scholarly journals Characterization of Frond and Flower Development and Identification of FT and FD Genes From Duckweed Lemna aequinoctialis Nd

2021 ◽  
Vol 12 ◽  
Author(s):  
Akiko Yoshida ◽  
Ken-ichiro Taoka ◽  
Aoi Hosaka ◽  
Keisuke Tanaka ◽  
Hisato Kobayashi ◽  
...  
Keyword(s):  
Flower Development ◽  
De Novo ◽  
Wide Distribution ◽  
Proximal Region ◽  
Flower Formation ◽  
Rna Seq ◽  
Flowering Locus T ◽  
Protein Protein Interaction ◽  
Transcriptional Complex

Duckweeds (Araceae: Lemnoideae) are aquatic monocotyledonous plants that are characterized by their small size, rapid growth, and wide distribution. Developmental processes regulating the formation of their small leaf-like structures, called fronds, and tiny flowers are not well characterized. In many plant species, flowering is promoted by the florigen activation complex, whose major components are florigen FLOWERING LOCUS T (FT) protein and transcription factor FD protein. How this complex is regulated at the molecular level during duckweed flowering is also not well understood. In this study, we characterized the course of developmental changes during frond development and flower formation in Lemna aequinoctialis Nd, a short-day plant. Detailed observations of frond and flower development revealed that cell proliferation in the early stages of frond development is active as can be seen in the separate regions corresponding to two budding pouches in the proximal region of the mother frond. L. aequinoctialis produces two stamens of different lengths with the longer stamen growing more rapidly. Using high-throughput RNA sequencing (RNA-seq) and de novo assembly of transcripts from plants induced to flower, we identified the L. aequinoctialis FT and FD genes, whose products in other angiosperms form a transcriptional complex to promote flowering. We characterized the protein-protein interaction of duckweed FT and FD in yeast and examined the functions of the two gene products by overexpression in Arabidopsis. We found that L. aequinoctialis FTL1 promotes flowering, whereas FTL2 suppresses flowering.

scholarly journals De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

2013 ◽  
Vol 14 (1) ◽  
pp. 58-67 ◽  
Author(s):  
Wei Wang ◽  
Cai-yan Li ◽  
Chu-tian Ge ◽  
Lei Lei ◽  
You-ling Gao ◽  
...  
Keyword(s):  
De Novo ◽  
Rna Seq ◽  
Pelodiscus Sinensis

scholarly journals Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data

2021 ◽  
pp. gr.271627.120
Author(s):  
Zhaozhao Zhao ◽  
Qiushi Xu ◽  
Ran Wei ◽  
Weixu Wang ◽  
Dong Ding ◽  
...  
Keyword(s):  
De Novo ◽  
Biological Significance ◽  
Rna Seq ◽  
Coding Region ◽  
Dynamic Changes ◽  
Cancer Tumor ◽  
Tumor Types ◽  
Pan Cancer ◽  
Intronic Poly

Intronic polyadenylation (IpA) usually leads to changes in coding region of an mRNA, and its implication in diseases has been recognized, though at its very beginning status. Conveniently and accurately identifying IpA is of great importance for further evaluating its biological significance. Here, we developed IPAFinder, a bioinformatic method for the de novo identification of intronic poly(A) sites and their dynamic changes from standard RNA-seq data. Applying IPAFinder to 256 pan-cancer tumor/normal pairs across six tumor types, we discovered 490 recurrent dynamically changed IpA events, some of which are novel and derived from cancer-associated genes such as TSC1, SPERD2, and CCND2. Furthermore, IPAFinder revealed that IpA could be regulated by factors related to splicing and m6A modification. In summary, IPAFinder enables the global discovery and characterization of biologically regulated IpA with standard RNA-seq data and should reveal the biological significance of IpA in various processes.

scholarly journals Gibberellin Induced Transcriptome Profiles Reveal Gene Regulation of Loquat Flowering

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuanyuan Jiang ◽  
Yicun Liu ◽  
Yongshun Gao ◽  
Jiangrong Peng ◽  
Wenbing Su ◽  
...  
Keyword(s):  
Flower Development ◽  
Crop Production ◽  
Gene Families ◽  
Fruit Trees ◽  
Flower Formation ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Autumn And Winter ◽  
And Control ◽  
Floral Bud

Flowering is an integral part of the life cycle of flowering plants, which is essential for plant survival and crop production. Most woody fruit trees such as apples and pears bloom in spring, but loquat blooms in autumn and winter. Gibberellin (GA) plays a key role in the regulation of plant flower formation. In this study, we sprayed loquat plants with exogenous GA3, which resulted in vigorous vegetative growth rather than floral bud formation. We then performed a comprehensive RNA-seq analysis on GA3-treated and control-treated leaves and buds over three time periods to observe the effects of exogenous GA3 application on floral initiation and development. The results showed that 111 differentially expressed genes (DEGs) and 563 DEGs were down-regulated, and 151 DEGs and 506 DEGs were up-regulated in buds and leaves, respectively, upon treatment with GA3. Among those that are homologs of the DELLA-mediated GA signal pathway genes, some may be involved in the positive regulation of flower development, including EjWRKY75, EjFT, EjSOC1, EjAGL24, EjSPL, EjLFY, EjFUL, and EjAP1; while some may be involved in the negative regulation of flower development, including EjDELLA, EjMYC3, EjWRKY12, and EjWRKY13. Finally, by analyzing the co-expression of DEGs and key floral genes EjSOC1s, EjLFYs, EjFULs, EjAP1s, 330 candidate genes that may be involved in the regulation of loquat flowering were screened. These genes belong to 74 gene families, including Cyclin_C, Histone, Kinesin, Lipase_GDSL, MYB, P450, Pkinase, Tubulin, and ZF-HD_dimer gene families. These findings provide new insights into the regulation mechanism of loquat flowering.

scholarly journals Usutu Virus NS5: Characterization of Polymerase Activity, Protein–Protein Interaction and Cellular Localization %MCEPASTEBIN%

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 98
Author(s):  
Laura Albentosa-González ◽  
Pilar Clemente-Casares ◽  
Rosario Sabariegos ◽  
Antonio Mas
Keyword(s):  
Rna Polymerase ◽  
Protein Interactions ◽  
Cellular Localization ◽  
De Novo ◽  
Subcellular Location ◽  
Polymerase Activity ◽  
Hill Coefficient ◽  
Usutu Virus ◽  
Protein Protein Interaction

Usutu virus (USUV) is a mosquito-borne arbovirus that has rapidly propagated in birds across several European countries over the last two decades, leading to substantial avian mortalities. USUV infection in humans has been associated with a growing number of cases of neurological disease in the last years, underlining the need for increased awareness and suitable treatments. Our group is working on the characterization of the NS5 protein of USUV. This protein is responsible for the replication activity of the viral genome and can be a suitable viral target to treat the infection. NS5 contains a RNA-dependent RNA polymerase (RdRpD) and a methyltransferase domains. Recombinant NS5 and RdRpD proteins expressed in bacteria were purified and biochemically characterized to determine the best conditions for their polymerase activities. Both proteins showed de novo and primer extension activities. Optimal RNA–polymerase reaction conditions included low NaCl (less than 20 mM), 2.5 mM MgCl2 and 5 mM MnCl2, 30 °C, and pH 7.25. Polymerase activity was cooperative for the polymerase domain (Hill coefficient = 5.8) but not for the complete NS5 (Hill coefficient = 1.2). To study their subcellular location, suitable sequences were cloned into a pcDNA3 vector and expressed in Huh7.5 and HEK293T cells. Both proteins were preferentially located in the cytoplasmic region, although a significant amount was found in the nucleus. Preliminary results showed that the concentration of sofosbuvir (SOFTP) necessary to achieve its incorporation by NS5 in 50% of the nascent RNA is higher than 100 µM, as already observed for dengue virus DENV. In this work, we describe the main features of the full-length USUV NS5, including the polymerase activity as well as the effect of protein–protein interactions and subcellular localization. Our results will be very useful for the study of this viral enzyme as a suitable target against the infection and the effect of antiviral drugs.

scholarly journals High throughput sequencing from Angolan citrus accessions discloses the presence of emerging CTV strains

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Aderito Tomàs Pais da Cunha ◽  
Michela Chiumenti ◽  
Laurindo Chambula Ladeira ◽  
Raied Abou Kubaa ◽  
Giuliana Loconsole ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Rna Seq ◽  
Citrus Industry ◽  
Certification Programs ◽  
Molecular Variants ◽  
Pooled Samples ◽  
Tristeza Virus

Abstract Background Citrus industry is worldwide dramatically affected by outbreaks of Citrus tristeza virus (CTV). Controls should be applied to nurseries, which could act as diversity hotspots for CTV. Early detection and characterization of dangerous or emerging strains of this virus greatly help to prevent outbreaks of disease. This is particularly relevant in those growing regions where no dedicated certification programs are currently in use. Methods Double-stranded RNA extracted from Citrus spp. samples, collected in two locations in Angola, were pooled and submitted to a random-primed RNA-seq. This technique was performed to acquire a higher amount of data in the survey, before the amplification and sequencing of genes from single plants. To confirm the CTV infection in individual plants, as suggested by RNA-seq information from the pooled samples, the analysis was integrated with multiple molecular marker amplification (MMM) for the main known CTV strains (T30, T36, VT and T3). Results From the analysis of HTS data, several assembled contigs were identified as CTV and classified according to their similarity to the established strains. By the MMM amplification, only five individual accessions out of the eleven pooled samples, resulted to be infected by CTV. Amplified coat protein genes from the five positive sources were cloned and sequenced and submitted to phylogenetic analysis, while a near-complete CTV genome was also reconstructed by the fusion of three overlapping contigs. Conclusion Phylogenetic analysis of the ORF1b and CP genes, retrieved by de novo assembly and RT-PCR, respectively, revealed the presence of a wide array of CTV strains in the surveyed citrus-growing spots in Angola. Importantly, molecular variants among those identified from HTS showed high similarity with known severe strains as well as to recently described and emerging strains in other citrus-growing regions, such as S1 (California) or New Clade (Uruguay).

scholarly journals Characterization of De Novo Synthesized GPCRs Supported in Nanolipoprotein Discs

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e44911 ◽  
Author(s):  
Tingjuan Gao ◽  
Jitka Petrlova ◽  
Wei He ◽  
Thomas Huser ◽  
Wieslaw Kudlick ◽  
...  
Keyword(s):  
De Novo

scholarly journals nanotatoR: a tool for enhanced annotation of genomic structural variants

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Surajit Bhattacharya ◽  
Hayk Barseghyan ◽  
Emmanuèle C. Délot ◽  
Eric Vilain
Keyword(s):  
De Novo ◽  
Genome Mapping ◽  
Gene List ◽  
Sufficient Information ◽  
Rna Seq ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Pathogenic Variants ◽  
Increased Sensitivity

Abstract Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. Results We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. Conclusions The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.

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