RNA-Seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification

ABSTRACTBackgroundSalicornia neei is a halophyte plant that has been proposed for phytoremediation of saline wastewater generated by land-based aquaculture, which usually contains elevated concentrations of ammonium resulting from protein metabolism. To identify the molecular mechanisms related to ammonium response through of analysis results in silico and the Michaelis–Menten ammonium removal biokinetics and the transcriptome of S. neei in response to growth in saline water containing 3 mM ammonium.ResultsThe parameters for ammonium uptake by S. neei root cuttings were estimated: 1) maximum uptake rate Imax = 7.07 ± 0.27 mM N g−1 fresh weight h−1; and 2) half-saturation constant Km = 0.85 ± 0.12 mM N L−1. Further, a total of 45,327 genes were annotated, which represents 51.2% of the contig predicted from de novo assembly. A total of 9,140 genes were differentially expressed in response to ammonium in saline water, but only 7,396 could be annotated against functional databases. According to the GO enrichment and as well as KEGG pathway analyses showed these upregulated genes were involved in pr cellular anatomical entity, cellular process, and metabolic process, including biological KEGG pathways linked to biosynthesis amino acid biosynthesis, nitrogen metabolism and autophagy and other. In addiction, a set of 72 genes were directly involved in ammonium metabolism, including glutamine synthetase 1 (GLN1), glutamate synthase 1 (GLT1), and ferredoxin-dependent glutamate synthase chloroplastic (Fd-GOGAT).ConclusionOur results support the hypothesis that an ammonium detoxification system mediated by glutamine and glutamate synthase was activated in S. neei when exposed to ammonium and saline water. These results provide novel insight into understanding the molecular mechanisms of ammonium nutrition and aid for investigating the response of halophyte plants to saline wastewater from land-based aquaculture

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De Novo Transcriptome Assembly of Isatis indigotica at Reproductive Stages and Identification of Candidate Genes Associated with Flowering Pathways

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04232-17 ◽

2018 ◽

Vol 143 (1) ◽

pp. 56-66

Author(s):

Yu Bai ◽

Ying Zhou ◽

Xiaoqing Tang ◽

Yu Wang ◽

Fangquan Wang ◽

...

Keyword(s):

Candidate Genes ◽

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Orthologous Group ◽

Rna Seq ◽

Isatis Indigotica ◽

Regulatory Pathways ◽

Kegg Pathways ◽

Bolting And Flowering

The appropriate timing of bolting and flowering is one of the keys to the reproductive success of Isatis indigotica. Several flowering regulatory pathways have been reported in plant species, but we know little about flowering regulatory in I. indigotica. In the present study, we performed RNA-seq and annotated I. indigotica transcriptome using RNA from five tissues (leaves, roots, flowers, fruit, and stems). Illumina sequencing generated 149,907,857 high-quality clean reads and 124,508 unigenes were assembled from the sequenced reads. Of these unigenes, 88,064 were functionally annotated by BLAST searches against the public protein databases. Functional classification and annotation assigned 55,991 and 23,072 unigenes to 52 gene ontology (GO) terms and 25 clusters of orthologous group (COG) categories, respectively. A total of 19,927 unigenes were assigned to 124 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 80 candidate genes related to plant circadian rhythm were identified. We also identified a number of differentially expressed genes (DEG) and 91 potential bolting and flowering-related genes from the RNA-seq data. This study is the first to identify bolting and flowering-related genes based on transcriptome sequencing and assembly in I. indigotica. The results provide foundations for the exploration of flowering pathways in I. indigotica and investigations of the molecular mechanisms of bolting and flowering in Brassicaceae plants.

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De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

International Journal of Molecular Sciences ◽

10.3390/ijms22189874 ◽

2021 ◽

Vol 22 (18) ◽

pp. 9874

Author(s):

Matin Miryeganeh ◽

Hidetoshi Saze

Keyword(s):

Stress Tolerance ◽

Molecular Mechanisms ◽

High Salinity ◽

De Novo ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Natural Habitats ◽

Mangrove Species ◽

Mangrove Tree ◽

Bruguiera Gymnorhiza

Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

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Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

International Journal of Molecular Sciences ◽

10.3390/ijms21217934 ◽

2020 ◽

Vol 21 (21) ◽

pp. 7934

Author(s):

Thiago Mateus Rosa-Santos ◽

Renan Gonçalves da Silva ◽

Poornasree Kumar ◽

Pratibha Kottapalli ◽

Chiquito Crasto ◽

...

Keyword(s):

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Arable Land ◽

Aluminum Tolerance ◽

Aluminum Stress ◽

Physiological Processes ◽

Aluminum Ions ◽

Detoxification Mechanism ◽

Genomic Studies

Some metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al3+) can be very toxic, especially in acidic soils. Considerable parts of the world’s arable land are acidic in nature; mechanistically elucidating a plant’s response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar.

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Transcriptome Analysis Reveals Higher Levels of Mobile Element-Associated Abnormal Gene Transcripts in Temporal Lobe Epilepsy Patients

Frontiers in Genetics ◽

10.3389/fgene.2021.767341 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kai Hu ◽

Ping Liang

Keyword(s):

Temporal Lobe Epilepsy ◽

Temporal Lobe ◽

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Genetic Research ◽

Mobile Element ◽

Mobile Elements ◽

Coding Sequences ◽

Gene Transcripts

Mesial temporal lobe epilepsy (MTLE) is the most common form of epilepsy, and temporal lobe epilepsy patients with hippocampal sclerosis (TLE-HS) show worse drug treatment effects and prognosis. TLE has been shown to have a genetic component, but its genetic research has been mostly limited to coding sequences of genes with known association to epilepsy. Representing a major component of the genome, mobile elements (MEs) are believed to contribute to the genetic etiology of epilepsy despite limited research. We analyzed publicly available human RNA-seq-based transcriptome data to determine the role of mobile elements in epilepsy by performing de novo transcriptome assembly, followed by identification of spliced gene transcripts containing mobile element (ME) sequences (ME-transcripts), to compare their frequency across different sample groups. Significantly higher levels of ME-transcripts in hippocampal tissues of epileptic patients, particularly in TLE-HS, were observed. Among ME classes, short interspersed nuclear elements (SINEs) were shown to be the most frequent contributor to ME-transcripts, followed by long interspersed nuclear elements (LINEs) and DNA transposons. These ME sequences almost in all cases represent older MEs normally located in the intron sequences. For protein coding genes, ME sequences were mostly found in the 3′-UTR regions, with a significant portion also in the coding sequences (CDSs), leading to reading frame disruption. Genes associated with ME-transcripts showed enrichment for the mRNA splicing process and an apparent bias in epileptic transcriptomes toward neural- and epilepsy-associated genes. The findings of this study suggest that abnormal splicing involving MEs, leading to loss of functions in critical genes, plays a role in epilepsy, particularly in TLE-HS, thus providing a novel insight into the molecular mechanisms underlying epileptogenesis.

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Comprehensive transcriptome analysis of grafting onto Artemisia scoparia W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

10.21203/rs.2.10583/v3 ◽

2019 ◽

Author(s):

Xue-ying Zhang ◽

Xian-zhi Sun ◽

Sheng Zhang ◽

Jing-hui Yang ◽

Fang-fang Liu ◽

...

Keyword(s):

Stress Responses ◽

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Chrysanthemum Morifolium ◽

The Self ◽

Rna Seq ◽

Aphid Infestation ◽

A Genome ◽

Artemisia Scoparia

Abstract Abstract Background: Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum ( Chrysanthemum morifolium T. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results : The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion: In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding. Key words : Chrysanthemum, Grafting, Aphid stress, Gene expression, RNA-Seq

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Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome

Genome Biology and Evolution ◽

10.1093/gbe/evz157 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2232-2243 ◽

Cited By ~ 5

Author(s):

Tsai-Ming Lu ◽

Miyuki Kanda ◽

Hidetaka Furuya ◽

Noriyuki Satoh

Keyword(s):

Molecular Mechanisms ◽

Hox Genes ◽

Transcriptome Assembly ◽

Repetitive Sequences ◽

Protein Coding ◽

Animal Group ◽

Kegg Pathways ◽

Genome Features ◽

Parasitic Lifestyle ◽

Mixed Stage

Abstract Dicyemids, previously called “mesozoans” (intermediates between unicellular protozoans and multicellular metazoans), are an enigmatic animal group. They have a highly simplified adult body, comprising only ∼30 cells, and they have a unique parasitic lifestyle. Recently, dicyemids were shown to be spiralians, with affinities to the Platyhelminthes. In order to understand molecular mechanisms involved in evolution of this odd animal, we sequenced the genome of Dicyema japonicum and a reference transcriptome assembly using mixed-stage samples. The D. japonicum genome features a high proportion of repetitive sequences that account for 49% of the genome. The dicyemid genome is reduced to ∼67.5 Mb with 5,012 protein-coding genes. Only four Hox genes exist in the genome, with no clustering. Gene distribution in KEGG pathways shows that D. japonicum has fewer genes in most pathways. Instead of eliminating entire critical metabolic pathways, parasitic lineages likely simplify pathways by eliminating pathway-specific genes, while genes with fundamental functions may be retained in multiple pathways. In principle, parasites can stand to lose genes that are unnecessary, in order to conserve energy. However, whether retained genes in incomplete pathways serve intermediate functions and how parasites overcome the physiological needs served by lost genes, remain to be investigated in future studies.

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Comparative Analysis of Transcriptome Responses to Cold Stress in Galeruca daurica (Coleoptera: Chrysomelidae)

Journal of Insect Science ◽

10.1093/jisesa/iez109 ◽

2019 ◽

Vol 19 (6) ◽

Author(s):

Xiao-Rong Zhou ◽

Yan-Min Shan ◽

Yao Tan ◽

Zhuo-Ran Zhang ◽

Bao-Ping Pang

Keyword(s):

Cold Stress ◽

Stress Responses ◽

Low Temperatures ◽

Fatty Acid Synthase ◽

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Glucose Dehydrogenase ◽

Insect Pest ◽

Cuticle Protein

Abstract Galeruca daurica (Joannis) has become a new insect pest in the Inner Mongolia grasslands since 2009, and its larvae and eggs have strong cold tolerance. To get a deeper insight into its molecular mechanisms of cold stress responses, we performed de novo transcriptome assembly for G. daurica by RNA-Seq and compared the transcriptomes of its larvae exposed to five different temperature treatments (−10, −5, 0, 5, and 25°C for 1 h and then recovered at 25°C for 1 h), respectively. Compared with the control (25°C), the numbers of differentially expressed genes (DEGs) decreased from 1,821 to 882, with the temperature declining from 5 to −10°C. Moreover, we obtained 323 coregulated DEGs under different low temperatures. Under four low temperatures (−10, −5, 0, and 5°C), a large number of genes were commonly upregulated during recovery from cold stresses, including those related to cuticle protein, followed by cytochrome P450, clock protein, fatty acid synthase, and fatty acyl-CoA reductase; meanwhile, lots of genes encoding cuticle protein, RNA replication protein, RNA-directed DNA polymerase, and glucose dehydrogenase were commonly downregulated. Our findings provide important clues for further investigations of key genes and molecular mechanisms involved in the adaptation of G. daurica to harsh environments.

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Transcriptomic Analysis Identifies New Non-Target Site Glyphosate-Resistance Genes in Conyza bonariensis

Plants ◽

10.3390/plants8060157 ◽

2019 ◽

Vol 8 (6) ◽

pp. 157 ◽

Cited By ~ 7

Author(s):

Cristiano Piasecki ◽

Yongil Yang ◽

Daiane P. Benemann ◽

Frederico S. Kremer ◽

Vanessa Galli ◽

...

Keyword(s):

Molecular Mechanisms ◽

Target Genes ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Glyphosate Resistance ◽

Target Site ◽

Differentially Expressed ◽

Irreversible Damage ◽

Conyza Bonariensis

Conyza bonariensis (hairy fleabane) is one of the most problematic and widespread glyphosate-resistant weeds in the world. This highly competitive weed species significantly interferes with crop growth and substantially decreases crop yield. Despite its agricultural importance, the molecular mechanisms of glyphosate resistance are still unknown. The present RNA-Seq study was performed with the goal of identifying differentially expressed candidate transcripts (genes) related to metabolism-based non-target site glyphosate resistance in C. bonariensis. The whole-transcriptome was de novo assembled from glyphosate-resistant and -sensitive biotypes of C. bonariensis from Southern Brazil. The RNA was extracted from untreated and glyphosate-treated plants at several timepoints up to 288 h after treatment in both biotypes. The transcriptome assembly produced 90,124 contigs with an average length of 777 bp and N50 of 1118 bp. In response to glyphosate treatment, differential gene expression analysis was performed on glyphosate-resistant and -sensitive biotypes. A total of 9622 genes were differentially expressed as a response to glyphosate treatment in both biotypes, 4297 (44.6%) being up- and 5325 (55.4%) down-regulated. The resistant biotype presented 1770 up- and 2333 down-regulated genes while the sensitive biotype had 2335 and 2800 up- and down-regulated genes, respectively. Among them, 974 up- and 1290 down-regulated genes were co-expressed in both biotypes. In the present work, we identified 41 new candidate target genes from five families related to herbicide transport and metabolism: 19 ABC transporters, 10 CYP450s, one glutathione S-transferase (GST), five glycosyltransferases (GT), and six genes related to antioxidant enzyme catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The candidate genes may participate in metabolic-based glyphosate resistance via oxidation, conjugation, transport, and degradation, plus antioxidation. One or more of these genes might ‘rescue’ resistant plants from irreversible damage after glyphosate treatment. The 41 target genes we report in the present study may inform further functional genomics studies, including gene editing approaches to elucidate glyphosate-resistance mechanisms in C. bonariensis.

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Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop

International Journal of Genomics ◽

10.1155/2019/7295859 ◽

2019 ◽

Vol 2019 ◽

pp. 1-14

Author(s):

Fahad Al-Qurainy ◽

Aref Alshameri ◽

Abdel-Rhman Gaafar ◽

Salim Khan ◽

Mohammad Nadeem ◽

...

Keyword(s):

De Novo ◽

Gene Annotation ◽

Transcriptome Assembly ◽

Average Frequency ◽

Cyamopsis Tetragonoloba ◽

Metabolic Pathway Analysis ◽

Illumina Hiseq ◽

Forage Crop ◽

Kegg Pathways ◽

Advanced Analysis

The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2×100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C. tetragonoloba under normal, heat, drought, and salinity conditions. Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers. A total of 218.2 million paired-end raw reads (~44 Gbp) were generated. Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes. There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta. Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated. A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected. Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively. The transcriptome was associated with 985 enzymes and 156 KEGG pathways. A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts. This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.

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Transcriptome analysis reveals higher levels of mobile element-associated abnormal gene transcripts in temporal lobe epilepsy patients

10.1101/2021.05.14.444199 ◽

2021 ◽

Author(s):

Hai Hu ◽

Ping Liang

Keyword(s):

Temporal Lobe Epilepsy ◽

Temporal Lobe ◽

Molecular Mechanisms ◽

De Novo ◽

Splice Variants ◽

Transcriptome Assembly ◽

Hippocampal Sclerosis ◽

Mobile Element ◽

Loss Of Function ◽

Gene Transcripts

Objective: To determine role of abnormal splice variants associated with mobile elements in epilepsy. Methods: Publicly available human RNA-seq-based transcriptome data for laser-captured dentate granule cells of post-mortem hippocampal tissues from temporal lobe epilepsy patients with (TLE, N=14 for 7 subjects) and without hippocampal sclerosis (TLE-HS, N=8 for 5 subjects) and healthy individuals (N=51), surgically resected bulk neocortex tissues from TLE patients (TLE-NC, N=17). For each individual sample, de novo transcriptome assembly was performed followed by identification of spliced gene transcripts containing mobile element (ME) sequences (ME-transcripts) to compare the ME-transcript frequency across the sample groups. Enrichment analysis for genes associated with ME-transcripts and detailed sequence examination for representative epileptic genes were performed to analyze the pattern and mechanism of ME-transcripts on gene function. Results: We observed significantly higher levels of ME-transcripts in the hippocampal tissues of epileptic patients, particularly in TLE-HS. Among ME classes, SINEs were shown to be the most frequent contributor to ME-transcripts followed by LINEs and DNA transposons. These ME sequences almost in all cases represent older MEs normally located in the intron sequences, leading abnormal splicing variants. For protein coding genes, ME sequences were mostly found in the 3-UTR regions, with a significant portion also in the coding sequences (CDS) leading to reading frame disruption. Genes associated with ME-transcripts showed enrichment for involvement in the mRNA splicing process in all sample groups, with bias towards neural and epilepsy-associated genes in the epileptic transcriptomes. Significance: Our data suggest that abnormal splicing involving MEs, leading to loss of function in critical genes, plays a role in epilepsy, particularly in TLE-HS, providing a novel insight on the molecular mechanisms underlying epileptogenesis.

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