De Novo assembly , function annotation and comparative transcriptome analysis for Isoetes sinensis in terrestrial and submerged environments
Background: Isoetes L. is an ancient genus of heterosporous lycopsids with a unique phylogenetic evolution position. Repeating adaptation to terrestrial and aquatic environments over time has led Isoetes to grow in various habitats，such as oligotrophic lakes, seasonal pools，and terrestrial areas. However, we know little about the adaptation mechanism of Isoetes in the various environments. Moreover, the transcriptional and genomic resources of Isoetes are limited in the public database. Isoetes sinensis is a kind of amphibious species growing in various environments, including terrestrial environment (TE) and submerged environment (SE). I. sinensis is an ideal model for Isoetes to research the adaptation mechanism in the various environments. In this study, I. sinensis was performed to demonstrate different regulatory mechanism in TE and SE using Illumina RNA-sequencing technology.  Results: We generated 89 million high-quality reads. The reads assembled de novo into 13,619 unigenes with the average length of 1,618 bp and N50 length of 2,350 bp. 1,740 differentially expressed genes were identified with 1,146 up-regulated and 594 down-regulated in TE. A high correlation was validated between the results of the transcriptome and quantitative real-time PCR. Gene ontology annotation revealed that stress-relevant categories were remarkably enriched, including response to abiotic or biotic stress, endogenous and external stimuli. The KEGG enrichment analysis showed that the plant hormone signaling pathways were influenced in the various environments, including ABA, ethylene, jasmonic acid, salicylic acid, cytokinin, auxin, and gibberellin. Analyses of transcription factors and carbohydrate metabolism revealed their potential function in I. sinensis for adapting to the various environments. In addition, repetitive sequences were detected，including 619 retroelements, 50 DNA transposons, and 1,092 simple sequence repeats.  Conclusions: This is the first report for Isoetes to generate substantial sequence resources by high-throughput sequencing approach. The potential adaptation mechanism for I. sinensis was elucidated in TE and SE, related to plant hormone signaling pathway, transcription factors, and carbohydrate metabolism. We have provided repetitive sequences that will be exploited for rapid genetic studies. The transcriptomic resources of I. sinensis are a foundation for in-depth investigation in the future.  Keywords: Isoetes L., Isoetes sinensis, transcriptome, submerged, terrestrial, stress, adaptation, various environments.