Gene prediction for N. salina CCMP1776 (version 2)

Overview
Analysis NameGene prediction for N. salina CCMP1776 (version 2)
Methodaugustus (augustus)
Sourceaugustus
Date performed2019-10-08

 

Gene model prediction for N. salina CCMP1776.

Transcriptomic data for N. salina CCMP 1776 that had not been previously published, were based on three independent repeats of RNA-seq for normal and nitrogen (N) limitation.

N. salina WT was cultivated under normal and N limitation condition to isolate RNA as described in [1, 2]. F2N medium was used for normal condition. F2N media with 75 mg/L NaNO3 50 g/L sea salt were used for N limitation and osmotic stress condition, respectively. The culture conditions were followings: 25°C, 120 rpm, under 120 µmol photons/m2/s of fluorescent light, and 0.5 vvm air containing 2% CO2. The samples were obtained at 4, 8, and 12 day to extract RNA. After cell harvest at the mid-exponential phase, 200 mg of wet biomass was used to obtain total RNA.

Reference

1.        Kang, N.K., et al., Effects of overexpression of a bHLH transcription factor on biomass and lipid production in Nannochloropsis salina. Biotechnol Biofuels, 2015. 8: p. 200.

2.        Kwon, S., et al., Enhancement of biomass and lipid productivity by overexpression of a bZIP transcription factor in Nannochloropsis salina. Biotechnol Bioeng, 2018. 115(2): p. 331-340.

The statistics of RNA-seq data used to assist gene model prediction are listed below:

Sample

Num. of
reads

Num. of
trimmed reads

Trimmed/
Raw(%)

reads mapping

Aligned
Pairs

Concordant
Pairs %

Mapped

rate

Normal_1

20,819,883

19,059,377

91.54

15,533,392

81.5

15,208,254

79.2

20,819,883

19,059,377

91.54

15,528,500

81.5

Normal_2

26,750,246

24,230,068

90.58

20,613,690

85.1

20,118,539

81.8

26,750,246

24,230,068

90.58

20,590,659

85.0

Normal_3

24,827,039

20,423,256

82.26

16,950,114

83.0

16,682,994

80.9

24,827,039

20,423,256

82.26

16,930,992

82.9

N-starvation_1

31,877,112

25,928,944

81.34

23,570,026

90.9

19,052,652

88.7

31,877,112

25,928,944

81.34

23,506,630

90.7

N-starvation_2

16,747,673

13,826,287

82.56

11,237,247

81.3

11,046,741

78.8

16,747,673

13,826,287

82.56

11,214,387

81.1

N-starvation_3

19,993,690

16,543,029

82.74

14,178,939

85.7

10,634,729

83.1

19,993,690

16,543,029

82.74

14,150,106

85.5

 

More details, please contact Prof. Byeong-ryool Jeong (bjeong@unist.ac.kr).

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