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

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.

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

Plant Genetic Resources ◽

10.1017/s1479262114000410 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S130-S133 ◽

Cited By ~ 7

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.

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De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.625520 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tao Liu ◽

Xiaoting Liu ◽

Rangrang Zhou ◽

Hong Chen ◽

Huaigang Zhang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Regulatory Mechanism ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Processing Technique ◽

Sodium Selenate ◽

Control Group ◽

Primary Mechanism ◽

High Selenium

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.

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De novo transcriptome assembly and analysis of the codon usage bias of the MADS-box gene family in Cymbidium kanran

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79.2.13 ◽

2019 ◽

Vol 79 (02) ◽

Author(s):

Boyun Yang ◽

Huolin Luo ◽

Yuan Tao ◽

Wenjing Yu ◽

Liping Luo

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Mads Box ◽

Illumina Hiseq ◽

Optimal Codons ◽

Mads Box Gene ◽

New Varieties

Cymbidium kanran is an important commercially grown member of the Chinese orchid family. However, little information regarding the molecular biology of this species is available. In this study, the C. kanran root, shoot, stem, leaf, and flower transcriptomes were sequenced with the Illumina HiSeq 4000 system, which resulted in 8.9 Gb of clean reads that were assembled into 74,620 unigenes, with an average length and N50 of 983 bp and 1,640 bp, respectively. The screening of seven databases (NR, NT, GO, KOG, KEGG, Swiss-Prot, and InterPro) for similar sequences resulted in the functional annotation of 49,813 unigenes. Additionally, 173 MADS-box genes, which help to control major aspects of plant development, were identified and their codon usage bias was analyzed. Only 26 genes had a low ENC (less than or equal to 35), suggesting the codon usage bias was weak. Base mutations were the major determinants of codon usage, although natural selection pressure also influenced codon usage bias. Moreover, 22 optimal codons were identified based on ΔRSCU, and 20 codons ended with A/U. The results of this study provide the foundation for the molecular breeding of new varieties

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

Forests ◽

10.3390/f10050393 ◽

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.

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Deciphering Novel Antimicrobial Peptides from the Transcriptome of Papilio xuthus

Insects ◽

10.3390/insects11110776 ◽

2020 ◽

Vol 11 (11) ◽

pp. 776

Author(s):

Joon Ha Lee ◽

Hoyong Chung ◽

Yong Pyo Shin ◽

Mi-Ae Kim ◽

Sathishkumar Natarajan ◽

...

Keyword(s):

Antimicrobial Peptides ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Swallowtail Butterfly ◽

Papilio Xuthus ◽

Antimicrobial Studies

An insect’s innate immune system is the front line of defense against many invading microorganisms. One of the important components of this defense system is antimicrobial peptides (AMPs). Papiliocin is a well-studied antimicrobial peptide (AMP) isolated from the swallowtail butterfly, Papilio xuthus, and it was previously reported to be effective against Gram-positive bacteria, Gram-negative bacteria, and fungi, particularly in drug resistant Gram-negative bacteria. Hence, we aimed to identify novel AMPs from Papilio xuthus using its transcriptome. We immunized the swallowtail butterfly with Escherichia coli, Staphylococcus aureus, Candida albicans, and the total RNA was isolated. De novo transcriptome assembly and functional annotations were conducted, and AMPs were predicted using an in-silico pipeline. The obtained 344,804,442 raw reads were then pre-processed to retrieve 312,509,806 (90.6%) total clean reads. A total of 38,272 unigenes were assembled with the average length of 1010 bp. Differential gene expression analysis identified 584 and 1409 upregulated and downregulated genes, respectively. The physicochemical, aggregation, and allergen propensity were used as filtration criteria. A total of 248 peptides were predicted using our in-house pipeline and the known AMPs were removed, resulting in 193 novel peptides. Finally, seven peptides were tested in vitro and three peptides (Px 5, 6, and 7) showed stronger antimicrobial activity against Gram-negative bacteria and yeast. All the tested peptides were non-allergens. The identified novel AMPs may serve as potential candidates for future antimicrobial studies.

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

10.21203/rs.2.9879/v1 ◽

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.

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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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De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

PLoS ONE ◽

10.1371/journal.pone.0120615 ◽

2015 ◽

Vol 10 (3) ◽

pp. e0120615 ◽

Cited By ~ 20

Author(s):

Mei Liang ◽

Xiaoming Yang ◽

Hang Li ◽

Shiying Su ◽

Hualin Yi ◽

...

Keyword(s):

Molecular Marker ◽

De Novo ◽

Transcriptome Assembly ◽

Marker Development ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Molecular Marker Development

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The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae)

International Journal of Molecular Sciences ◽

10.3390/ijms222111964 ◽

2021 ◽

Vol 22 (21) ◽

pp. 11964

Author(s):

Matin Miryeganeh ◽

Hidetoshi Saze

Keyword(s):

Salt Stress ◽

De Novo ◽

Saline Water ◽

Average Length ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Natural Populations ◽

Rhizophora Stylosa ◽

Salt Stress Response ◽

Mangrove Tree

Mangroves are salt-tolerant plant species that grow in coastal saline water and are adapted to harsh environmental conditions. In this study, we de novo assembled and functionally annotated the transcriptome of Rhizophora stylosa, the widely distributed mangrove from the largest mangrove family (Rhizophoraceae). The final transcriptome consists of 200,491 unigenes with an average length, and N50 of 912.7 and 1334 base pair, respectively. We then compared the genome-wide expression profiles between the two morphologically distinct natural populations of this species growing under different levels of salinity depending on their distance from the ocean. Among the 200,491 unigenes, 40,253 were identified as differentially expressed between the two populations, while 15,741 and 24,512 were up- and down-regulated, respectively. Functional annotation assigned thousands of upregulated genes in saline environment to the categories related to abiotic stresses such as response to salt-, osmotic-, and oxidative-stress. Validation of those genes may contribute to a better understanding of adaptation in mangroves species. This study reported, for the first time, the transcriptome of R. stylosa, and the dynamic of it in response to salt stress and provided a valuable resource for elucidation of the molecular mechanism underlying the salt stress response in mangroves and other plants that live under stress.

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De novo Transcriptome Assembly of Myllocerinus aurolineatus Voss in Tea Plants

Frontiers in Sustainable Food Systems ◽

10.3389/fsufs.2021.631990 ◽

2021 ◽

Vol 5 ◽

Author(s):

Xin Xie ◽

Junmei Jiang ◽

Meiqing Chen ◽

Maoxi Huang ◽

Linhong Jin ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Nucleotide Polymorphisms ◽

Illumina Hiseq ◽

Single Nucleotide ◽

Functional Studies ◽

Myllocerinus Aurolineatus ◽

Tea Plants ◽

The Trinity ◽

Simple Sequence

Myllocerinus aurolineatus Voss is a species of the insecta class in the arthropod. In this study, we first observed and identified M. aurolineatus Voss in tea plants in Guizhou, China, where it caused severe quantity and quality losses in tea plants. Knowledge on M. aurolineatus Voss genome is inadequate, especially for biological or functional research. We performed the first transcriptome sequencing by using the Illumina Hiseq™ technique on M. aurolineatus Voss. Over 55.9 million high-quality paired-end reads were generated and assembled into 69,439 unigenes using the Trinity short read software, resulting in a cluster of 1,207 bp of the N50 length. A total of 69,439 genes were predicted by BLAST to known proteins in the NCBI database and were distributed into Gene Ontology (20,190), eukaryotic complete genomes (12,488), and the Kyoto Encyclopedia of Genes and Genomes (3,170). We also identified 96,790 single-nucleotide polymorphisms and 13,121 simple sequence repeats in these unigenes. Our transcriptome data provide a useful resource for future functional studies of M. aurolineatus Voss for dispersal control in tea plants.

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