Transcriptome-Wide Identification and Prediction of miRNAs and Their Targets in Paris polyphylla var. yunnanensis by High-Throughput Sequencing Analysis

Abstract

Long dormancy period of seeds limits the large-scale artificial cultivation of the scarce Paris polyphylla var. yunnanensis, an important traditional Chinese medicine. Characterizing miRNAs and their targets is crucial to understanding the role of miRNAs during seed dormancy in this species. Considering the limited genome information of this species, we first sequenced and assembled the transcriptome data of dormant seeds and their seed coats as the reference genome. A total of 146,671 unigenes with an average length of 923 bp were identified and showed functional diversity based on different annotation methods. Two small RNA libraries from respective seeds and seed coats were sequenced and the combining data indicates that 263 conserved miRNAs belonging to at least 83 families and 768 novel miRNAs in 1174 transcripts were found. The annotations of the predicted putative targets of miRNAs suggest that these miRNAs were mainly involved in the cell, metabolism and genetic information processing by direct and indirect regulation patterns in dormant seeds of P. polyphylla var. yunnanensis. Therefore, we provide the first known miRNA profiles and their targets, which will assist with further study of the molecular mechanism of seed dormancy in P. polyphylla var. yunnanensis.

Comparative transcriptomic analysis reveals genes regulating the germination of morphophysiologically dormant Paris polyphylla seeds during a warm stratification

“…dactylifera and M . acuminata , the top matched species in Ling’s transcriptome data [17] differed from those of our current study. Additionally, our transcriptome include only two homologous unigenes from Nelumbo nucifera , which is the third most common species in a previous study [17].…”

“…acuminata , the top matched species in Ling’s transcriptome data [17] differed from those of our current study. Additionally, our transcriptome include only two homologous unigenes from Nelumbo nucifera , which is the third most common species in a previous study [17]. We suspect that these differences in species distributions between two transcriptome annotations of the same plant species may have been due to differences in sequencing depth, assembled unigenes lengths, and especially the studied tissues because different sets of genes are expressed in diverse tissues.…”

“…The top four matched species were Phoenix dactylifera (22.8%), Musa acuminata (7.9%), Vitis vinifera (4.8%) and Hordeum vulgare (3.4%) (S3C Fig), which contrasted with the previous annotations of P . polyphylla transcriptomes for mature dormant seeds and seed coats [17]. For example, except for P .…”

Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis

“…The raw mass data were used to search against the ‘non-redundant protein sequences (nr)’ database by the blast program. Protein identification was performed using the Mascot sever (Version 2.3.02) against the transcriptome data published in our previous study ( Ling et al, 2017 ; Zhang & Ling, 2019 ). The confident protein identification involved at least one matched unique peptide with a confidence interval ≥95% according to the mascot probability scores.…”

Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus

“…Gene expression profiles during secondary metabolism are complex. RNA-Seq has been applied to investigate active ingredient accumulation of several traditional Chinese medicine, such as Ganoderma lucidum [16], Paris polyphylla [17], and Panax japonicas [18]. e use of the RNA-Seq technique identified many DEGs that were associated with secondary metabolism.…”