Response mechanism of growth and gypenosides content for Gynostemma longipes cultivated at two altitude habitats to fine root morphological characteristics

IntroductionFine roots are the critical functional organs of plants to absorb water and nutrients from the soil environment, while the relation between fine root morphological characteristics and yield & quality has received less attention for medicinal plants.MethodsTherefore, we investigated the relationship between fine root morphological characteristics and biomass & gypenosides content. We explored the primary environmental drivers of fine root indicators for Gynostemma longipes from three provenances cultivated at two altitude habitats.ResultsAt the end of the growing season, compared with the low-altitude habitat, the underground biomass of G. longipes in the high-altitude habitat increased significantly by 200%~290% for all three provenances. The response of gypenosides content to different altitude habitats varied with provenance and plant organs. The biomass of G. longipes strongly depended on the fine root characteristic indicators (P < 0.001), fine root length density, and fine root surface area. Our results also showed that the harvest yield of G. longipes could be effectively increased by promoting the growth of fine roots per unit leaf weight (P < 0.001, R2 = 0.63). Both fine root length density and fine root surface area had strong positive correlations with soil nutrient factors (R2 > 0.55) and a strong negative correlation with soil pH (R2 > 0.48). In a word, the growth of G. longipes is strongly controlled by the fine root morphological characteristics through the response of fine roots to soil nutrient factors and pH.DiscussionOur findings will help to deepen the understanding of the root ecophysiological basis driven by soil factors for the growth and secondary metabolites formation of G. longipes and other medicinal plants under changing habitat conditions. In future research, we should investigate how environmental factors drive plant morphological characteristics (e.g., fine roots) to affect the growth & quality of medicinal plants over a longer time scale

Comprehensive Analysis of Alternative Splicing in <i>Digitalis purpurea</i> by Strand-Specific RNA-Seq

<div><p><i>Digitalis purpurea</i> (<i>D. purpurea</i>) is one of the most important medicinal plants and is well known in the treatment of heart failure because of the cardiac glycosides that are its main active compounds. However, in the absence of strand specific sequencing information, the post-transcriptional mechanism of gene regulation in <i>D. purpurea</i> thus far remains unknown. In this study, a strand-specific RNA-Seq library was constructed and sequenced using Illumina HiSeq platforms to characterize the transcriptome of <i>D. purpurea</i> with a focus on alternative splicing (AS) events and the effect of AS on protein domains. <i>De novo</i> RNA-Seq assembly resulted in 48,475 genes. Based on the assembled transcripts, we reported a list of 3,265 AS genes, including 5,408 AS events in <i>D. purpurea</i>. Interestingly, both glycosyltransferases and monooxygenase, which were involved in the biosynthesis of cardiac glycosides, are regulated by AS. A total of 2,422 AS events occurred in coding regions, and 959 AS events were located in the regions of 882 unique protein domains, which could affect protein function. This <i>D. purpurea</i> transcriptome study substantially increased the expressed sequence resource and presented a better understanding of post-transcriptional regulation to further facilitate the medicinal applications of <i>D. purpurea</i> for human health.</p></div

The complete chloroplast genome of Epimedium elachyphyllum Stearn (Berberidaceae), an endangered species endemic to China

Epimedium elachyphyllum, which belongs to Berberidaceae, is only distributed in Guizhou province of China. In this study, the complete chloroplast (cp)genome of E. elachyphyllum was sequenced and assembled. The circular genome is 157,201 bp in length, which comprises of a large single-copy region (LSC, 88,519 bp), a small single-copy region (SSC, 17,042 bp), and a pair of inverted repeat regions (IRa and IRb, 25,820 bp). The genome of E. elachyphyllum contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 18 complete cp genome sequences indicated that E. elachyphyllum was closely related to E. dolichostemon

Most significant functional groups (p-value<0.05) of AS genes.

<p>The most significant functional groups (p-value<0.05) are presented graphically. The X-axis represents log10 of the enrichment P value. The Y-axis indicates the number of AS genes in log2 value. The size of each point is proportional to the percentage (AS genes associated with GO terms/All genes associated with GO terms).</p

Venn diagram showing annotated genes by SP, NR, NT, and KEGG.

<p>The number of genes annotated is listed in each diagram component.</p

Sequence length distribution of assembled transcripts.

<p>The X-axis indicates the length range of the transcript sequences. The Y-axis indicates the percentage of transcript sequences with a certain length.</p

AS validation of 14 selected genes by RT-PCR.

<p>The splicing patterns of selected AS genes were analyzed using RT-PCR to validate the RNA sequencing results. Electrophoretic analysis of amplified products from RT-PCR with 3% agarose gel. M, DL500 marker, and the size of specific bands are indicated. The numbers 1–14 represent the PCR products of contig name comp 65400_c0, comp 62996_c0, comp69107_c0, comp65089_c0, comp67573_c0, comp67051_c1, comp68099_c0, comp68043_c2, comp57809_c0, comp66555_c0, comp66894_c0, comp63097_c0, comp64465_c1, and comp5406_c0, respectively.</p

The complete chloroplast genome of Epimedium xichangense Y. J. Zhang (Berberidaceae)

Epimedium xichangense, a critically endangered herb with limited population, mainly distributes in Sichuan province, China. In our study, we obtained the complete chloroplast genome of E. xichangense with a length of 158,955 bp, including a large single copy region of 86,478 bp, small single copy region of 17,027 bp, and a pair of inverted repeat regions of 27,725 bp. The GC content in the whole chloroplast genome of E. xichangense is 38.81%. Among the 112 unique genes in the circular genome, 30 tRNA, four rRNA and 78 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 26 species, and came to the conclusion that E. xichangense was phylogenetically closely related to E. acuminatum and E. chlorandrum

The complete chloroplast genome of Epimedium trifoliolatobinatum (Koidz.) Koidz. (Berberidaceae)

Epimedium L. is an important genus in the family Berberidaceae. Epimedium trifoliolatobinatum (Koidz.) Koidz. 1939 is inhabited on the west side of the Shikoku, Japan. In this study, the first complete chloroplast genome of E. trifoliolatobinatum was assembled with Illumina paired-end sequencing data, which was 157,272 bp in length with a total GC content of 38.70%. A total of 112 unique genes were annotated, comprising 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis suggested that E. trifoliolatobinatum was sister to E. koreanum. The current results provided fundamental information for further conducting molecular systematics and phylogenetic research of Epimedium genus

The complete chloroplast genome of Epimedium brevicornu (Berberidaceae), a traditional Chinese medicinal herb

Epimedii Folium has been used as a common traditional Chinese medicine for more than 2000 years in China. In this study, we assembled the complete chloroplast (cp) genome of Epimedium brevicornu. The whole cp genome of E. brevicornu is 158,658 bp in length, comprising a pair of inverted repeat (IR) regions (27,699 bp) separated by a large single copy (LSC) region (86,558 bp) and a small single copy (SSC) region (16,702bp). The E. brevicornu cp genome contains 129 genes, of which 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis shows that E. brevicornu is closely clustered with E. wushanense, E. lishihchenii, and E. sagittatum. The published E. brevicornu chloroplast genome will provide useful information for the phylogenetic and evolutionary study on Epimedium family of Berberidaceae