Abstract
BackgroundDryopteris 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.ResultsUsing 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.ConclusionsThis 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.
Highlights
Dryopteris fragrans (D. fragrans) is a potential medicinal fern distributed in volcanic magmatic rock areas under tough environmental condition
A total of 52,995 Unigenes were expressed in three periods, and the numbers of genes expressed in stage A, B and C were 4988, 3366 and 14,516, respectively
10,584 Simple Sequence Repeats (SSRs) markers and 349,885 Single Nucleotide Polymorphisms (SNPs) were obtained through data analysis
Summary
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. A number of investigations of the morphological development, evolution and functions of the sporangium have been reported [1,2,3,4], but little is known regarding the transcriptome of fern sporangium. D. fragrans (L.) Schott, known as lava grass in China, is a perennial fern in the Dryopteris genus of the Dryopteris family. This species belongs to the single Fragrantes clade of a sister to the rest of Dryopteris in a molecular circumscription study [5]. The plants have a slight fragrance and are called D. fragrans
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