Laboratory of Plant Research, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin, 150040, China.
BMC Genomics. 2018 Jun 18;19(1):471. doi: 10.1186/s12864-018-4843-2.
Dryopteris fragrans (D. fragrans) is a potential medicinal fern distributed in volcanic magmatic rock areas under tough environmental condition. Sporangia are important organs for fern reproduction. This study was designed to characterize the transcriptome characteristics of the wild D. fragrans sporangia in three stages (stage A, B, and C) with the aim of uncovering its molecular mechanism of growth and development.
Using a HiSeq 4000, 79.81 Gb clean data (each sample is at least 7.95 GB) were obtained from nine samples, with three being supplied from each period, and assembled into 94,705 Unigenes, among which 44,006 Unigenes were annotated against public protein databases (NR, Swiss-Prot, KEGG, COG, KOG, GO, eggNOG and Pfam). Furthermore, we observed 7126 differentially expressed genes (DEG) (Fold Change > 4, FDR < 0.001), 349,885 SNP loci, and 10,584 SSRs. DEGs involved in DNA replication and homologous recombination were strongly expressed in stage A, and several DEGs involved in cutin, suberin and wax biosynthesis had undergone dramatic changes during development, which was consistent with morphological observations. DEGs responsible for secondary metabolism and plant hormone signal transduction changed clearly in the last two stages. DEGs homologous to those known genes associated with the development of reproductive organs of flowering plants have also been validated and discussed, such as AGL61, AGL62, ONAC010. In particular, a Unigene encoding TFL1, an important flower-development regulator in flowering plants, was identified and exhibited the highest expression level in stage B in D. fragrans sporangia.
This study is the first report on global transcriptome analysis in the development of sporangia of wild D. fragrans. DEGs related to development and homologous to flower-seed development in flowering plants were discussed. All DEGs involved in DNA replication and homologous recombination were consistent with morphological observations of paraffin slices. The results of this study provide rare resources for further investigation of the D. fragrans sporangium development, stress resistance and secondary metabolism.
凤尾蕨（D. fragrans）是一种分布在火山岩浆岩地区的潜在药用蕨类植物，生长环境条件十分苛刻。孢子囊是蕨类植物繁殖的重要器官。本研究旨在对野生凤尾蕨三个发育阶段（A、B 和 C 期）的孢子囊进行转录组特征分析，以揭示其生长发育的分子机制。
使用 HiSeq 4000，从 9 个样本中获得了 79.81 Gb 的清洁数据（每个样本至少 7.95GB），每个样本来自三个时期，共组装成 94705 个 Unigenes，其中 44006 个 Unigenes被注释到公共蛋白数据库（NR、Swiss-Prot、KEGG、COG、KOG、GO、eggNOG 和 Pfam）。此外，我们观察到 7126 个差异表达基因（DEG）（Fold Change > 4，FDR < 0.001），349885 个 SNP 位点和 10584 个 SSRs。在 A 期，与 DNA 复制和同源重组相关的 DEG 强烈表达，在发育过程中，一些参与角质、栓质和蜡生物合成的 DEG 发生了剧烈变化，这与形态学观察结果一致。在最后两个阶段，参与次生代谢和植物激素信号转导的 DEG 发生了明显变化。与开花植物生殖器官发育相关的已知基因同源的 DEG 也得到了验证和讨论，如 AGL61、AGL62、ONAC010。特别是，我们鉴定了一个编码 TFL1 的 Unigene，TFL1 是开花植物中重要的花发育调控因子，在凤尾蕨孢子囊中 B 期表达水平最高。
本研究首次对野生凤尾蕨孢子囊发育的全转录组进行了分析。讨论了与发育相关的 DEG 及其与开花植物花-种发育的同源性。所有与 DNA 复制和同源重组相关的 DEG 都与石蜡切片的形态学观察结果一致。本研究结果为进一步研究凤尾蕨孢子囊发育、抗逆性和次生代谢提供了难得的资源。
