Comparative transcriptomic analysis reveals key components controlling spathe color in Anthurium andraeanum (Hort.)

Anthurium andraeanum (Hort.) is an important ornamental in the tropical cut-flower industry. However, there is currently insufficient information to establish a clear connection between the genetic model(s) proposed and the putative genes involved in the differentiation between colors. In this study, 18 cDNA libraries related to the spathe color and developmental stages of A. andraeanum were characterized by transcriptome sequencing (RNA-seq). For the de novo transcriptome, a total of 114,334,082 primary sequence reads were obtained from the Illumina sequencer and were assembled into 151,652 unigenes. Approximately 58,476 transcripts were generated and used for comparative transcriptome analysis between three cultivars that differ in spathe color (‘Sasha’ (white), ‘Honduras’ (red), and ‘Rapido’ (purple)). A large number of differentially expressed genes (8,324), potentially involved in multiple biological and metabolic pathways, were identified, including genes in the flavonoid and anthocyanin biosynthetic pathways. Our results showed that the chalcone isomerase (CHI) gene presented the strongest evidence for an association with differences in color and the highest correlation with other key genes (flavanone 3-hydroxylase (F3H), flavonoid 3’5’ hydroxylase (F3’5’H)/ flavonoid 3’-hydroxylase (F3’H), and leucoanthocyanidin dioxygenase (LDOX)) in the anthocyanin pathway. We also identified a differentially expressed cytochrome P450 gene in the late developmental stage of the purple spathe that appeared to determine the difference between the red- and purple-colored spathes. Furthermore, transcription factors related to putative MYB-domain protein that may control anthocyanin pathway were identified through a weighted gene co-expression network analysis (WGCNA). The results provided basic sequence information for future research on spathe color, which have important implications for this ornamental breeding strategies.

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Comparative transcriptomic analysis reveals key components controlling spathe color in Anthurium andraeanum (Hort.)

10.1101/2020.12.29.424726 ◽

2020 ◽

Author(s):

Jaime A. Osorio-Guarín ◽

David Gopaulchan ◽

Corey Quackenbush ◽

Adrian M. Lennon ◽

Pathmanathan Umaharan ◽

...

Keyword(s):

Developmental Stage ◽

Biosynthetic Pathway ◽

Differentially Expressed ◽

Cdna Libraries ◽

Future Research ◽

Sequence Information ◽

List Type ◽

Domain Protein ◽

Anthurium Andraeanum ◽

Myb Domain

ABSTRACTAnthurium andraeanum (Hort.) is an important ornamental in the tropical cut-flower industry. However, there is currently not enough information to establish a clear connection between the genetic model(s) proposed and the putative genes involved in the differentiation between colors. In this study, 18 cDNA libraries related to the spathe color and developmental stages of A. andraeanum cut-flowers were characterized by transcriptome sequencing technology. For the de novo transcriptome, a total of 114,334,082 primary sequence reads were obtained from the Illumina sequencer and were assembled into 151,652 unigenes. Approximately 58,476 transcripts were generated and used for comparative transcriptome analysis between three varieties that differ in spathe color (‘Sasha’ (white), ‘Honduras’ (red), and ‘Rapido’ (purple)). A large number of differentially expressed genes (8,324) that were potentially involved in multiple biological and metabolic pathways were identified, including the flavonoid and anthocyanin biosynthetic pathways. Our results showed that chalcone synthase (CHS) and flavonoid 3’-hydroxylase (F3’H) were the main genes differentially expressed in the white/red/purple comparison. We also identified a differentially expressed cytochrome P450 in the late developmental stage of the purple spathe that appeared to determine the difference between the red- and purple-colored spathes. Additionally, putative MYB-domain protein candidates that could be responsible for the control of the biosynthetic pathway were identified. The results provided basic sequence information for future research on spathe color, which have important implications for breeding strategies in this ornamental.Core ideasRNA-seq was performed on three anthurium varieties.Gene expression was compared for developmental stage and spathe color.Differentially expressed unigenes were identified.Putative MYB-domain protein candidates of the anthocyanin biosynthetic pathway were identified.

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CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure

PLoS Computational Biology ◽

10.1371/journal.pcbi.1009631 ◽

2021 ◽

Vol 17 (11) ◽

pp. e1009631

Author(s):

Raquel Linheiro ◽

John Archer

Keyword(s):

De Novo ◽

Simulated Data ◽

Real Data ◽

Gene Families ◽

Classification Systems ◽

Whole Body ◽

Cdna Libraries ◽

Sequence Information ◽

Rna Seq ◽

High Quality

With the exponential growth of sequence information stored over the last decade, including that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric sequences has become essential when assembling read data. In transcriptomics, de novo assembled chimeras can closely resemble underlying transcripts, but patterns such as those seen between co-evolving sites, or mapped read counts, become obscured. We have created a de Bruijn based de novo assembler for RNA-Seq data that utilizes a classification system to describe the complexity of underlying graphs from which contigs are created. Each contig is labelled with one of three levels, indicating whether or not ambiguous paths exist. A by-product of this is information on the range of complexity of the underlying gene families present. As a demonstration of CStones ability to assemble high-quality contigs, and to label them in this manner, both simulated and real data were used. For simulated data, ten million read pairs were generated from cDNA libraries representing four species, Drosophila melanogaster, Panthera pardus, Rattus norvegicus and Serinus canaria. These were assembled using CStone, Trinity and rnaSPAdes; the latter two being high-quality, well established, de novo assembers. For real data, two RNA-Seq datasets, each consisting of ≈30 million read pairs, representing two adult D. melanogaster whole-body samples were used. The contigs that CStone produced were comparable in quality to those of Trinity and rnaSPAdes in terms of length, sequence identity of aligned regions and the range of cDNA transcripts represented, whilst providing additional information on chimerism. Here we describe the details of CStones assembly and classification process, and propose that similar classification systems can be incorporated into other de novo assembly tools. Within a related side study, we explore the effects that chimera’s within reference sets have on the identification of differentially expression genes. CStone is available at: https://sourceforge.net/projects/cstone/.

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Transcriptome dynamics underlying flower color in marigold (Tagetes erecta L.)

10.21203/rs.2.17549/v2 ◽

2019 ◽

Author(s):

Huali Zhang ◽

Shiya Zhang ◽

Hua Zhang ◽

Xi Chen ◽

Fang Liang ◽

...

Keyword(s):

Inbred Line ◽

Developmental Stages ◽

De Novo ◽

Flower Color ◽

Carotenoid Biosynthesis ◽

Cdna Libraries ◽

Carotenoid Content ◽

Tagetes Erecta ◽

Tagetes Erecta L ◽

Carotenoid Degradation

Abstract Background: Marigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of flower colors. Despite its economic value, few biochemical and molecular studies have explored the generation of flower color in this species. Results: To study the mechanism underlying marigold petal color, we performed a metabolomics analysis and de novo cDNA sequencing on the inbred line ‘V-01’ and its petal color mutant ‘V-01M’ at four flower developmental stages. A total of 49,217 unigenes were identified from 24 cDNA libraries. Based on our transcriptomic and metabolomic analyses, we present an overview of carotenoid biosynthesis, degradation, and accumulation in marigold flowers. The carotenoid content of the yellow mutant ‘V-01M’ was higher than that of the orange inbred line ‘V-01’, and the abundances of the yellow compounds lutein, neoxanthin, violaxanthin, zeaxanthin, and antheraxanthin were significantly higher in the mutant. During flower development, the carotenoid biosynthesis genes were upregulated in both ‘V-01’ and ‘V-01M’, with no significant differences between the two lines. By contrast, the carotenoid degradation genes were dramatically downregulated in the yellow mutant ‘V-01M’. Conclusions: We therefore speculate that the carotenoid degradation genes are the key factors regulating the carotenoid content of marigold flowers. Our research provides a large amount of transcriptomic data and insights into the marigold color metabolome.

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Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

Journal of Insect Science ◽

10.1093/jisesa/iew053 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 7

Author(s):

Juan Ma ◽

Rongyan Wang ◽

Xiuhua Li ◽

Bo Gao ◽

Shulong Chen

Keyword(s):

Sweet Potato ◽

Molecular Mechanisms ◽

Developmental Stages ◽

De Novo ◽

Average Length ◽

Expression Profiles ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Cylas Formicarius ◽

Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

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Leishmania infection induces a limited differential gene expression in the sand fly midgut

10.21203/rs.2.17551/v2 ◽

2020 ◽

Author(s):

Iliano V. Coutinho-Abreu ◽

Tiago D. Serafim ◽

Claudio Meneses ◽

Shaden Kamhawi ◽

Fabiano Oliveira ◽

...

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

De Novo ◽

Early Time ◽

Differentially Expressed ◽

Sand Fly ◽

Leishmania Infection ◽

Lutzomyia Longipalpis ◽

Late Time ◽

Time Points

Abstract Background: Phlebotomine sand flies are the vectors of Leishmania worldwide. To develop in the sand fly midgut, Leishmania multiplies and undergoes multiple stage differentiations leading to the infective form, the metacyclic promastigotes. To gain a better understanding of the influence of Leishmania infection on midgut gene expression, we performed RNA-Seq comparing uninfected and Leishmania infantum -infected Lutzomyia longipalpis midguts at seven time points which cover the various Leishmania developmental stages including early time points when blood digestion is taking place, and late time points when the parasites are undergoing metacyclogenesis. Results: Out of over 13,841 transcripts assembled de novo , only 113 sand fly transcripts, about 1%, were differentially expressed. Further, we observed a low overlap of differentially expressed sand fly transcripts across different time points suggesting that each Leishmania stage influences midgut gene expression in a specific manner. Two main patterns of sand fly gene expression modulation were noted. At early time points (days 1-4), more transcripts were down-regulated by Leishmania infection at large fold changes (> -32 fold). Among the down-regulated genes, the transcription factor Forkhead/HNF-3 and hormone degradation enzymes were differentially regulated on day 4 and appear to be the upstream regulators of nutrient transport, digestive enzymes, and peritrophic matrix proteins. Conversely, at later time points (days 6 onwards), most of the differentially expressed transcripts were up-regulated by small fold changes (< 32 fold). The molecular function of these genes has been associated with the metabolism of lipids and detoxification of xenobiotics. Conclusion: Overall, it appears that Leishmania modulates sand fly gene expression early on in order to overcome the barriers imposed by the midgut, yet it behaves like a commensal at later time points, where a massive number of parasites in the anterior midgut results only in modest changes in midgut gene expression.

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Transcriptomic and proteomic analyses of a new cytoplasmic male sterile line with a wild Gossypium bickii genetic background

BMC Genomics ◽

10.1186/s12864-020-07261-y ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Haiyan Zhao ◽

Jianshe Wang ◽

Yunfang Qu ◽

Renhai Peng ◽

Richard Odongo Magwanga ◽

...

Keyword(s):

Genetic Background ◽

Developmental Stages ◽

Interaction Network ◽

Differentially Expressed ◽

Future Research ◽

Glutathione S Transferase ◽

Male Sterile ◽

Genomic Databases ◽

Wild Cotton ◽

Pathway Analyses

Abstract Background Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B. Results We detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background. Conclusion We first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching.

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A study of the heterochronic sense/antisense RNA representation in florets of sexual and apomictic Paspalum notatum

BMC Genomics ◽

10.1186/s12864-021-07450-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Maricel Podio ◽

Carolina Colono ◽

Lorena Siena ◽

Juan Pablo A. Ortiz ◽

Silvina Claudia Pessino

Keyword(s):

Comparative Analysis ◽

Developmental Stages ◽

De Novo ◽

Wrky Transcription Factor ◽

Hormonal Control ◽

Differentially Expressed ◽

Paspalum Notatum ◽

Antisense Transcripts ◽

Antisense Gene ◽

Heritable Trait

Abstract Background Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of maternal seeds. Recently, reference floral transcriptomes were generated from sexual and apomictic biotypes of Paspalum notatum, one of the most well-known plant models for the study of apomixis. However, the transcriptome dynamics, the occurrence of apomixis vs. sexual expression heterochronicity across consecutive developmental steps and the orientation of transcription (sense/antisense) remain unexplored. Results We produced 24 Illumina TruSeq®/ Hiseq 1500 sense/antisense floral transcriptome libraries covering four developmental stages (premeiosis, meiosis, postmeiosis, and anthesis) in biological triplicates, from an obligate apomictic and a full sexual genotype. De novo assemblies with Trinity yielded 103,699 and 100,114 transcripts for the apomictic and sexual samples respectively. A global comparative analysis involving reads from all developmental stages revealed 19,352 differentially expressed sense transcripts, of which 13,205 (68%) and 6147 (32%) were up- and down-regulated in apomictic samples with respect to the sexual ones. Interestingly, 100 differentially expressed antisense transcripts were detected, 55 (55%) of them up- and 45 (45%) down-regulated in apomictic libraries. A stage-by-stage comparative analysis showed a higher number of differentially expressed candidates due to heterochronicity discrimination: the highest number of differential sense transcripts was detected at premeiosis (23,651), followed by meiosis (22,830), postmeiosis (19,100), and anthesis (17,962), while the highest number of differential antisense transcripts were detected at anthesis (495), followed by postmeiosis (164), meiosis (120) and premeiosis (115). Members of the AP2, ARF, MYB and WRKY transcription factor families, as well as the auxin, jasmonate and cytokinin plant hormone families appeared broadly deregulated. Moreover, the chronological expression profile of several well-characterized apomixis controllers was examined in detail. Conclusions This work provides a quantitative sense/antisense gene expression catalogue covering several subsequent reproductive developmental stages from premeiosis to anthesis for apomictic and sexual P. notatum, with potential to reveal heterochronic expression between reproductive types and discover sense/antisense mediated regulation. We detected a contrasting transcriptional and hormonal control in apomixis and sexuality as well as specific sense/antisense modulation occurring at the onset of parthenogenesis.

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De Novo Assembly and Transcriptome Profiling of Ethiopian Lowland Bamboo Oxytenanthera Abyssinica (A. rich) Munro Under Drought and Salt Stresses

The Open Biotechnology Journal ◽

10.2174/1874070701913010006 ◽

2019 ◽

Vol 13 (1) ◽

pp. 6-17

Author(s):

Muhamed Adem ◽

Dereje Beyene ◽

Tileye Feyissa ◽

Kai Zhao ◽

Tingbo Jiang

Keyword(s):

Differentially Expressed Genes ◽

De Novo ◽

Transcriptome Profiling ◽

Global Gene Expression ◽

Perennial Grasses ◽

Differentially Expressed ◽

Cdna Libraries ◽

Protein Families ◽

Sequencing Platform ◽

Genome Wide

Background: Bamboos are perennial grasses classified under family Poaceae and subfamily Bambusoideae and are among the fastest growing plants on earth. Despite ecological and economic significances, Ethiopian lowland bamboo (O. abyssinica) lacks global gene expression under abiotic stress. Methods: Plastic pot germinated seedlings of O. abyssinica were subjected to 200 µm NaCl and 25% PEG-6000 (Poly Ethylene glycol) to induce salt and drought stress, respectively. Using the Illumina sequencing platform, fifteen cDNA libraries were constructed and sequenced to generate the first drought and salt stress transcriptome profiling of the species so as to elucidate genome-wide transcriptome changes in response to such stresses. Results: Following quality control, 754,444,646 clean paired-ends reads were generated, and then de novo assembled into 406,181 unigenes. Functional annotation against the public databases presented annotation of 217,067 (53.4%) unigenes, where NCBI-Nr 203,777, Swissport 115,741, COG 81,632 and KEGG 80,587. Prediction of Transcripts Factors (TFs) have generated 4,332 TFs organized into 64 TF families. Analysis of Differentially Expressed Genes (DEGs) provided 65,471 genes where 569 genes belong to all stresses. Protein families with a higher number of differentially expressed genes include bZIP (49), WRKY (43), MYB (38), AP2/ERF (30), HD-ZIP (25) and MYB related (21). Conclusion: In addition to revealing the genome-wide level appraisal of transcriptome resources of the species, this study also uncovered the comprehensive understanding of key stress responsive protein-coding genes, protein families and pathways which could be used as the basis for further studies.

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Carotenoid metabolite and transcriptome dynamics underlying flower color in marigold (Tagetes erecta L.)

Scientific Reports ◽

10.1038/s41598-020-73859-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Huali Zhang ◽

Shiya Zhang ◽

Hua Zhang ◽

Xi Chen ◽

Fang Liang ◽

...

Keyword(s):

Inbred Line ◽

Developmental Stages ◽

De Novo ◽

Economic Value ◽

Flower Color ◽

Carotenoid Biosynthesis ◽

Cdna Libraries ◽

Carotenoid Content ◽

Tagetes Erecta ◽

Carotenoid Degradation

Abstract Marigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of flower colors. Despite its economic value, few biochemical and molecular studies have explored the generation of flower color in this species. To study the mechanism underlying marigold petal color, we performed a metabolite analysis and de novo cDNA sequencing on the inbred line ‘V-01’ and its petal color mutant ‘V-01M’ at four flower developmental stages. A total of 49,217 unigenes were identified from 24 cDNA libraries. Based on our metabolites and transcriptomic analyses, we present an overview of carotenoid biosynthesis, degradation, and accumulation in marigold flowers. The carotenoid content of the yellow mutant ‘V-01M’ was higher than that of the orange inbred line ‘V-01’, and the abundances of the yellow compounds lutein, neoxanthin, violaxanthin, zeaxanthin, and antheraxanthin were significantly higher in the mutant. During flower development, the carotenoid biosynthesis genes were upregulated in both ‘V-01’ and ‘V-01M’, with no significant differences between the two lines. By contrast, the carotenoid degradation genes were dramatically downregulated in the yellow mutant ‘V-01M’. We therefore speculate that the carotenoid degradation genes are the key factors regulating the carotenoid content of marigold flowers. Our research provides a large amount of transcriptomic data and insights into the marigold color metabolome.

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Transcriptome Analysis of Larval Segment Formation and Secondary Loss in the Echiuran Worm Urechis unicinctus

International Journal of Molecular Sciences ◽

10.3390/ijms20081806 ◽

2019 ◽

Vol 20 (8) ◽

pp. 1806 ◽

Cited By ~ 4

Author(s):

Xitan Hou ◽

Maokai Wei ◽

Qi Li ◽

Tingting Zhang ◽

Di Zhou ◽

...

Keyword(s):

Developmental Stages ◽

Average Length ◽

Expression Profiles ◽

Evolutionary Relationship ◽

Cdna Libraries ◽

Future Research ◽

Molecular Evidence ◽

Axis Formation ◽

Urechis Unicinctus ◽

Secondary Loss

The larval segment formation and secondary loss in echiurans is a special phenomenon, which is considered to be one of the important characteristics in the evolutionary relationship between the Echiura and Annelida. To better understand the molecular mechanism of this phenomenon, we revealed the larval transcriptome profile of the echiuran worm Urechis unicinctus using RNA-Seq technology. Twelve cDNA libraries of U. unicinctus larvae, late-trochophore (LT), early-segmentation larva (ES), segmentation larva (SL), and worm-shaped larva (WL) were constructed. Totally 243,381 unigenes were assembled with an average length of 1125 bp and N50 of 1836 bp, and 149,488 unigenes (61.42%) were annotated. We obtained 70,517 differentially expressed genes (DEGs) by pairwise comparison of the larval transcriptome data at different developmental stages and clustered them into 20 gene expression profiles using STEM software. Based on the typical profiles during the larval segment formation and secondary loss, eight signaling pathways were enriched, and five of which, mTOR, PI3K-AKT, TGF-β, MAPK, and Dorso-ventral axis formation signaling pathway, were proposed for the first time to be involved in the segment formation. Furthermore, we identified 119 unigenes related to the segment formation of annelids, arthropods, and chordates, in which 101 genes were identified in Drosophila and annelids. The function of most segment polarity gene homologs (hedgehog, wingless, engrailed, etc.) was conserved in echiurans, annelids, and arthropods based on their expression profiles, while the gap and pair-rule gene homologs were not. Finally, we verified that strong positive signals of Hedgehog were indeed located on the boundary of larval segments using immunofluorescence. Data in this study provide molecular evidence for the understanding of larval segment development in echiurans and may serve as a blueprint for segmented ancestors in future research.

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