Illumina Sequencing of Common (Short) Ragweed (Ambrosia artemisiifolia L.) Reproductive Organs and Leaves

Virág, Eszter; Hegedűs, Géza; Barta, Endre; Nagy, Erzsébet; Mátyás, Kinga; Kolics, Balázs; Taller, János

doi:10.3389/fpls.2016.01506

Cited by 11 publications

(24 citation statements)

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“…In the present work we report Illumina RNA-sequencing of two developmental stages of female flowers compared with male and leaf transcriptomic data. Diversity of differentially expressed transcripts between female and male inflorescence as well as leaves were analyzed comparing with previously reported transcript datasets (Virág E et al 2016). Differences between expression levels of the above described flowering pathways and two gene categories such as MIGs and…”

Section: )mentioning

confidence: 99%

“…Node segments (1.5 -2 cm long) were excised from 21-day-old plants and transferred to above described MS medium. transcriptoms (Virág E. et al 2016). For gene expression comparision we used 1M and 2M libraries as indicated in the Figure 1 (J-L, 1M; P-Q, 2M).…”

Section: Plant Materials and Cultivation Conditionsmentioning

confidence: 99%

“…2.0 μg of total RNA from 1F, 1M and 2F, 2M samples were used as starting material for cDNA synthesis and library construction. Enrichment of mRNA, cDNA synthesis and library preparation for Illumina NextSeq paired-end sequencing were carried out using TruSeq™ RNA sample preparation kit (Low-Throughput protocol) using an oligo(dT) 18 as described by Virág E et al 2016. The RNA-Seq was performed using Illumina NextSeq5000 system.…”

Section: Rna-seq Library Construction and Sequencingmentioning

confidence: 99%

“…Sequence reads of male inflorescence (M), leaves (L) and female (F) inflorescence containing all nine developmental stages were used from earlier reported and deposited data in National Centre for Biotechnology Information's (NCBI) Sequence Read Archive (SRA) under the accession SRP08007 (Virág E et al 2016).…”

Section: Rna-seq Library Construction and Sequencingmentioning

confidence: 99%

“…In detaile. First, a combined read set was assembled from the three sample libraries (M, F and L) to generate a 'reference' de novo transcriptome assembly that was deposited in the NCBI TSA database under the accession GEZL00000000 and reported in our prior study (Virág et al 2016). During this processes, reads with certain length of overlap were combined to form contigs (kmer size, K, = 25).…”

Section: Construction Of a Artemisiifolia Transcript Datasets Identmentioning

confidence: 99%

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Peer Review #1 of "Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weed Ambrosia artemisiifolia L. (Asteraceae) (v0.2)"

Rocheta¹

2019

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The highly allergenic and invasive weed Ambrosia artemisiifolia L. (A. artemisiifolia) is a monoecius plant with separated male and female flowers. The genetic regulation of floral morphogenesis is a less understood field in the reproduction biology of this species. Therefore the objective of this work was to investigate the genetic control of sex determination during floral organogenesis. To this end we performed a genome-wide transcriptional profiling of vegetative and generative tissues during the plant development comparing wild-growing and in vitro cultivated plants. RNA-seq on Illumina NextSeq 500 platform with an integrative bioinformatics analysis indicated differences in 80 floral gene expressions depending on photoperiodic and endogenous initial signals. Sex specificity of genes was validated based on RT-qPCR experiments. We found 11 and 16 uniquely expressed genes in female and male transcriptomes that were responsible particularly to maintain fertility and against abiotic stress. High gene expression of homologous such as FD, FT, TFL1 and CAL, SOC1, AP1 were characteristic to male and female floral meristems during organogenesis. Homologues transcripts of LFY and FLC were not found in the investigated generative and vegetative tissues. The repression of AP1 by TFL1 homolog was demonstrated in male flowers resulting exclusive expression of AP2 and PI that controlled stamen and carpel formation in the generative phase. Alterations of male and female floral meristem differentiation were demonstrated under photoperiodic and hormonal condition changes by applying in vitro treatments.

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Section: )mentioning

confidence: 99%

Section: Plant Materials and Cultivation Conditionsmentioning

confidence: 99%

Section: Rna-seq Library Construction and Sequencingmentioning

confidence: 99%

Section: Rna-seq Library Construction and Sequencingmentioning

confidence: 99%

Section: Construction Of a Artemisiifolia Transcript Datasets Identmentioning

confidence: 99%

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Peer Review #1 of "Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weed Ambrosia artemisiifolia L. (Asteraceae) (v0.2)"

Rocheta¹

2019

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Illumina sequencing of the chloroplast genome of common ragweed ( Ambrosia artemisiifolia L.)

et al. 2017

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Common ragweed (Ambrosia artemisiifolia L.) is the most widespread weed and the most dangerous pollen allergenic plant in large areas of the temperate zone. Since herbicides like PSI and PSII inhibitors have their target genes in the chloroplast genome, understanding the chloroplast genome may indirectly support the exploration of herbicide resistance and development of novel control methods. The aim of the present study was to sequence and reconstruct for the chloroplast genome of A. artemisiifolia and establish a molecular dataset. We used an Illumina MiSeq protocol to sequence the chloroplast genome of isolated intact organelles of ragweed plants grown in our experimental garden. The assembled chloroplast genome was found to be 152,215 bp (GC: 37.6%) in a quadripartite structure, where 80 protein coding genes, 30 tRNA and 4 rRNA genes were annotated in total. We also report the complete sequence of 114 genes encoded in A. artemisiifolia chloroplast genome supported by both MIRA and Velvet de novo assemblers and ordered to Helianthus annuus L. using the Geneious software.

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Evidence for contemporary plant mitoviruses

et al. 2018

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Mitoviruses have small RNA(+) genomes, replicate in mitochondria, and have been shown to infect only fungi to date. For this report, sequences that appear to represent nearly complete plant mitovirus genomes were recovered from publicly available transcriptome data. Twenty of the refined sequences, 2684-2898 nt long and derived from 10 different species of land plants, appear to encompass the complete coding regions of contemporary plant mitoviruses, which furthermore constitute a monophyletic cluster within genus Mitovirus. Complete coding sequences of several of these viruses were recovered from multiple transcriptome (but not genome) studies of the same plant species and also from multiple plant tissues. Crop plants among implicated hosts include beet and hemp. Other new results suggest that such genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes. Whether these mitoviruses are wholly cryptic with regard to plant health remains to be investigated.

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Illumina Sequencing of Common (Short) Ragweed (Ambrosia artemisiifolia L.) Reproductive Organs and Leaves

Cited by 11 publications

References 5 publications

Peer Review #1 of "Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weed Ambrosia artemisiifolia L. (Asteraceae) (v0.2)"

Peer Review #1 of "Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weed Ambrosia artemisiifolia L. (Asteraceae) (v0.2)"

Illumina sequencing of the chloroplast genome of common ragweed ( Ambrosia artemisiifolia L.)

Evidence for contemporary plant mitoviruses

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