Gene prediction for N. salina CCMP1776 (version 2) | NanDeSyn: Nannochloropsis Design & Synthesis Initiative

Overview


Analysis Name	Gene prediction for N. salina CCMP1776 (version 2)
Method	augustus (augustus)
Source	augustus
Date performed	2019-10-08

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 %
Sample	Num. of reads	Num. of trimmed reads	Trimmed/ Raw(%)	Mapped	rate	Aligned Pairs	Concordant Pairs %
Normal_1	20,819,883	19,059,377	91.54	15,533,392	81.5	15,208,254	79.2
Normal_1	20,819,883	19,059,377	91.54	15,528,500	81.5	15,208,254	79.2
Normal_2	26,750,246	24,230,068	90.58	20,613,690	85.1	20,118,539	81.8
Normal_2	26,750,246	24,230,068	90.58	20,590,659	85.0	20,118,539	81.8
Normal_3	24,827,039	20,423,256	82.26	16,950,114	83.0	16,682,994	80.9
Normal_3	24,827,039	20,423,256	82.26	16,930,992	82.9	16,682,994	80.9
N-starvation_1	31,877,112	25,928,944	81.34	23,570,026	90.9	19,052,652	88.7
N-starvation_1	31,877,112	25,928,944	81.34	23,506,630	90.7	19,052,652	88.7
N-starvation_2	16,747,673	13,826,287	82.56	11,237,247	81.3	11,046,741	78.8
N-starvation_2	16,747,673	13,826,287	82.56	11,214,387	81.1	11,046,741	78.8
N-starvation_3	19,993,690	16,543,029	82.74	14,178,939	85.7	10,634,729	83.1
N-starvation_3	19,993,690	16,543,029	82.74	14,150,106	85.5	10,634,729	83.1

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

Properties