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

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.

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

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

Universal and differential transcriptional regulatory pathways involved in the preparation of summer and winter diapauses in Pieris melete

2021 ◽  
pp. 1-8
Author(s):  
Ting Jiang ◽  
Yulin Zhu ◽  
Yingchuan Peng ◽  
Wanna Zhang ◽  
Haijun Xiao
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Orthologous Group ◽  
Seasonal Adaptation ◽  
Environmental Signals ◽  
Regulatory Pathways ◽  
Kegg Pathways ◽  
Summer Diapause ◽  
Transcriptional Regulatory

Abstract Much progress has been made in understanding the environmental and hormonal systems regulating winter diapause. However, transcriptional regulation of summer diapause is still largely unknown, making it difficult to understand an all-around regulation profile of seasonal adaptation. To bridge this gap, comparison RNA-seq to profile the transcriptome and to examine differential gene expression profiles between non-diapause, summer diapause, and winter diapause groups were performed. A total number of 113 million reads were generated and assembled into 79,117 unigenes, with 37,492 unigenes categorized into 58 functional gene ontology groups, 25 clusters of orthologous group categories, and 256 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG analysis mapped 2108 differentially expressed genes to 48 and 67 pathways for summer and winter diapauses, respectively. Enrichment statistics showed that 11 identical pathways similarly overlapped in the top 20 enriched functional groups both related to summer and winter diapauses. We also identified 35 key candidate genes for universal and differential functions related to summer and winter diapause preparation. Furthermore, we identified some genes involved in the signaling and metabolic pathways that may be the key drivers to integrate environmental signals into the summer and winter diapause preparation. The current study provided valuable insights into global molecular mechanisms underpinning diapause preparation.

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

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

scholarly journals De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico)

2018 ◽  
Author(s):  
Federico Vita ◽  
Amedeo Alpi ◽  
Edoardo Bertolini
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Genetic Studies ◽  
Protein Coding ◽  
Important Species ◽  
White Truffle ◽  
Tuber Magnatum ◽  
Insight Into

AbstractThe Italian white truffle (Tuber magnatum Pico) is a gastronomic delicacy that dominates the worldwide truffle market. Despite its importance, the genomic resources currently available for this species are still limited. Here we present the first de novo transcriptome assembly of T. magnatum. Illumina RNA-seq data were assembled using a single-k-mer approach into 22,932 transcripts with N50 of 1,524 bp. Our approach allowed to predict and annotate 12,367 putative protein coding sequences, reunited in 6,723 loci. In addition, we identified 2,581 gene-based SSR markers. This work provides the first publicly available reference transcriptome for genomics and genetic studies providing insight into the molecular mechanisms underlying the biology of this important species.

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

2021 ◽  
Author(s):  
Mónica Díaz-Silva ◽  
Jonathan Maldonado ◽  
Nicol Delgado ◽  
Pamela Veloso ◽  
Herman Silva ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Saline Water ◽  
Transcriptome Assembly ◽  
Glutamate Synthase ◽  
Ammonium Uptake ◽  
Saline Wastewater ◽  
Anatomical Entity ◽  
Kegg Pathways ◽  
Pathway Analyses

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

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

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

scholarly journals Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress

2020 ◽  
Vol 21 (3) ◽  
pp. 1067 ◽  
Author(s):  
Zhaoyang Hu ◽  
Yufei Zhang ◽  
Yue He ◽  
Qingqing Cao ◽  
Ting Zhang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Italian Ryegrass ◽  
Full Length ◽  
Rna Seq ◽  
Cd Stress ◽  
Toxic Heavy Metal ◽  
Regulatory Pathways ◽  
A Genome ◽  
Cd Translocation

Cadmium (Cd) is a toxic heavy metal element. It is relatively easily absorbed by plants and enters the food chain, resulting in human exposure to Cd. Italian ryegrass (Lolium multiflorum Lam.), an important forage cultivated widely in temperate regions worldwide, has the potential to be used in phytoremediation. However, genes regulating Cd translocation and accumulation in this species are not fully understood. Here, we optimized PacBio ISO-seq and integrated it with RNA-seq to construct a de novo full-length transcriptomic database for an un-sequenced autotetraploid species. With the database, we identified 2367 differentially expressed genes (DEGs) and profiled the molecular regulatory pathways of Italian ryegrass with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in response to Cd stress. Overexpression of a DEG LmAUX1 in Arabidopsis thaliana significantly enhanced plant Cd concentration. We also unveiled the complexity of alternative splicing (AS) with a genome-free strategy. We reconstructed full-length UniTransModels using the reference transcriptome, and 29.76% of full-length models had more than one isoform. Taken together, the results enhanced our understanding of the genetic diversity and complexity of Italian ryegrass under Cd stress and provided valuable genetic resources for its gene identification and molecular breeding.

scholarly journals Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12454
Author(s):  
Zehu Yuan ◽  
Ling Ge ◽  
Jingyi Sun ◽  
Weibo Zhang ◽  
Shanhe Wang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Messenger Rna ◽  
Molecular Mechanisms ◽  
Alternative Polyadenylation ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Protein Protein Interaction ◽  
Kegg Pathways ◽  
Novel Transcripts

Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear. Methods In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs. Results In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.

scholarly journals The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 7
Author(s):  
Nur Lina Rahmat ◽  
Anis Nadyra Zifruddin ◽  
Cik Mohd Rizuan Zainal Abidin ◽  
Nor-Azlan Nor Muhammad ◽  
Maizom Hassan
Keyword(s):  
Oil Palm ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Instar Larva ◽  
Orthologous Group ◽  
Kegg Pathways ◽  
Developmental Gene Expression ◽  
Functional Studies

Bagworm, Metisa plana (Lepidoptera: Psychidae) is a ubiquitous insect pest in the oil palm plantations. M. plana infestation could reduce the oil palm productivity by 40% if it remains untreated over two consecutive years. Despite the urgency to tackle this issue, the genome and transcriptome of M. plana have not yet been fully elucidated. Here, we report a comprehensive transcriptome dataset from four different developmental stages of M. plana, comprising of egg, third instar larva, pupa and female adult. The de novo transcriptome assembly of the raw data had produced a total of 193,686 transcripts, which were then annotated against UniProt, NCBI non-redundant (NR) database, Gene Ontology, Cluster of Orthologous Group, and Kyoto Encyclopedia of Genes and Genomes databases. From this, 46,534 transcripts were annotated and mapped to 146 known metabolic or signalling KEGG pathways. The paper further identified 41 differentially expressed transcripts encoding seven genes in the chitin biosynthesis pathways, and their expressions across each developmental stage were further analysed. The genetic diversity of M. plana was profiled whereby there were 21,516 microsatellite sequences and 379,895 SNPs loci found in the transcriptome of M. plana. These datasets add valuable transcriptomic resources for further study of developmental gene expression, transcriptional regulations and functional gene activities involved in the development of M. plana. Identification of regulatory genes in the chitin biosynthesis pathway may also help in developing an RNAi-mediated pest control management by targeting certain pathways, and functional studies of the genes in M. plana.

scholarly journals De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (Solanum betaceum Cav.) with Different Fruit Color

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 431
Author(s):  
Juan Pacheco ◽  
Santiago Vilanova ◽  
Rubén Grillo-Risco ◽  
Francisco Garcia-Garcia ◽  
Jaime Prohens ◽  
...  
Keyword(s):  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Orthologous Group ◽  
Significant Similarity ◽  
Single Nucleotide ◽  
Kegg Pathways ◽  
Tomato Cultivars ◽  
Solanum Betaceum ◽  
Tree Tomato

The tree tomato (Solanum betaceum Cav.) is an underutilized fruit crop native to the Andean region and phylogenetically related to the tomato and potato. Tree tomato fruits have a high amount of nutrients and bioactive compounds. However, so far there are no studies at the genome or transcriptome level for this species. We performed a de novo assembly and transcriptome annotation for purple-fruited (A21) and an orange-fruited (A23) accessions. A total of 174,252 (A21) and 194,417 (A23) transcripts were assembled with an average length of 851 and 849 bp. A total of 34,636 (A21) and 36,224 (A23) transcripts showed a significant similarity to known proteins. Among the annotated unigenes, 22,096 (A21) and 23,095 (A23) were assigned to the Gene Ontology (GO) term and 14,035 (A21) and 14,540 (A23) were found to have Clusters of Orthologous Group (COG) term classifications. Furthermore, 22,096 (A21) and 23,095 (A23) transcripts were assigned to 155 and 161 (A23) KEGG pathways. The carotenoid biosynthetic process GO terms were significantly enriched in the purple-fruited accession A21. Finally, 68,647 intraspecific single-nucleotide variations (SNVs) and almost 2 million interspecific SNVs were identified. The results of this study provide a wealth of genomic data for the genetic improvement of the tree tomato.

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