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1.
BMC Genomics ; 22(1): 637, 2021 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-34479505

RESUMO

BACKGROUND: The pond snail, Lymnaea stagnalis (L. stagnalis), has served as a valuable model organism for neurobiology studies due to its simple and easily accessible central nervous system (CNS). L. stagnalis has been widely used to study neuronal networks and recently gained popularity for study of aging and neurodegenerative diseases. However, previous transcriptome studies of L. stagnalis CNS have been exclusively carried out on adult L. stagnalis only. As part of our ongoing effort studying L. stagnalis neuronal growth and connectivity at various developmental stages, we provide the first age-specific transcriptome analysis and gene annotation of young (3 months), adult (6 months), and old (18 months) L. stagnalis CNS. RESULTS: Using the above three age cohorts, our study generated 55-69 millions of 150 bp paired-end RNA sequencing reads using the Illumina NovaSeq 6000 platform. Of these reads, ~ 74% were successfully mapped to the reference genome of L. stagnalis. Our reference-based transcriptome assembly predicted 42,478 gene loci, of which 37,661 genes encode coding sequences (CDS) of at least 100 codons. In addition, we provide gene annotations using Blast2GO and functional annotations using Pfam for ~ 95% of these sequences, contributing to the largest number of annotated genes in L. stagnalis CNS so far. Moreover, among 242 previously cloned L. stagnalis genes, we were able to match ~ 87% of them in our transcriptome assembly, indicating a high percentage of gene coverage. The expressional differences for innexins, FMRFamide, and molluscan insulin peptide genes were validated by real-time qPCR. Lastly, our transcriptomic analyses revealed distinct, age-specific gene clusters, differentially expressed genes, and enriched pathways in young, adult, and old CNS. More specifically, our data show significant changes in expression of critical genes involved in transcription factors, metabolisms (e.g. cytochrome P450), extracellular matrix constituent, and signaling receptor and transduction (e.g. receptors for acetylcholine, N-Methyl-D-aspartic acid, and serotonin), as well as stress- and disease-related genes in young compared to either adult or old snails. CONCLUSIONS: Together, these datasets are the largest and most updated L. stagnalis CNS transcriptomes, which will serve as a resource for future molecular studies and functional annotation of transcripts and genes in L. stagnalis.


Assuntos
Perfilação da Expressão Gênica , Lymnaea , Animais , Sistema Nervoso Central , Lymnaea/genética , Anotação de Sequência Molecular , Transcriptoma
2.
Int J Mol Sci ; 22(16)2021 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-34445259

RESUMO

The increasing number and complexity of structures containing RNA chains in the Protein Data Bank (PDB) have led to the need for automated structure annotation methods to replace or complement expert visual curation. This is especially true when searching for tertiary base motifs and substructures. Such base arrangements and motifs have diverse roles that range from contributions to structural stability to more direct involvement in the molecule's functions, such as the sites for ligand binding and catalytic activity. We review the utility of computational approaches in annotating RNA tertiary base motifs in a dataset of PDB structures, particularly the use of graph theoretical algorithms that can search for such base motifs and annotate them or find and annotate clusters of hydrogen-bond-connected bases. We also demonstrate how such graph theoretical algorithms can be integrated into a workflow that allows for functional analysis and comparisons of base arrangements and sub-structures, such as those involved in ligand binding. The capacity to carry out such automatic curations has led to the discovery of novel motifs and can give new context to known motifs as well as enable the rapid compilation of RNA 3D motifs into a database.


Assuntos
Algoritmos , Bases de Dados de Ácidos Nucleicos , Anotação de Sequência Molecular , Motivos de Nucleotídeos , RNA/química , Software , RNA/genética , Fluxo de Trabalho
3.
Science ; 373(6555): 655-662, 2021 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-34353948

RESUMO

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.


Assuntos
Genoma de Planta , Anotação de Sequência Molecular , Zea mays/genética , Centrômero/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Metilação de DNA , Resistência à Doença/genética , Genes de Plantas , Variação Genética , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Herança Multifatorial/genética , Fenótipo , Doenças das Plantas , Polimorfismo de Nucleotídeo Único , Sequências Reguladoras de Ácido Nucleico , Análise de Sequência de DNA , Tetraploidia , Transcriptoma , Sequenciamento Completo do Genoma
4.
J Med Microbiol ; 70(8)2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34397349

RESUMO

Introduction. Lactococcus petauri LZys1 (L. petauri LZys1) is a type of lactic acid bacteria (LAB), which was initially isolated from healthy human gut.Hypothesis/Gap Statement. It was previously anticipated that L. petauri LZys1 has potential characteristics of probiotic properties. The genetic structure and the regulation functions of L. petauri LZys1 need to be better revealed.Aim. The aim of this study was to detect the probiotic properties L. petauri LZys1 and to reveal the genome information related to its genetic adaptation and probiotic profiles.Methodology. Multiple in vitro experiments were carried out to evaluate its lactic acid-producing ability, resistance to pathogenic bacterial strains, auto-aggregation and co-aggregation ability, and so on. Additionally, complete genome sequencing, gene annotation, and probiotic associated gene analysis were performed.Results. The complete genome of L. petauri LZys1 comprised of 1 985 765 bp, with a DNA G+C content of 38.07 %, containing 50 tRNA, seven rRNA, and four sRNA. A total of 1931 genes were classified into six functional categories by Kyoto Encyclopaedia of Genes and Genomes (KEGG) database. The neighbour-joining phylogeny tree based on the whole genome of L. petauri LZys1 and other probiotics demonstrated that L. petauri LZys1 has a significant similarity to Lactococcus garvieae. The functional genes were detected to expound the molecular mechanism and biochemical processes of its potential probiotic properties, such as atpB gene.Conclusion. All the results described in this study, together with relevant information previously reported, made L. prtauri LZys1 a very interesting potential strain to be considered as a prominent candidate for probiotic use.


Assuntos
Trato Gastrointestinal/microbiologia , Genoma Bacteriano , Lactococcus , Probióticos , Animais , Bactérias/crescimento & desenvolvimento , Bactérias/patogenicidade , Sequência de Bases , Fezes/microbiologia , Genes Bacterianos , Humanos , Lactococcus/citologia , Lactococcus/genética , Lactococcus/isolamento & purificação , Lactococcus/fisiologia , Masculino , Anotação de Sequência Molecular , Mariposas/microbiologia , Filogenia , Polissacarídeos Bacterianos/biossíntese , Polissacarídeos Bacterianos/genética , Sequenciamento Completo do Genoma , Adulto Jovem
5.
BMC Plant Biol ; 21(1): 365, 2021 Aug 11.
Artigo em Inglês | MEDLINE | ID: mdl-34380415

RESUMO

BACKGROUND: Kiwifruit (Actinidia Lindl.) is considered an important fruit species worldwide. Due to its temperate origin, this species is highly vulnerable to freezing injury while under low-temperature stress. To obtain further knowledge of the mechanism underlying freezing tolerance, we carried out a hybrid transcriptome analysis of two A. arguta (Actinidi arguta) genotypes, KL and RB, whose freezing tolerance is high and low, respectively. Both genotypes were subjected to - 25 °C for 0 h, 1 h, and 4 h. RESULTS: SMRT (single-molecule real-time) RNA-seq data were assembled using the de novo method, producing 24,306 unigenes with an N50 value of 1834 bp. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that they were involved in the 'starch and sucrose metabolism', the 'mitogen-activated protein kinase (MAPK) signaling pathway', the 'phosphatidylinositol signaling system', the 'inositol phosphate metabolism', and the 'plant hormone signal transduction'. In particular, for 'starch and sucrose metabolism', we identified 3 key genes involved in cellulose degradation, trehalose synthesis, and starch degradation processes. Moreover, the activities of beta-GC (beta-glucosidase), TPS (trehalose-6-phosphate synthase), and BAM (beta-amylase), encoded by the abovementioned 3 key genes, were enhanced by cold stress. Three transcription factors (TFs) belonging to the AP2/ERF, bHLH (basic helix-loop-helix), and MYB families were involved in the low-temperature response. Furthermore, weighted gene coexpression network analysis (WGCNA) indicated that beta-GC, TPS5, and BAM3.1 were the key genes involved in the cold response and were highly coexpressed together with the CBF3, MYC2, and MYB44 genes. CONCLUSIONS: Cold stress led various changes in kiwifruit, the 'phosphatidylinositol signaling system', 'inositol phosphate metabolism', 'MAPK signaling pathway', 'plant hormone signal transduction', and 'starch and sucrose metabolism' processes were significantly affected by low temperature. Moreover, starch and sucrose metabolism may be the key pathway for tolerant kiwifruit to resist low temperature damages. These results increase our understanding of the complex mechanisms involved in the freezing tolerance of kiwifruit under cold stress and reveal a series of candidate genes for use in breeding new cultivars with enhanced freezing tolerance.


Assuntos
Aclimatação/genética , Actinidia/genética , Actinidia/fisiologia , Congelamento , Regulação da Expressão Gênica de Plantas , Frutas/genética , Frutas/fisiologia , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Sistema de Sinalização das MAP Quinases , Anotação de Sequência Molecular , Fosfatidilinositóis/metabolismo , Melhoramento Vegetal , Reguladores de Crescimento de Plantas/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Amido/metabolismo , Sacarose/metabolismo
6.
BMC Plant Biol ; 21(1): 370, 2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34384392

RESUMO

BACKGROUND: To adapt seasonal climate changes under natural environments, Polygonatum sibiricum seeds have a long period of epicotyl morphophysiological dormancy, which limits their wide-utilization in the large-scale plant progeny propagation. It has been proven that the controlled consecutive warm and cold temperature treatments can effectively break and shorten this seed dormancy status to promote its successful underdeveloped embryo growth, radicle emergence and shoot emergence. To uncover the molecular basis of seed dormancy release and seedling establishment, a SMRT full-length sequencing analysis and an Illumina sequencing-based comparison of P. sibiricum seed transcriptomes were combined to investigate transcriptional changes during warm and cold stratifications. RESULTS: A total of 87,251 unigenes, including 46,255 complete sequences, were obtained and 77,148 unigenes (88.42%) were annotated. Gene expression analyses at four stratification stages identified a total of 27,059 DEGs in six pairwise comparisons and revealed that more differentially expressed genes were altered at the Corm stage than at the other stages, especially Str_S and Eme. The expression of 475 hormone metabolism genes and 510 hormone signaling genes was modulated during P. sibiricum seed dormancy release and seedling emergence. One thousand eighteen transcription factors and five hundred nineteen transcription regulators were detected differentially expressed during stratification and germination especially at Corm and Str_S stages. Of 1246 seed dormancy/germination known DEGs, 378, 790, and 199 DEGs were associated with P. sibiricum MD release (Corm vs Seed), epicotyl dormancy release (Str_S vs Corm), and the seedling establishment after the MPD release (Eme vs Str_S). CONCLUSIONS: A comparison with dormancy- and germination-related genes in Arabidopsis thaliana seeds revealed that genes related to multiple plant hormones, chromatin modifiers and remodelers, DNA methylation, mRNA degradation, endosperm weakening, and cell wall structures coordinately mediate P. sibiricum seed germination, epicotyl dormancy release, and seedling establishment. These results provided the first insights into molecular regulation of P. sibiricum seed epicotyl morphophysiological dormancy release and seedling emergence. They may form the foundation of future studies regarding gene interaction and the specific roles of individual tissues (endosperm, newly-formed corm) in P. sibiricum bulk seed dormancy.


Assuntos
Dormência de Plantas/genética , Polygonatum/crescimento & desenvolvimento , Polygonatum/genética , Temperatura , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Germinação/genética , Anotação de Sequência Molecular , Reguladores de Crescimento de Plantas/genética , Transdução de Sinais/genética , Fatores de Transcrição/metabolismo , Transcriptoma
7.
Methods Mol Biol ; 2351: 67-90, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34382184

RESUMO

The Cap Analysis of Gene Expression (CAGE) is a powerful method to identify Transcription Start Sites (TSSs) of capped RNAs while simultaneously measuring transcripts expression level. CAGE allows mapping at single nucleotide resolution at all active promoters and enhancers. Large CAGE datasets have been produced over the years from individual laboratories and consortia, including the Encyclopedia of DNA Elements (ENCODE) and Functional Annotation of the Mammalian Genome (FANTOM) consortia. These datasets constitute open resource for TSS annotations and gene expression analysis. Here, we provide an experimental protocol for the most recent CAGE method called Low Quantity (LQ) single strand (ss) CAGE "LQ-ssCAGE", which enables cost-effective profiling of low quantity RNA samples. LQ-ssCAGE is especially useful for samples derived from cells cultured in small volumes, cellular compartments such as nuclear RNAs or for samples from developmental stages. We demonstrate the reproducibility and effectiveness of the method by constructing 240 LQ-ssCAGE libraries from 50 ng of THP-1 cell extracted RNAs and discover lowly expressed novel enhancer and promoter-derived lncRNAs.


Assuntos
Biologia Computacional/métodos , Elementos Facilitadores Genéticos , Regiões Promotoras Genéticas , Capuzes de RNA , Sítio de Iniciação de Transcrição , Bases de Dados Genéticas , Regulação da Expressão Gênica , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Anotação de Sequência Molecular , Sequências Reguladoras de Ácido Nucleico , Reprodutibilidade dos Testes , Fluxo de Trabalho
8.
BMC Bioinformatics ; 22(1): 399, 2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376148

RESUMO

Numerous genomes are sequenced and made available to the community through the NCBI portal. However, and, unlike what happens for gene function annotation, annotation of promoter sequences and the underlying prediction of regulatory associations is mostly unavailable, severely limiting the ability to interpret genome sequences in a functional genomics perspective. Here we present an approach where one can download a genome of interest from NCBI in the GenBank Flat File (.gbff) format and, with a minimum set of commands, have all the information parsed, organized and made available through the platform web interface. Also, the new genomes are compared with a given genome of reference in search of homologous genes, shared regulatory elements and predicted transcription associations. We present this approach within the context of Community YEASTRACT of the YEASTRACT + portal, thus benefiting from immediate access to all the comparative genomics queries offered in the YEASTRACT + portal. Besides the yeast community, other communities can install the platform independently, without any constraints. In this work, we exemplify the usefulness of the presented tool, within Community YEASTRACT, in constructing a dedicated database and analysing the genome of the highly promising oleaginous red yeast species Rhodotorula toruloides currently poorly studied at the genome and transcriptome levels and with limited genome editing tools. Regulatory prediction is based on the conservation of promoter sequences and available regulatory networks. The case-study examined is focused on the Haa1 transcription factor-a key regulator of yeast resistance to acetic acid, an important inhibitor of industrial bioconversion of lignocellulosic hydrolysates. The new tool described here led to the prediction of a RtHaa1 regulon with expected impact in the optimization of R. toruloides robustness for lignocellulosic and pectin-rich residue biorefinery processes.


Assuntos
Regulon , Leveduras , Anotação de Sequência Molecular , Rhodotorula , Fatores de Transcrição , Leveduras/genética
9.
Fa Yi Xue Za Zhi ; 37(3): 318-324, 2021 Jun.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-34379899

RESUMO

Abstract: Objective To study the growth regulation, environmental adaption and epigenetic regulation of Chrysomyia Megacephala pupae, in order to obtain the transcriptome data of Chrysomyia Megacephala in different growing periods, and lay the foundation for forensic application. Methods The Chrysomyia Megacephala was cultivated and after pupation, 3 pupae were collected every 24 h from pupation to emergence, and stored at -80 ℃ for later use. High-throughput sequencing was performed by Illumina Hiseq 4000 and Unigenes were obtained. The Unigenes were compared by comparison tool BLAST from NCBI in databases such as NR, STRING, SWISS-PROT (including Pfam), GO, COG, KEGG in order to obtain the corresponding annotation information. The expression amount of Unigenes obtained by sequencing in Chrysomyia Megacephala in six different growing periods was calculated by FPKM method, and the discrepant genes were screened according to the following standards: the log2 multiple absolute value of FPKM expression amount between two different growing periods must be larger than 1 (log2|FC|>1), and the false discovery rate must be less than 0.05. Results When the mean temperature was 25.6 ℃, Chrysomyia Megacephala emerged 6 d after they pupated. A total of 43 408 pieces of Unigenes were obtained and their mean length was 905 bp, of which 32 500, 18 720, 13 542, 9 191 and 18 720 pieces were annotated by NR, SWISS-PORT, Pfam, STRING and KEGG databases. According to the discrepant gene analysis of pupae in two different growing periods, the number of genes with variants ranged from 801 to 5 307, and the total number of discrepant genes was 45 676. Conclusion The gene expressions of the transcriptome data of Chrysomyia Megacephala pupae in different growing periods are different. The results provided a good foundation for further research on the transcriptome changes in each period of the pupae of sarcosaprophagous flies and provided the basis for exploring the genes associated with the growth of Chrysomyia Megacephala pupae.


Assuntos
Epigênese Genética , Transcriptoma , Animais , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Pupa/genética
10.
Molecules ; 26(15)2021 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-34361782

RESUMO

Thermal treatments of milk induce changes in the properties of milk whey proteins. The aim of this study was to investigate the specific changes related to nutrients in the whey proteins of dairy cow milk after pasteurization at 85 °C for 15 s or ultra-high temperature (UHT) at 135 °C for 15 s. A total of 223 whey proteins were confidently identified and quantified by TMT-based global discovery proteomics in this study. We found that UHT thermal treatment resulted in an increased abundance of 17 proteins, which appeared to show heat insensitivity. In contrast, 15 heat-sensitive proteins were decreased in abundance after UHT thermal treatment. Some of the heat-sensitive proteins were connected with the biological immune functionality, suggesting that UHT thermal treatment results in a partial loss of immune function in the whey proteins of dairy cow milk. The information reported here will considerably expand our knowledge about the degree of heat sensitivity in the whey proteins of dairy cow milk in response to different thermal treatments and offer a knowledge-based reference to aid in choosing dairy products. It is worth noting that the whey proteins (lactoperoxidase and lactoperoxidase) in milk that were significantly decreased by high heat treatment in a previous study (142 °C) showed no significant difference in the present study (135 °C). These results may imply that an appropriately reduced heating intensity of UHT retains the immunoactive proteins to the maximum extent possible.


Assuntos
Leite/química , Pasteurização/métodos , Proteínas do Soro do Leite/química , Soro do Leite/química , Animais , Feminino , Temperatura Alta , Leite/imunologia , Anotação de Sequência Molecular , Estabilidade Proteica , Proteômica/métodos , Soro do Leite/imunologia , Proteínas do Soro do Leite/classificação , Proteínas do Soro do Leite/imunologia , Proteínas do Soro do Leite/isolamento & purificação
11.
Int J Mol Sci ; 22(14)2021 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-34299026

RESUMO

Pseudomonas aeruginosa and Sphingobacterium sp. are well known for their ability to decontaminate many environmental pollutants while Geobacillus sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of P. aeruginosa S3, Sphingobacterium S2 and Geobacillus EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of Sphinogobacterium strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of P. aeruginosa strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile Geobacillus strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.


Assuntos
Proteínas de Bactérias/genética , Biofilmes/crescimento & desenvolvimento , Genoma Bacteriano , Geobacillus/genética , Poliésteres/metabolismo , Pseudomonas aeruginosa/genética , Sphingobacterium/genética , Biodegradação Ambiental , DNA Bacteriano/análise , DNA Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Filogenia
12.
Int J Biol Macromol ; 185: 582-591, 2021 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-34216660

RESUMO

The effects of a novel Flammulina velutipes polysaccharide (FVP) on intestinal microbiota, immune repertoire and heart transcriptome were investigated in this study. The results showed that FVP treatment could effectively regulate the abundance of colonic microbiota. And FVP exhibited obvious immunoregulatory effect by influencing V gene and J gene fragments usage on TCRα chain. The usage frequency of TRBV1, TRBJ1-6 and TRBJ1-5 were significantly altered, and 41 V-J pairs were identified with obvious difference after FVP treatment. Furthermore, the mRNA of mice heart was analyzed by transcriptome assay. Total 525 genes and 1587 mRNA were significantly changed after FVP treatment. KEGG annotation indicated that the up-regulated mRNA was enriched in 17 pathways including adherens junction, mTOR signaling pathway, insulin signaling pathway, mitophagy, tight junction, PPAR signaling pathway and TNF signaling pathway, etc. Meanwhile, the down-regulated mRNA was gathered in AMPK signaling pathway, metabolism of xenobiotics by cytochrome P450, apelin signaling pathway, PPAR signaling pathway, PI3K-Akt signaling pathway, insulin signaling pathway, cardiac muscle contraction, adrenergic signaling in cardiomyocytes, Fc gamma R-mediated phagocytosis, etc. The great potential exhibited by FVP could make it an ideal candidate as complementary medicine or functional food for promotion of health.


Assuntos
Bactérias/isolamento & purificação , Flammulina/química , Perfilação da Expressão Gênica/métodos , Miocárdio/química , Polissacarídeos/administração & dosagem , Receptores de Antígenos de Linfócitos T alfa-beta/genética , Animais , Bactérias/efeitos dos fármacos , Bactérias/genética , Microbioma Gastrointestinal/efeitos dos fármacos , Regulação da Expressão Gênica/efeitos dos fármacos , Coração/efeitos dos fármacos , Masculino , Camundongos , Anotação de Sequência Molecular , Filogenia , Polissacarídeos/farmacologia , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Análise de Sequência de RNA , Xenobióticos
13.
Methods Mol Biol ; 2328: 277-285, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34251633

RESUMO

The identification and characterization of non-coding RNAs (ncRNAs) in prokaryotes is an important step in the study of the interaction of these molecules with mRNAs-or target proteins, in the post-transcriptional regulation process. Here, we describe one of the main in silico prediction methods in prokaryotes, using the TargetRNA2 tool to predict target mRNAs.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Genoma Microbiano/genética , Células Procarióticas/metabolismo , RNA não Traduzido/metabolismo , Simulação por Computador , Bases de Dados Genéticas , Anotação de Sequência Molecular , RNA não Traduzido/genética , RNA-Seq , Software
14.
BMC Res Notes ; 14(1): 261, 2021 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-34233731

RESUMO

OBJECTIVES: Sengon (Falcataria moluccana) is a popular tree species in community plantation forests in Java, Indonesia due to its fast-growing and multipurpose characteristics. However, without effective control measures sengon plantations are vulnerable to boktor stem borer (Xystrocera festiva) infestation. Previous research found some boktor-resistant trees amid mostly susceptible individuals. Resistant trees have higher levels of enzyme inhibitory activity than susceptible ones. However, efforts to differentiate between the two accessions using microsatellite markers failed to provide satisfactory answers. This dataset was created to study differences in gene expressions between resistant and susceptible accessions, and to identify candidate genes involved in boktor resistance in sengon. DATA DESCRIPTION: RNA was extracted from fresh wood samples collected from two individual trees: one heavily infested with boktor larvae, and the other showing no signs of infestation. The sample trees grow in close proximity to each other within the same plantation. The RNA was sequenced using the BGISEQ-500 platform and produced 78.5 million raw reads. De novo transcriptome were assembled using Trinity and produced 96,164 contigs after filtering and clustering. This transcriptome data is important for understanding pest resistance mechanisms in sengon trees, serving as basis for an improvement program for resistance to boktor pest.


Assuntos
Besouros , Fabaceae , Animais , Humanos , Indonésia , Anotação de Sequência Molecular , Transcriptoma/genética , Árvores/genética
15.
Int J Mol Sci ; 22(12)2021 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-34199260

RESUMO

The phenylpropanoid pathway is a major secondary metabolite pathway that helps plants overcome biotic and abiotic stress and produces various byproducts that promote human health. Its byproduct caffeoylquinic acid is a soluble phenolic compound present in many angiosperms. Hydroxycinnamate-CoA shikimate/quinate transferase is a significant enzyme that plays a role in accumulating CQA biosynthesis. This study analyzed transcriptome-wide identification of the phenylpropanoid to caffeoylquinic acid biosynthesis candidate genes in A. spathulifolius flowers and leaves. Transcriptomic analyses of the flowers and leaves showed a differential expression of the PPP and CQA biosynthesis regulated unigenes. An analysis of PPP-captive unigenes revealed a major duplication in the following genes: PAL, 120 unigenes in leaves and 76 in flowers; C3'H, 169 unigenes in leaves and 140 in flowers; 4CL, 41 unigenes in leaves and 27 in flowers; and C4H, 12 unigenes in leaves and 4 in flowers. The phylogenetic analysis revealed 82 BAHDs superfamily members in leaves and 72 in flowers, among which five unigenes encode for HQT and three for HCT. The three HQT are common to both leaves and flowers, whereas the two HQT were specialized for leaves. The pattern of HQT synthesis was upregulated in flowers, whereas HCT was expressed strongly in the leaves of A. spathulifolius. Overall, 4CL, C4H, and HQT are expressed strongly in flowers and CAA and HCT show more expression in leaves. As a result, the quantification of HQT and HCT indicates that CQA biosynthesis is more abundant in the flowers and synthesis of caffeic acid in the leaves of A. spathulifolius.


Assuntos
Aciltransferases/genética , Asteraceae/enzimologia , Asteraceae/genética , Vias Biossintéticas , Ácido Quínico/análogos & derivados , Transcriptoma/genética , Vias Biossintéticas/genética , Flores/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Anotação de Sequência Molecular , Filogenia , Folhas de Planta/genética , Propanóis/metabolismo , Ácido Quínico/metabolismo
16.
BMC Plant Biol ; 21(1): 319, 2021 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-34217205

RESUMO

BACKGROUND: PTI1 (Pto-interacting 1) protein kinase belongs to the receptor-like cytoplasmic kinase (RLCK) group of receptor-like protein kinases (RLK), but lack extracellular and transmembrane domains. PTI1 was first identified in tomato (Solanum lycopersicum) and named SlPTI1, which has been reported to interact with bacterial effector Pto, a serine/threonine protein kinase involved in plant resistance to bacterial disease. Briefly, the host PTI1 specifically recognizes and interacts with the bacterial effector AvrPto, which triggers hypersensitive cell death to inhibit the pathogen growth in the local infection site. Previous studies have demonstrated that PTI1 is associated with oxidative stress and hypersensitivity. RESULTS: We identified 12 putative PTI1 genes from the genome of foxtail millet (Setaria italica) in this study. Gene replication analysis indicated that both segmental replication events played an important role in the expansion of PTI1 gene family in foxtail millet. The PTI1 family members of model plants, i.e. S. italica, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), maize (Zea mays), S. lycopersicum, and soybean (Glycine max), were classified into six major categories according to the phylogenetic analysis, among which the PTI1 family members in foxtail millet showed higher degree of homology with those of rice and maize. The analysis of a complete set of SiPTI1 genes/proteins including classification, chromosomal location, orthologous relationships and duplication. The tissue expression characteristics revealed that SiPTI1 genes are mainly expressed in stems and leaves. Experimental qRT-PCR results demonstrated that 12 SiPTI1 genes were induced by multiple stresses. Subcellular localization visualized that all of foxtail millet SiPTI1s were localized to the plasma membrane. Additionally, heterologous expression of SiPTI1-5 in yeast and E. coli enhanced their tolerance to salt stress. CONCLUSIONS: Our results contribute to a more comprehensive understanding of the roles of PTI1 protein kinases and will be useful in prioritizing particular PTI1 for future functional validation studies in foxtail millet.


Assuntos
Genoma de Planta , Família Multigênica , Proteínas de Plantas/genética , Salinidade , Setaria (Planta)/genética , Setaria (Planta)/fisiologia , Cromossomos de Plantas/genética , Escherichia coli/metabolismo , Duplicação Gênica/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Anotação de Sequência Molecular , Motivos de Nucleotídeos/genética , Filogenia , Proteínas de Plantas/metabolismo , Saccharomyces cerevisiae/metabolismo , Estresse Fisiológico/genética , Sintenia/genética
17.
Sci Data ; 8(1): 174, 2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34267227

RESUMO

LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.


Assuntos
Genoma de Planta , Plantas/genética , Retroelementos , Sequências Repetidas Terminais , Evolução Molecular , Anotação de Sequência Molecular
18.
Nat Commun ; 12(1): 4571, 2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34315874

RESUMO

Understanding mechanisms of hepatocellular damage may lead to new treatments for liver disease, and genome-wide association studies (GWAS) of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) serum activities have proven useful for investigating liver biology. Here we report 100 loci associating with both enzymes, using GWAS across 411,048 subjects in the UK Biobank. The rare missense variant SLC30A10 Thr95Ile (rs188273166) associates with the largest elevation of both enzymes, and this association replicates in the DiscovEHR study. SLC30A10 excretes manganese from the liver to the bile duct, and rare homozygous loss of function causes the syndrome hypermanganesemia with dystonia-1 (HMNDYT1) which involves cirrhosis. Consistent with hematological symptoms of hypermanganesemia, SLC30A10 Thr95Ile carriers have increased hematocrit and risk of iron deficiency anemia. Carriers also have increased risk of extrahepatic bile duct cancer. These results suggest that genetic variation in SLC30A10 adversely affects more individuals than patients with diagnosed HMNDYT1.


Assuntos
Alanina Transaminase/sangue , Aspartato Aminotransferases/sangue , Proteínas de Transporte de Cátions/genética , Estudo de Associação Genômica Ampla , Manganês/sangue , Mutação/genética , Proteínas de Transporte de Cátions/metabolismo , Regulação da Expressão Gênica , Ligação Genética , Loci Gênicos , Genoma Humano , Células HeLa , Hematócrito , Heterozigoto , Homeostase , Humanos , Fígado/patologia , Manganês/metabolismo , Anotação de Sequência Molecular , Fenótipo , Reprodutibilidade dos Testes
19.
Int J Mol Sci ; 22(12)2021 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-34204216

RESUMO

From mammals to fish, reproduction is driven by luteinizing hormone (LH) and follicle-stimulating hormone (FSH) temporally secreted from the pituitary gland. Teleost fish are an excellent model for addressing the unique regulation and function of each gonadotropin cell since, unlike mammals, they synthesize and secrete LH and FSH from distinct cells. Only very distant vertebrate classes (such as fish and birds) demonstrate the mono-hormonal strategy, suggesting a potential convergent evolution. Cell-specific transcriptome analysis of double-labeled transgenic tilapia expressing GFP and RFP in LH or FSH cells, respectively, yielded genes specifically enriched in each cell type, revealing differences in hormone regulation, receptor expression, cell signaling, and electrical properties. Each cell type expresses a unique GPCR signature that reveals the direct regulation of metabolic and homeostatic hormones. Comparing these novel transcriptomes to that of rat gonadotrophs revealed conserved genes that might specifically contribute to each gonadotropin activity in mammals, suggesting conserved mechanisms controlling the differential regulation of gonadotropins in vertebrates.


Assuntos
Peixes/genética , Hormônio Foliculoestimulante/genética , Regulação da Expressão Gênica , Gonadotropinas/genética , Hormônio Luteinizante/genética , Hipófise/metabolismo , Animais , Biomarcadores , Separação Celular , Biologia Computacional/métodos , Peixes/classificação , Imunofluorescência , Perfilação da Expressão Gênica , Anotação de Sequência Molecular , Filogenia , Hipófise/citologia , Ratos
20.
Nat Commun ; 12(1): 4247, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34253727

RESUMO

The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's longevity and tolerance to temperature, nutrient and water stress.


Assuntos
Cycadopsida/genética , Clima Desértico , Genoma de Planta , África , Metilação de DNA/genética , Evolução Molecular , Geografia , Meristema/genética , Anotação de Sequência Molecular , Folhas de Planta/genética , Chuva , Análise de Sequência de DNA , Especificidade da Espécie , Transcriptoma/genética
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