Alterations in the Transcriptome of Rye Plants Following the Microdochium nivale Infection: Identification of Resistance/Susceptibility-Related Reactions Based on RNA-Seq Analysis

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromosome-scale assembly of rye genome has improved whole-genome studies of this crop. In the present work, the first transcriptome study of the M. nivale-infected crop plant (rye) with the detailed functional gene classification was carried out, along with the physiological verification of the RNA-Seq data. The results revealed plant reactions that contributed to their resistance or susceptibility to M. nivale. Phytohormone abscisic acid was shown to promote plant tolerance to M. nivale. Flavonoids were proposed to contribute to plant resistance to this pathogen. The upregulation of plant lipase encoding genes and the induction of lipase activity in M. nivale-infected plants revealed in our study were presumed to play an important role in plant susceptibility to the studied phytopathogen. Our work disclosed important aspects of plant-M. nivale interactions, outlined the directions for future studies on poorly characterized plant diseases caused by this phytopathogen, and provided new opportunities to improve cereals breeding and food security strategies.

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Transcriptional and morphological profiling of parvalbumin interneuron subpopulations in the mouse hippocampus

Nature Communications ◽

10.1038/s41467-020-20328-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Lin Que ◽

David Lukacsovich ◽

Wenshu Luo ◽

Csaba Földy

Keyword(s):

Large Scale ◽

Cell Types ◽

Rna Seq ◽

Neuronal Identity ◽

Parvalbumin Interneurons ◽

Different Types ◽

Parvalbumin Interneuron ◽

Cam Profile ◽

Developmental Domains

AbstractThe diversity reflected by >100 different neural cell types fundamentally contributes to brain function and a central idea is that neuronal identity can be inferred from genetic information. Recent large-scale transcriptomic assays seem to confirm this hypothesis, but a lack of morphological information has limited the identification of several known cell types. In this study, we used single-cell RNA-seq in morphologically identified parvalbumin interneurons (PV-INs), and studied their transcriptomic states in the morphological, physiological, and developmental domains. Overall, we find high transcriptomic similarity among PV-INs, with few genes showing divergent expression between morphologically different types. Furthermore, PV-INs show a uniform synaptic cell adhesion molecule (CAM) profile, suggesting that CAM expression in mature PV cells does not reflect wiring specificity after development. Together, our results suggest that while PV-INs differ in anatomy and in vivo activity, their continuous transcriptomic and homogenous biophysical landscapes are not predictive of these distinct identities.

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Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽

10.1186/s12864-021-07605-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qi Wu ◽

Yiming Luo ◽

Xiaoyong Wu ◽

Xue Bai ◽

Xueling Ye ◽

...

Keyword(s):

Expression Profiles ◽

Functional Characterization ◽

Chenopodium Quinoa ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Rna Seq ◽

Short Day ◽

Homologous Genes ◽

The Relationship ◽

Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

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Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants

Microorganisms ◽

10.3390/microorganisms8111679 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1679

Author(s):

Valentina Méndez ◽

Miryam Valenzuela ◽

Francisco Salvà-Serra ◽

Daniel Jaén-Luchoro ◽

Ximena Besoain ◽

...

Keyword(s):

Virulence Factors ◽

Phylogenetic Analyses ◽

Plant Diseases ◽

Genomic Diversity ◽

Clavibacter Michiganensis ◽

Tomato Plants ◽

Clavibacter Michiganensis Subsp ◽

Genomic Analyses ◽

Encoding Genes ◽

Genomic Similarity

The genus Clavibacter has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean C. michiganensis subsp. michiganensis strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, Clavibacter michiganensis. VL527 and MSF322 genomes possess 3,396,632 and 3,399,199 bp, respectively, with a pCM2-like plasmid in strain VL527, with pCM1- and pCM2-like plasmids in strain MSF322. OP3 genome is composed of a chromosome and three plasmids (including pCM1- and pCM2-like plasmids) of 3,466,104 bp. Genomic analyses confirmed the phylogenetic relationships of the Chilean strains among C.michiganensis subsp. michiganensis and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the pelA1 gene (chp/tomA region)—that grouped Chilean strains in three distinct clusters—and proteases and hydrolases encoding genes, exclusive for each of the Chilean strains, may be involved in these observed virulence levels. Based on genomic similarity (ANIm) analyses, a proposal to combine and reclassify C. michiganensis subsp. phaseoli and subsp. chilensis at the species level, as C. phaseoli sp. nov., as well as to reclassify C. michiganensis subsp. californiensis as the species C. californiensis sp. nov. may be justified.

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KEANEKARAGAMAN JENIS TUMBUHAN MASA LAMPAU DI SITUS PEMUTERAN, KABUPATEN BULELENG, PROVINSI BALI (Kajian berdasarkan analisis palinology)

Berkala Arkeologi ◽

10.30883/jba.v31i1.415 ◽

2011 ◽

Vol 31 (1) ◽

pp. 12-30

Author(s):

Vita Vita

Keyword(s):

Plant Species ◽

Plant Communities ◽

Environmental Conditions ◽

Fossil Pollen ◽

Plant Tolerance ◽

The Past ◽

Soil Sediment ◽

The Family ◽

Different Types ◽

Excavation Site

A variety of plant species that exist today reflect the diversity of plant species as well as how pre-existing or in the past, the area along the environmental conditions are not much changed significantly. Plant communities in a region will illustrate the diversity of plant species tolerant to environmental conditions in the area. The power plant tolerance to different environmental factors will lead to different types of plants that live in the area By using HF method and Acetolysis, then the results of the identification of fossil pollen (pollen analysis) that has been done specifically on a sample of soil /sediment from the findings of pottery, as well as the box has been opened at the excavation site Pemuteran, Buleleng Regency, Bali Province randomly, especially in layer B in test pit 4 and 5, the types derived from fossil pollen from plants derived from plants that are useful in the family Compositae, Poaceae, Malvaceae and Papilionaceae. In addition, there is also a pollen that is not available on the site around Pemuteran, such as the family Pinaceae, Fagaceae, Daphnae, Sequoia, Geraniaceae, Cupressus.

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Pleiotropic Effects of RsmA and RsmE Proteins in Pseudomonas Fluorescens 2P24

10.21203/rs.3.rs-29303/v1 ◽

2020 ◽

Author(s):

Yang Zhang ◽

Bo Zhang ◽

Haiyan Wu ◽

Xiaogang Wu ◽

Qing Yan ◽

...

Keyword(s):

Pseudomonas Fluorescens ◽

Double Mutant ◽

Secretion System ◽

Plant Diseases ◽

Fine Tuning ◽

Substantial Portion ◽

Rna Seq ◽

Gene Encoding ◽

Rhizosphere Bacterium ◽

Production Cell

Abstract Background: Pseudomonas fluorescens 2P24 is a rhizosphere bacterium that produces 2,4-diacetyphloroglucinol (2,4-DAPG) as the decisive secondary metabolite to suppress soilborne plant diseases. The biosynthesis of 2,4-DAPG is strictly regulated by the RsmA family proteins RsmA and RsmE. However, mutation of both of rsmA and rsmE genes results in reduced bacterial growth.Results: In this study, we showed that overproduction of 2,4-DAPG in the rsmA rsmE double mutant influenced the growth of strain 2P24. This delay of growth could be partially reversal when the phlD gene was deleted or overexpression of the phlG gene encoding the 2,4-DAPG hydrolase in the rsmA rsmE double mutant. RNA-seq analysis of the rsmA rsmE double mutant revealed that a substantial portion of the P. fluorescens genome was regulated by RsmA family proteins. These genes are involved in the regulation of 2,4-DAPG production, cell motility, carbon metabolism, and type six secretion system.Conclusions: These results suggest that RsmA and RsmE are the important regulators of genes involved in the plant-associated strain 2P24 ecologic fitness and operate a sophisticated mechanism for fine-tuning the concentration of 2,4-DAPG in the cells.

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Animal, fungi, and plant genome sequences harbour different non-canonical splice sites

10.1101/616565 ◽

2019 ◽

Cited By ~ 2

Author(s):

Katharina Frey ◽

Boas Pucker

Keyword(s):

Splice Site ◽

Plant Genome ◽

Fungal Genome ◽

Rna Seq ◽

Splice Sites ◽

Genome Sequences ◽

Oikopleura Dioica ◽

Protein Encoding ◽

Encoding Genes ◽

Splice Site Usage

AbstractMost protein encoding genes in eukaryotes contain introns which are interwoven with exons. After transcription, introns need to be removed in order to generate the final mRNA which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5’ end and AG at the 3’ end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations which have been known for years. During the last years, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here we expand systematic investigations of non-canonical splice site combinations in plants to all eukaryotes by analysing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences such as a substantially increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts could be one explanation for this observation. In addition, high numbers of GA-AG splice site combinations were observed in Eurytemora affinis and Oikopleura dioica. A variant in one U1 snRNA isoform might allow the recognition of GA as 5’ splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3’ splice site compared to the 5’ splice site across animals, fungi, and plants.

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Standardizing unique molecular identifiers in SAM flags would benefit more than RNA-Seq

10.7287/peerj.preprints.2465v1 ◽

2016 ◽

Author(s):

Elisha D Roberson

Keyword(s):

Pcr Amplification ◽

Amplicon Sequencing ◽

Abundance Estimation ◽

Rna Seq ◽

Specific Expression ◽

High Coverage ◽

Different Types ◽

Pcr Duplicates ◽

Allele Specific ◽

Break Points

Unique Molecular Identifiers (UMIs) have been incorporated into RNA-Seq experiments to overcome issues with abundance estimation from samples that may have many PCR amplification cycles. However, the use of UMIs in many different types of sequencing experiments could be beneficial, including amplicon sequencing, ATAC-Seq, and ChIP-Seq. Furthermore, UMIs help to overcome artifacts in high-coverage DNA-Seq, and would enable more accurate RNA-Seq genotyping and allele-specific expression calculation. The main advantage of using UMIs is that identical molecules that are true PCR duplicates can be discerned from unique molecules with identical break points.

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Selenium Effect on Rye Malt Quality

Proceedings of the Latvian Academy of Sciences Section B Natural Exact and Applied Sciences ◽

10.2478/prolas-2013-0062 ◽

2013 ◽

Vol 67 (4-5) ◽

pp. 394-398

Author(s):

Kristīne Antoņenko ◽

Viesturs Kreicbergs ◽

Māra Dūma ◽

Sandra Ozola

Keyword(s):

Selenium Concentration ◽

Total Phenol ◽

Sodium Selenate ◽

Substantial Part ◽

Total Phenol Content ◽

Malt Extract ◽

Cereal Crop ◽

Quality Indices ◽

Bread Making ◽

Secale Cereale L

Abstract Rye (Secale cereale L.) is the most important cereal crop after wheat, rice and maize. A substantial part of the rye yield is used for bread making, especially in European countries. There have been numerous studies on grain enrichment with selenium (Se), as it is known that selenium is a fundamental trace element essential for human health and in the form of selenoproteins plays key structural and enzymic roles. The main aim of this study was to investigate the effect of different selenium concentrations on quality indices of rye malt - the content of malt extract, diastase activity, selenium and total phenol content in malt. Rye grain of 95% viability was soaked and germinated at temperature +6 ± 2 °C for three days +18 ± 2 °C, using sodium selenate Na2SeO4 solutions (Se concentration 3 mg l-1, 5 mg l-1, 10 mg l-1), and dried in an oven for 24 hours at temperature +70 - 112 °C. Germination of grain with deionised water served as a control. The obtained results showed that an increase of selenium concentration caused increase of malt extract concentration (from 74 to 80%), selenium concentration (from 0.0139 to 0.3251 mg kg-1) and total phenol concentration (from 3.13 to 3.63 mg GAE g-1 DW) in rye malt, while diastase activity decreased from 330 to 216.

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Standardizing unique molecular identifiers in SAM flags would benefit more than RNA-Seq

10.7287/peerj.preprints.2465 ◽

2016 ◽

Author(s):

Elisha D Roberson

Keyword(s):

Pcr Amplification ◽

Amplicon Sequencing ◽

Abundance Estimation ◽

Rna Seq ◽

Specific Expression ◽

High Coverage ◽

Different Types ◽

Pcr Duplicates ◽

Allele Specific ◽

Break Points

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Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions

PeerJ ◽

10.7717/peerj.7241 ◽

2019 ◽

Vol 7 ◽

pp. e7241 ◽

Cited By ~ 6

Author(s):

Ikuko Yuyama ◽

Tomihiko Higuchi

Keyword(s):

Matrix Protein ◽

Organic Matrix ◽

Matrix Proteins ◽

Rna Seq ◽

Coral Skeletons ◽

Different Types ◽

Key Factor ◽

Acropora Tenuis ◽

Differential Gene ◽

Selective Formation

Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO3.

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