Wang Wenlei, Li Huanqin, Lin Xiangzhi, Yang Shanjun, Wang Zhaokai, Fang Baishan
Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Fujian, 361005, China.
College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China.
Sci Rep. 2015 Dec 11;5:17099. doi: 10.1038/srep17099.
Tissue culture could solve the problems associated with Gracilaria cultivation, including the consistent supply of high-quality seed stock, strain improvement, and efficient mass culture of high-yielding commercial strains. However, STC lags behind that of higher plants because of the paucity of genomic information. Transcriptome analysis and the identification of potential unigenes involved in the formation and regeneration of callus or direct induction of ABs are essential. Herein, the CK, EWAB and NPA G. lichenoides transcriptomes were analyzed using the Illumina sequencing platform in first time. A total of 17,922,453,300 nucleotide clean bases were generated and assembled into 21,294 unigenes, providing a total gene space of 400,912,038 nucleotides with an average length of 1,883 and N 50 of 5,055 nucleotides and a G + C content of 52.02%. BLAST analysis resulted in the assignment of 13,724 (97.5%), 3,740 (26.6%), 9,934 (70.6%), 10,611 (75.4%), 9,490 (67.4%), and 7,773 (55.2%) unigenes were annotated to the NR, NT, Swiss-Prot, KEGG, COG, and GO databases, respectively, and the total of annotated unigenes was 14,070. A total of 17,099 transcripts were predicted to possess open reading frames, including 3,238 predicted and 13,861 blasted based on protein databases. In addition, 3,287 SSRs were detected in G.lichenoides, providing further support for genetic variation and marker-assisted selection in the future. Our results suggest that auxin polar transport, auxin signal transduction, crosstalk with other endogenous plant hormones and antioxidant systems, play important roles for ABs formation in G. lichenoides explants in vitro. The present findings will facilitate further studies on gene discovery and on the molecular mechanisms underlying the tissue culture of seaweed.
组织培养可以解决与江蓠属栽培相关的问题，包括持续供应高质量的种苗、菌株改良以及高产商业菌株的高效大规模培养。然而，由于基因组信息匮乏，江蓠属的体细胞胚胎发生技术落后于高等植物。转录组分析以及鉴定参与愈伤组织形成与再生或直接诱导体细胞胚的潜在单基因至关重要。在此，首次使用Illumina测序平台对嗜热栖热菌、嗜热栖热菌EWAB和嗜热栖热菌NPA的转录组进行了分析。共产生了17922453300个核苷酸的纯净碱基，并组装成21294个单基因，提供了400912038个核苷酸的总基因空间，平均长度为1883个核苷酸，N50为5055个核苷酸，G + C含量为52.02%。BLAST分析结果显示，分别有13724个（97.5%）、3740个（26.6%）、9934个（70.6%）、10611个（75.4%）、9490个（67.4%）和7773个（55.2%）单基因被注释到NR、NT、Swiss-Prot、KEGG、COG和GO数据库中，并得到注释的单基因总数为14070个。总共预测有17099个转录本具有开放阅读框，其中基于蛋白质数据库预测了3238个，比对到13861个。此外，在嗜热栖热菌中检测到3287个简单重复序列（SSR），为未来的遗传变异和标记辅助选择提供了进一步的支持。我们的研究结果表明，生长素极性运输、生长素信号转导、与其他植物内源激素的相互作用以及抗氧化系统，在嗜热栖热菌外植体体外体细胞胚形成中发挥重要作用。本研究结果将有助于进一步开展基因发现以及海藻组织培养潜在分子机制的研究。
