De novo transcriptome analysis of an Arctic microalga, Chlamydomonas sp.

Kim, Sanghee; Kim, Min Jung; Jung, Min Gui; Lee, Soo-Yong; Baek, Ye-Seul; Kang, Sung‐Ho; Choi, Han-Gu

doi:10.1007/s13258-013-0085-5

Cited by 15 publications

(5 citation statements)

References 37 publications

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“…These unigenes had a mean length of 580 bp (Table 1). Our data indicated that the C. nasus unigenes were roughly shorter than the average lengths of unigenes that were previously reported in other species such as Eriocheir sinensis (382 bp) (He et al, 2012), Acropora millepora (440 bp) (Meyer et al, 2009), Pinus contorta (500 bp) (Parchman et al, 2010), Chlamydomonas spp (665 bp) (Kim et al, 2013), and Camellia sinensis (733 bp) (Wu et al, 2013). These results provide sequence information for future gene cloning and transgenic engineering stud ies.…”

Section: Illumina Sequencing and Assembly Of The Transcriptomesupporting

confidence: 46%

Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing

Fang¹,

Zhou²,

Duan³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. RNA-Seq technology has been widely applied to transcriptomics, genomics, molecular marker development, and functional gene studies. In the genome, microsatellites are simple sequence repeats (SSR) with a high degree of polymorphism that are used as DNA markers in many molecular genetic studies. Using traditional methods such as magnetic bead enrichment, only a few microsatellite markers have been isolated. Coilia nasus is an anadromous, small-to-moderately sized fish species that is famous as an important fishery resource. Here, we have identified a large number of microsatellites from the fish brains by using Illumina sequencing. About 20 million Illumina reads were assembled into 148,845 unigenes. A total of 13,038 SSR motifs were identified via analysis of 3,958,293,117 (3.96 Gb) nucleotides to produce a comprehensive transcript dataset for the C. nasus brain, including mono-, di-, tri-, tetra-, and penta-repeat motifs. The most abundant type of repeat motif was di-nucleotide (42.97%), followed by mono-nucleotide (38.86%), tri-nucleotide (16.21%), tetra-nucleotide (1.83%), and penta-nucleotide (0.05%) repeat units, which is similar to the results obtained in studies in other species. These data provide a base of sequence informa tion to improve molecular-assisted markers to study C. nasus genetic diversity.

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Section: Illumina Sequencing and Assembly Of The Transcriptomesupporting

confidence: 46%

Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing

Fang¹,

Zhou²,

Duan³

et al. 2015

Genet. Mol. Res.

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“…Membrane remodelling is one of the most wide-spread adaptations observed in cold growing organisms and upregulation of related enzymes has been seen in numerous psychrophiles (Gao et al, 2006;Bergholz et al, 2009;Kim et al, 2013;Mykytczuk et al, 2013). Modifications to fatty acid and membrane biosynthesis allow organisms to overcome decreased membrane fluidity at lower temperatures.…”

Section: Fatty Acid and Lipid Synthesis And Modificationsmentioning

confidence: 99%

Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis

Raymond-Bouchard

Chourey

Altshuler

et al. 2017

Environmental Microbiology

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The eurypsychrophilic bacterium Planococcus halocryophilus is capable of growth down to -15°C, making it ideal for studying adaptations to subzero growth. To increase our understanding of the mechanisms and pathways important for subzero growth, we performed proteomics on P. halocryophilus grown at 23°C, 23°C with 12% w/v NaCl and -10°C with 12% w/v NaCl. Many proteins with increased abundances at -10°C versus 23°C also increased at 23C-salt versus 23°C, indicating a closely tied relationship between salt and cold stress adaptation. Processes which displayed the largest changes in protein abundance were peptidoglycan and fatty acid (FA) synthesis, translation processes, methylglyoxal metabolism, DNA repair and recombination, and protein and nucleotide turnover. We identified intriguing targets for further research at -10°C, including PlsX and KASII (FA metabolism), DD-transpeptidase and MurB (peptidoglycan synthesis), glyoxalase family proteins (reactive electrophile response) and ribosome modifying enzymes (translation turnover). PemK/MazF may have a crucial role in translational reprogramming under cold conditions. At -10°C P. halocryophilus induces stress responses, uses resources efficiently, and carefully controls its growth and metabolism to maximize subzero survival. The present study identifies several mechanisms involved in subzero growth and enhances our understanding of cold adaptation.

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“…The transcriptome analysis has been conducted on a cold Arctic strain of Chlamydomonas sp. [ 11 ], showing the responsible genes for cold tolerance, photosynthesis activity and fatty acid (FA) biosynthesis, and also identifying the putative homologs of antifreeze protein in microalgae. Similarly, the lipid metabolism on Nannochloropsis sp .…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by Salicylic Acid (SA) and Jasmonic Acid (JA)

Gao

et al. 2015

PLoS ONE

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Haematococcus pluvialis is an astaxanthin-rich microalga that can increase its astaxanthin production by salicylic acid (SA) or jasmonic acid (JA) induction. The genetic transcriptome details of astaxanthin biosynthesis were analyzed by exposing the algal cells to 25 mg/L of SA and JA for 1, 6 and 24 hours, plus to the control (no stress). Based on the RNA-seq analysis, 56,077 unigenes (51.7%) were identified with functions in response to the hormone stress. The top five identified subcategories were cell, cellular process, intracellular, catalytic activity and cytoplasm, which possessed 5600 (~9.99%), 5302 (~9.45%), 5242 (~9.35%), 4407 (~7.86%) and 4195 (~7.48%) unigenes, respectively. Furthermore, 59 unigenes were identified and assigned to 26 putative transcription factors (TFs), including 12 plant-specific TFs. They were likely associated with astaxanthin biosynthesis in Haematococcus upon SA and JA stress. In comparison, the up-regulation of differential expressed genes occurred much earlier, with higher transcript levels in the JA treatment (about 6 h later) than in the SA treatment (beyond 24 h). These results provide valuable information for directing metabolic engineering efforts to improve astaxanthin biosynthesis in H. pluvialis.

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De novo transcriptome analysis of an Arctic microalga, Chlamydomonas sp.

Cited by 15 publications

References 37 publications

Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing

Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing

Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis

Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by Salicylic Acid (SA) and Jasmonic Acid (JA)

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