, DNA repair mechanism, and different developmental stages of the protozoon. Therefore, this study finding will provide pivotal information to future aspirants upon Bovine Neosporosis. It will also serve as the baseline information for further studies of the bioinformatics approach to identify other protozoal miRNAs.

Analysis of expressed sequence tags from biodiesel plant Jatropha curcas embryos at different developmental stages

Plant Science ◽  
2011 ◽  
Vol 181 (6) ◽  
pp. 696-700 ◽  
Author(s):  
Mao-Sheng Chen ◽  
Gui-Juan Wang ◽  
Ru-Ling Wang ◽  
Jun Wang ◽  
Song-Quan Song ◽  
...  
Keyword(s):  
Jatropha Curcas ◽  
Expressed Sequence Tags ◽  
Developmental Stages ◽  
Expressed Sequence

Generation, Identification, and Evaluation of Expressed Sequence Tags from Different Developmental Stages of the Asian Blood FlukeSchistosoma japonicum

1998 ◽  
Vol 252 (2) ◽  
pp. 348-356 ◽  
Author(s):  
Jinjiang Fan ◽  
Dennis J. Minchella ◽  
Sharon R. Day ◽  
Donald P. McManus ◽  
Wilfred U. Tiu ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Developmental Stages ◽  
Expressed Sequence

Expressed sequence tags from persimmon at different developmental stages

2008 ◽  
Vol 27 (5) ◽  
pp. 931-938 ◽  
Author(s):  
T. Nakagawa ◽  
A. Nakatsuka ◽  
K. Yano ◽  
S. Yasugahira ◽  
R. Nakamura ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Developmental Stages ◽  
Expressed Sequence

scholarly journals Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 176 ◽  
Author(s):  
Jason W Abernathy ◽  
Peng Xu ◽  
Ping Li ◽  
De-Hai Xu ◽  
Huseyin Kucuktas ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Protozoan Parasite ◽  
Ichthyophthirius Multifiliis ◽  
Ciliate Protozoan ◽  
Expressed Sequence

scholarly journals Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense

2009 ◽  
Vol 168 (1) ◽  
pp. 34-42 ◽  
Author(s):  
Jared R. Helm ◽  
Christiane Hertz-Fowler ◽  
Martin Aslett ◽  
Matthew Berriman ◽  
Mandy Sanders ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Developmental Stages ◽  
Trypanosoma Congolense ◽  
Expressed Sequence

scholarly journals Identification and Characterization of Microsatellites in Expressed Sequence Tags and Their Cross Transferability in Different Plants

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Shamshad ul Haq ◽  
Rohit Jain ◽  
Meenakshi Sharma ◽  
Sumita Kachhwaha ◽  
S. L. Kothari
Keyword(s):  
Expressed Sequence Tags ◽  
Polymorphic Information Content ◽  
Average Density ◽  
Trinucleotide Repeats ◽  
Homology Search ◽  
Potential Source ◽  
Genomic Studies ◽  
Identification And Characterization ◽  
Expressed Sequence

Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.

scholarly journals Analysis of Medicago truncatula Nodule Expressed Sequence Tags

2000 ◽  
Vol 13 (1) ◽  
pp. 62-71 ◽  
Author(s):  
János Györgyey ◽  
Danièle Vaubert ◽  
José I. Jiménez-Zurdo ◽  
Celine Charon ◽  
Liliane Troussard ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expressed Sequence Tags ◽  
Sinorhizobium Meliloti ◽  
Expression Patterns ◽  
Homology Search ◽  
Cdna Clones ◽  
Systematic Analysis ◽  
And Function ◽  
Nodulin Genes ◽  
Expressed Sequence

Systematic sequencing of expressed sequence tags (ESTs) can give a global picture of the assembly of genes involved in the development and function of organs. Indeterminate nodules representing different stages of the developmental program are especially suited to the study of organogenesis. With the vector λHybriZAP, a cDNA library was constructed from emerging nodules of Medicago truncatula induced by Sinorhizobium meliloti. The 5′ ends of 389 cDNA clones were sequenced, then these ESTs were analyzed both by sequence homology search and by studying their expression in roots and nodules. Two hundred fifty-six ESTs exhibited significant similarities to characterized data base entries and 40 of them represented 26 nodulin genes, while 133 had no similarity to sequences with known function. Only 60 out of the 389 cDNA clones corresponded to previously submitted M. truncatula EST sequences. For 117 cDNAs, reverse Northern (RNA) hybridization with root and nodule RNA probes revealed enhanced expression in the nodule, 48 clones are likely to code for novel nodulins, 33 cDNAs are clones of already known nodulin genes, and 36 clones exhibit similarity to other characterized genes. Thus, systematic analysis of the EST sequences and their expression patterns is a powerful way to identify nodule-specific and nodulation-related genes.

scholarly journals Gene Discovery and Expression Profile Analysis through Sequencing of Expressed Sequence Tags from Different Developmental Stages of the Chytridiomycete Blastocladiella emersonii

2005 ◽  
Vol 4 (2) ◽  
pp. 455-464 ◽  
Author(s):  
Karina F. Ribichich ◽  
Silvia M. Salem-Izacc ◽  
Raphaela C. Georg ◽  
Ricardo Z. N. Vêncio ◽  
Luci D. Navarro ◽  
...  
Keyword(s):  
Life Cycle ◽  
Expression Profile ◽  
Expressed Sequence Tags ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Protein Biosynthesis ◽  
Northern Analysis ◽  
Cdna Clones ◽  
Blastocladiella Emersonii ◽  
Expressed Sequence

ABSTRACT Blastocladiella emersonii is an aquatic fungus of the chytridiomycete class which diverged early from the fungal lineage and is notable for the morphogenetic processes which occur during its life cycle. Its particular taxonomic position makes this fungus an interesting system to be considered when investigating phylogenetic relationships and studying the biology of lower fungi. To contribute to the understanding of the complexity of the B. emersonii genome, we present here a survey of expressed sequence tags (ESTs) from various stages of the fungal development. Nearly 20,000 cDNA clones from 10 different libraries were partially sequenced from their 5′ end, yielding 16,984 high-quality ESTs. These ESTs were assembled into 4,873 putative transcripts, of which 48% presented no matches with existing sequences in public databases. As a result of Gene Ontology (GO) project annotation, 1,680 ESTs (35%) were classified into biological processes of the GO structure, with transcription and RNA processing, protein biosynthesis, and transport as prevalent processes. We also report full-length sequences, useful for construction of molecular phylogenies, and several ESTs that showed high similarity with known proteins, some of which were not previously described in fungi. Furthermore, we analyzed the expression profile (digital Northern analysis) of each transcript throughout the life cycle of the fungus using Bayesian statistics. The in silico approach was validated by Northern blot analysis with good agreement between the two methodologies.

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