A web accessible resource for investigating cassava phenomics and genomics information: BIOGEN BASE

Jayakodi, Murukarthick; selvan, Sreedevi Ghokhilamani; Natesan, Senthil; Raveendran, M.; Duraisamy, Raghu; Ramineni, Jana Jeevan; Rathinasamy, Sakthi Ambothi; Karuppusamy, Nageswari; Lakshmanan, P.; Chokkappan, Mohan

doi:10.6026/97320630006391

Cited by 4 publications

(3 citation statements)

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“…Two groups of samples, including the PRRSV-infected PTR2 cells and the normal control group with three replicates, were collected; thus, a total of six samples (MOCK1 MOCK2, MOCK3, PRRSV1, PRRSV2, and PRRSV3) were subjected to Next Generation Sequencing (NGS, Illumina PE150/SE50). The original image file was designed using CASAVA base identification of the sequence-read section [ 15 ]. A small number of reads with sequence joints or low sequencing quality were filtered out and the sequence error rate and GC content distribution were checked out.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide mRNA and Long Non-Coding RNA Analysis of Porcine Trophoblast Cells Infected with Porcine Reproductive and Respiratory Syndrome Virus Associated with Reproductive Failure

Zhang

Liu

Peng

et al. 2023

IJMS

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Porcine reproductive and respiratory syndrome (PRRS) is a vertically transmitted reproductive disorder that is typically characterized by miscarriage, premature birth, and stillbirth in pregnant sows after infection. Such characteristics indicate that PRRSV can infect and penetrate the porcine placental barrier to infect fetus piglets. The porcine trophoblast is an important component of the placental barrier, and secretes various hormones, including estrogen and progesterone, to maintain normal pregnancy and embryonic development during pregnancy. It is conceivable that the pathogenic effects of PRRSV infection on porcine trophoblast cells may lead to reproductive failure; however, the underlying detailed mechanism of the interaction between porcine trophoblast (PTR2) cells and PRRSV is unknown. Therefore, we conducted genome-wide mRNA and long non-coding RNA (lncRNA) analysis profiling in PRRSV-infected PTR2. The results showed that 672 mRNAs and 476 lncRNAs were significantly different from the control group after viral infection. Target genes of the co-expression and co-location of differential mRNAs and lncRNAs were enriched by GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, revealing that most of the pathways were involved in cell nutrient metabolism, cell proliferation, and differentiation. Specifically, the estrogen signaling pathway, the PI3K (PhosphoInositide-3 Kinase)-Akt (serine/threonine kinase) signaling pathway, and the insulin secretion related to embryonic development were selected for analysis. Further research found that PRRSV inhibits the expression of G-protein-coupled estrogen receptor 1 (GPER1), thereby reducing estrogen-induced phosphorylation of AKT and the mammalian target of rapamycin (mTOR). The reduction in the phosphorylation of AKT and mTOR blocks the activation of the GPER1- PI3K-AKT-mTOR signaling pathway, consequently restraining insulin secretion, impacting PTR2 cell proliferation, differentiation, and nutrient metabolism. We also found that PRRSV triggered trophoblast cell apoptosis, interrupting the integrity of the placental villus barrier. Furthermore, the interaction network diagram of lncRNA, regulating GPER1 and apoptosis-related genes, was constructed, providing a reference for enriching the functions of these lncRNA in the future. In summary, this article elucidated the differential expression of mRNA and lncRNA in trophoblast cells infected with PRRSV. This infection could inhibit the PI3K-AKT-mTOR pathway and trigger apoptosis, providing insight into the mechanism of the vertical transmission of PRRSV and the manifestation of reproductive failure.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide mRNA and Long Non-Coding RNA Analysis of Porcine Trophoblast Cells Infected with Porcine Reproductive and Respiratory Syndrome Virus Associated with Reproductive Failure

Zhang

Liu

Peng

et al. 2023

IJMS

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“…The user-friendly interface, i.e. the client tier, was developed using PHP (v4.3.9) and JavaScript [ 39 - 41 ]. In the database tier, all information related to the mTEs is stored in a MySQL (v4.1.20) database.…”

Section: Resultsmentioning

confidence: 99%

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

et al. 2014

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BackgroundMITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops.FindingsWe have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences.ConclusionsBrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php.

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“…A ‘precise query’ is formulated in such a way that it returns what the user wants without superfluous results. To enable precision in a query, an appropriate set of relational operators, as well as direct access to the underlying data, must be provided [2, 3]. MySQL is a data storage area in which small sections called TABLES.…”

Section: Methodsmentioning

confidence: 99%

MAGICdb – Mango Genetic stocks Identification and Characterisation database

Asaithambi

Natesan²,

Venkatesan³

et al. 2013

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MAGICdb is a unique database that integrates the morphological, fruit quality and the marker data of most popular and widely cultivated commercially important mango cultivars. The main objective of MAGICdb is to provide the end users with an integrated dataset of each mango variety cultivated widely in Tamil Nadu. MAGICdb structure is categorized in to three domains namely Morphological Data Search, Fruit Quality Search and Marker Search which in further contains details on Tree Character, Bearing Habit, Season of fruiting, Number of inflorescence/Sq.m, Percentage of hermaphrodite flower(%), Fruit set percentage(%), Number of fruits/ tree, Fruit weight (g) and, Yield (Kg/ tree). This database is equipped with a user friendly interface enabling the users to retrieve the information with ease. Database is available at http://www.tnaugenomics.com/mango/index.php

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A web accessible resource for investigating cassava phenomics and genomics information: BIOGEN BASE

Cited by 4 publications

References 0 publications

Genome-Wide mRNA and Long Non-Coding RNA Analysis of Porcine Trophoblast Cells Infected with Porcine Reproductive and Respiratory Syndrome Virus Associated with Reproductive Failure

Genome-Wide mRNA and Long Non-Coding RNA Analysis of Porcine Trophoblast Cells Infected with Porcine Reproductive and Respiratory Syndrome Virus Associated with Reproductive Failure

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

MAGICdb – Mango Genetic stocks Identification and Characterisation database

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