Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research

Xu, Jiajia; Li, Yuanyuan; Ma, Xiuling; Ding, Jianfeng; Wang, Kai; Wang, Sisi; Tian, Ye; Zhang, Hui; Zhu, Xin‐Guang

doi:10.1007/s11103-013-0025-4

Cited by 53 publications

(37 citation statements)

References 50 publications

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“…The copy numbers of the characteristic C4 enzyme genes in E. vivipara, Z. mays and S. bicolor were similar to those in rice (Table 4), which is consistent with the previous observation (Xu et al, 2013), suggesting that increase of the copy number of the C4 related enzyme genes may not be a prerequisite for C4 development.…”

Section: Identification Of Unigenes Coding For C4 Enzymessupporting

confidence: 90%

De novo Short Read Assembly and Functional Annotation of Eleocharis vivipara, a C3/C4 Interconvertible Sedge Plant

Harada

Yamato

Izui

et al. 2018

ecb

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Eleocharis vivipara is an amphibious sedge that displays C4 traits under terrestrial environments and C3 traits in submerged environments. This plant is thus potentially advantageous for screening genes indispensable to the development of C4 photosynthesis. In this study, we performed de novo transcriptome analysis of E. vivipara using its terrestrial-and submerged-type plants. By next-generation sequencing (NGS), approximately 90 and 89 million reads were yielded for the terrestrial and submerged types, respectively, and were assembled into 27,249 unigenes. Of these de novo consensus sequences, 94.5% showed similarities to database-registered sequences, and 69.4% were assigned with Gene Ontology terms. Our de novo assembled sequence data should provide a foundation for genetic analysis of the C4 photosynthetic system.

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Section: Identification Of Unigenes Coding For C4 Enzymessupporting

confidence: 90%

De novo Short Read Assembly and Functional Annotation of Eleocharis vivipara, a C3/C4 Interconvertible Sedge Plant

Harada

Yamato

Izui

et al. 2018

ecb

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“…), which belongs to family Poaceae, has gained the attention of plant scientists due mainly to its inherent C4 traits. Brutnell et al, (2010) proposed to make this weed a model species for C4 photosynthesis research [1], and there is a progressive support and acceptance to the proposal [2,3]. About 125 species are identified under genus Setaria [4], and S. viridis is considered the ancestral stock of this genus.…”

Section: Introductionmentioning

confidence: 99%

Study of Flowering Pattern in Setaria viridis, a Proposed Model Species for C4 Photosynthesis Research

et al. 2013

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Green foxtail millet (Setaria viridis) has NADP-ME type of C4 photosynthesis. Because of its short life cycle, small genome size of ∼515 Mb, small plant stature, high number of seed set, simple growth requirements, and wide adaptability, this diploid (2 = 18) weed is proposed to be a model species for the study of C4 photosynthesis. It is also a representative of bioenergy grasses and a model for genetic study of invasive weeds. Despite having all traits of a model species, it is difficult to cross-pollinate because its flowering behavior is not well studied. We used time lapse digital recording to study the flowering time and pattern along a single panicle. We found that flowering in Setaria was triggered by the darkness of the night and when the temperature was lower than 35 ∘ C. The anthesis of all the spikelets in a panicle took up-to three nights flowering from 9:30 pm to 10:00 am in the morning. Each spikelet has three phases of anthesis during which pollination occurs. A spikelet remains open for less than three hours. The pollination time for each spikelet is less than 60 minutes. Information from this study will facilitate the geneticists and plant breeders to plan for efficient crossing of Setaria.

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“…Raw reads were filtered and examined using the following steps: 1) trimming down the first 10 bases due to unstable performance in the sequence component using the FASTX-toolkit pipeline version 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/); 2) discarding low quality reads to ensure that more than 80% bases of each reserved read possessed an Illumina quality greater than 20 (q20 indicating 1% sequencing error rate); 3) examining the sequencing quality of the reads using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/) (Xu et al 2013).…”

Section: Illumina Sequencingmentioning

confidence: 99%

Increased expression of mitochondria-localized carbonic anhydrase activity resulted in an increased biomass accumulation in Arabidopsis thaliana

Jiang

Tholen

et al. 2014

J. Plant Biol.

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Carbonic anhydrase (CA; EC 4.2.1.1) catalyzes the interconversion of CO 2 and HCO 3 − and plays an important role in photosynthetic carbon assimilation. We report that the effect of manipulating AtβCA6 expression on the growth and biomass accumulation of Arabidopsis thaliana shows that AtβCA6 was expressed in mitochondria. Overexpression of AtβCA6 increased the fresh weight, dry weight and rosette leaf area and it was also linked to a slight decrease in the rate of respiration. By contrast, when the respiration rate in the AtβCA6 knock-out mutant SALK_065611 increased, the fresh weight, dry weight and rosette leaf area decreased. The expression level of AtβCA6 mainly affected the expression of the genes that were related to metabolism, photosynthesis and respiration. We discuss these data with respect to a potential role of AtβCA6 in refixation of CO 2 released from respiration and its potential as an option to increase biomass production.

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Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research

Cited by 53 publications

References 50 publications

<i>De novo</i> Short Read Assembly and Functional Annotation of <i>Eleocharis vivipara</i>, a C<sub>3</sub>/C<sub>4</sub> Interconvertible Sedge Plant

<i>De novo</i> Short Read Assembly and Functional Annotation of <i>Eleocharis vivipara</i>, a C<sub>3</sub>/C<sub>4</sub> Interconvertible Sedge Plant

Study of Flowering Pattern in Setaria viridis, a Proposed Model Species for C4 Photosynthesis Research

Increased expression of mitochondria-localized carbonic anhydrase activity resulted in an increased biomass accumulation in Arabidopsis thaliana

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