De novo transcriptome assembly of Vitis flexuosa grapevines inoculated with Elsinoe ampelina

2014 ◽  
Vol 12 (S1) ◽  
pp. S130-S133 ◽  
Author(s):  
Soon Young Ahn ◽  
Seon Ae Kim ◽  
Sung Hwan Jo ◽  
Hae Keun Yun
Keyword(s):  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Optimal Parameters ◽  
De Novo Transcriptome ◽  
Illumina Platform ◽  
Oxidoreductase Activity ◽  
Elsinoe Ampelina ◽  
Functional Molecular Markers

In this study, the transcriptome of Vitis flexuosa leaves inoculated with Elsinoe ampelina was analysed to identify useful genes and elucidate their function and differential expression patterns through assembly and annotation gene ontology of data from sequencing short reads on the Illumina platform. We assembled ~121 million high-quality trimmed reads using Velvet and Oases with optimal parameters into a non-redundant set of 70,899 transcripts ( ≥ 200 bp in length). The transcripts exhibited an average length of 1138 bp and a N50 length of 1695 bp, with the largest contig length being 9623 bp. Functional categorization revealed the conservation of genes involved in various molecular functions, including protein binding (21.1%) and oxidoreductase activity (11.7%), in V. flexuosa. The V. flexuosa transcript set generated in this study will serve as a resource for gene discovery and development of functional molecular markers.

scholarly journals De novo Characterization of the Platycladus orientalis Transcriptome and Analysis of Photosynthesis-Related Genes during Aging

Forests ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 393
Author(s):  
Ermei Chang ◽  
Jin Zhang ◽  
Xiamei Yao ◽  
Shuo Tang ◽  
Xiulian Zhao ◽  
...  
Keyword(s):  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Age And Growth ◽  
Potential Candidate ◽  
Platycladus Orientalis ◽  
Oxidation Reduction ◽  
Old Trees

In China, Platycladus orientalis has a lifespan of thousands of years. The long lifespan of these trees may be relevant for the characterization of plant aging at the molecular level. However, the molecular mechanism of the aging process of P. orientalis is still unknown. To explore the relationship between age and growth of P. orientalis, we analyzed physiological changes during P. orientalis senescence. The malondialdehyde content was greater in 200-, 700-, and 1100-year-old ancient trees than in 20-year-old trees, whereas the peroxidase and superoxide dismutase activities, as well as the soluble protein content, exhibited the opposite trend. Furthermore, we performed a de novo transcriptome assembly using RNA-Seq and obtained 48,044 unigenes with an average length of 896 bp. A total of 418 differentially expressed genes were identified in different stages of aging of P. orientalis. Clustering analysis revealed distinct timepoints at which the oxidation–reduction and photosynthesis pathways changed. Eight clusters with distinct expression patterns were identified. The expression levels of photosynthesis-, oxidation–reduction-, and transporter-related genes were down-regulated, whereas those of transcription-, signaling-, and senescence-related genes were up-regulated during aging. In addition, consistent with the most obviously down-regulated genes of photosynthesis-related genes, the photosynthetic indexes including chlorophyll a and b levels decreased steadily during P. orientalis aging. This study combined transcriptome with physiological and biochemical data, revealing potential candidate genes influencing senescence during P. orientalis aging.

De novo transcriptome assembly of four organs of Collichthys lucidus and identification of genes involved in sex determination and reproduction

2019 ◽  
Author(s):  
Wei Song ◽  
Yi-Bing Zhang ◽  
Xiao-Juan Zhang ◽  
Jianfang Gui
Keyword(s):  
Sex Determination ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Sex Differentiation ◽  
Molecular Regulation ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Sexual Characteristics ◽  
Collichthys Lucidus

Abstract Background Spinyhead croaker (Collichthys lucidus) is an important kind of fish for commercial fishery because of its delicious meat and abundant resource. However, the resource has been declining with the overfishing and environmental disruption. Unfortunately, the mechanism of sex determination and reproduction in Collichthys lucidus is still confusing, which has largely hindered molecular regulation and reproduction studies. Results Based on transcripts sequencing in brain, liver, ovary and testis, a de novo transcriptome assembly of Collichthys lucidus was performed. Totally, 131,168 non-redundant unigenes with an average length of 644 bp and an N50 value of 1033 bp, among which 2,143, 304, 333 and 556 were found specifically expressing in brain, liver, ovary and testis, respectively. Importantly, 1288 genes were differently expressed between ovary and testis, including 442 up- and 846 down-regulated in ovary. The differently expressed genes were involved in function of sexual reproduction, sex differentiation, development of primary male sexual characteristics, female gamete generation, and male sex differentiation. HYAL and SYCP3, two genes which were reported to play dominant roles in reproduction, may regulated the key of fertilization and meiosis in Collichthys lucidus. Meanwhile, 35,476 simple sequence repeats (SSRs) were identified, which would contribute to further genetic and mechanism researches. Conclusions The studies of genetic information, molecular regulation and reproduction of Collichthys lucidus would be expand due to the sequencing and de novo assembling on the transcripts of major organs. In addition, the identification of candidate genes involved in reproduction will be useful for protecting the resource of Collichthys lucidus.

scholarly journals De Novo Transcriptome Assembly and SNP Discovery for the Development of dCAPS Markers in Oat

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 184
Author(s):  
Tae-Heon Kim ◽  
Young-Mi Yoon ◽  
Jin-Cheon Park ◽  
Jong-Ho Park ◽  
Kyong-Ho Kim ◽  
...  
Keyword(s):  
Dna Markers ◽  
Dna Marker ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Seedling Stage ◽  
Marker Development ◽  
Illumina Platform ◽  
Functional Studies ◽  
Parent Term

Cultivated oat (Avena sativa L.) is an important cereal crop that has captured interest worldwide due to its nutritional properties and associated health benefits. Despite this interest, oat has lagged behind other cereal crops in genome studies and the development of DNA markers due to its large and complex genome. RNA-Seq technology has been widely used for transcriptome analysis, functional gene study, and DNA marker development. In this study, we performed the transcriptome sequencing of 10 oat varieties at the seedling stage using the Illumina platform for the development of DNA markers. In total, 31,187,392~41,304,176 trimmed reads (an average of 34,322,925) were generated from 10 oat varieties. All of the trimmed reads of these varieties were assembled and generated, yielding a total of 128,244 assembled unigenes with an average length of 1071.7 bp and N50 of 1752 bp. According to gene ontology (GO) analysis, 30.7% of unigenes were assigned to the “catalytic activity” of the parent term in the molecular function category. Of the 1273 dCAPS markers developed using 491 genotype-specific SNPs, 30 markers exhibiting polymorphism in 28 oat varieties were finally selected. The transcriptome data of oat varieties could be used for functional studies about the seedling stage of oat and information about sequence variations in DNA marker development. These 30 dCAPS markers will be utilized for oat genetic analysis, cultivar identification, and breeders’ rights protection.

scholarly journals Transcriptome Analysis of Melocactus glaucescens (Cactaceae) Reveals Metabolic Changes During in vitro Shoot Organogenesis Induction

2021 ◽  
Vol 12 ◽  
Author(s):  
Gabriela Torres-Silva ◽  
Ludmila Nayara Freitas Correia ◽  
Diego Silva Batista ◽  
Andréa Dias Koehler ◽  
Sheila Vitória Resende ◽  
...  
Keyword(s):  
De Novo ◽  
Shoot Organogenesis ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Genetic Regulation ◽  
Pairwise Comparison ◽  
Illumina Hiseq ◽  
Real Time Quantitative Pcr

Melocactus glaucescens is an endangered cactus highly valued for its ornamental properties. In vitro shoot production of this species provides a sustainable alternative to overharvesting from the wild; however, its propagation could be improved if the genetic regulation underlying its developmental processes were known. The present study generated de novo transcriptome data, describing in vitro shoot organogenesis induction in M. glaucescens. Total RNA was extracted from explants before (control) and after shoot organogenesis induction (treated). A total of 14,478 unigenes (average length, 520 bases) were obtained using Illumina HiSeq 3000 (Illumina Inc., San Diego, CA, USA) sequencing and transcriptome assembly. Filtering for differential expression yielded 2,058 unigenes. Pairwise comparison of treated vs. control genes revealed that 1,241 (60.3%) unigenes exhibited no significant change, 226 (11%) were downregulated, and 591 (28.7%) were upregulated. Based on database analysis, more transcription factor families and unigenes appeared to be upregulated in the treated samples than in controls. Expression of WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) and CALMODULIN (CaM) genes, both of which were upregulated in treated samples, was further validated by real-time quantitative PCR (RT-qPCR). Differences in gene expression patterns between control and treated samples indicate substantial changes in the primary and secondary metabolism of M. glaucescens after the induction of shoot organogenesis. These results help to clarify the molecular genetics and functional genomic aspects underlying propagation in the Cactaceae family.

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals Sub-Chronic Effects of Slight PAH- and PCB-Contaminated Mesocosms in Paracentrotus lividus Lmk: A Multi-Endpoint Approach and De Novo Transcriptomic

2021 ◽  
Vol 22 (13) ◽  
pp. 6674
Author(s):  
Luisa Albarano ◽  
Valerio Zupo ◽  
Davide Caramiello ◽  
Maria Toscanesi ◽  
Marco Trifuoggi ◽  
...  
Keyword(s):  
De Novo ◽  
Sea Urchins ◽  
Transcriptome Assembly ◽  
Paracentrotus Lividus ◽  
Marine Biota ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Limit Values ◽  
The Impact ◽  
Endpoint Approach

Sediment pollution is a major issue in coastal areas, potentially endangering human health and the marine environments. We investigated the short-term sublethal effects of sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on the sea urchin Paracentrotus lividus for two months. Spiking occurred at concentrations below threshold limit values permitted by the law (TLVPAHs = 900 µg/L, TLVPCBs = 8 µg/L, Legislative Italian Decree 173/2016). A multi-endpoint approach was adopted, considering both adults (mortality, bioaccumulation and gonadal index) and embryos (embryotoxicity, genotoxicity and de novo transcriptome assembly). The slight concentrations of PAHs and PCBs added to the mesocosms were observed to readily compartmentalize in adults, resulting below the detection limits just one week after their addition. Reconstructed sediment and seawater, as negative controls, did not affect sea urchins. PAH- and PCB-spiked mesocosms were observed to impair P. lividus at various endpoints, including bioaccumulation and embryo development (mainly PAHs) and genotoxicity (PAHs and PCBs). In particular, genotoxicity tests revealed that PAHs and PCBs affected the development of P. lividus embryos deriving from exposed adults. Negative effects were also detected by generating a de novo transcriptome assembly and its annotation, as well as by real-time qPCR performed to identify genes differentially expressed in adults exposed to the two contaminants. The effects on sea urchins (both adults and embryos) at background concentrations of PAHs and PCBs below TLV suggest a need for further investigations on the impact of slight concentrations of such contaminants on marine biota.

scholarly journals De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e96855 ◽  
Author(s):  
Samuel E. Fox ◽  
Matthew Geniza ◽  
Mamatha Hanumappa ◽  
Sushma Naithani ◽  
Chris Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Triticum Monococcum ◽  
Diploid Wheat ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome
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