Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in <i>Panax ginseng</i>

Waminal, Nomar Espinosa; Pellerin, Remnyl Joyce; Jang, Woojong; Kim, Hyun Hee; Yang, Tae-Jin

doi:10.9787/pbb.2018.6.1.74

Cited by 14 publications

(6 citation statements)

References 33 publications

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“…Owing to recent advances in sequencing technology, the draft genome sequence of P. ginseng has been released by two research groups [37,38]. In addition, we also previously reported the precise transcript sequences of P. ginseng using PacBio single-molecule realtime (SMRT) isoform sequencing (Iso-seq) analysis [39].…”

Section: Introductionmentioning

confidence: 99%

“…Herein, we demonstrate for the first time that GA promotes storage root secondary growth in P. ginseng. We identified eight putative homologs of the AtGID1 gene in P. ginseng (PgGID1s), based on its draft genome sequence and SMRT Iso-seq data [37][38][39]. Functional genomic analysis of four representative PgGID1s (PgGID1A-D) revealed that the functions of PgGIDs are evolutionarily conserved.…”

Section: Introductionmentioning

confidence: 99%

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Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng

Hong

Kim

Lee

et al. 2021

IJMS

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Gibberellins (GAs) are an important group of phytohormones associated with diverse growth and developmental processes, including cell elongation, seed germination, and secondary growth. Recent genomic and genetic analyses have advanced our knowledge of GA signaling pathways and related genes in model plant species. However, functional genomics analyses of GA signaling pathways in Panax ginseng, a perennial herb, have rarely been carried out, despite its well-known economical and medicinal importance. Here, we conducted functional characterization of GA receptors and investigated their physiological roles in the secondary growth of P. ginseng storage roots. We found that the physiological and genetic functions of P. ginseng gibberellin-insensitive dwarf1s (PgGID1s) have been evolutionarily conserved. Additionally, the essential domains and residues in the primary protein structure for interaction with active GAs and DELLA proteins are well-conserved. Overexpression of PgGID1s in Arabidopsis completely restored the GA deficient phenotype of the Arabidopsis gid1a gid1c (atgid1a/c) double mutant. Exogenous GA treatment greatly enhanced the secondary growth of tap roots; however, paclobutrazol (PCZ), a GA biosynthetic inhibitor, reduced root growth in P. ginseng. Transcriptome profiling of P. ginseng roots revealed that GA-induced root secondary growth is closely associated with cell wall biogenesis, the cell cycle, the jasmonic acid (JA) response, and nitrate assimilation, suggesting that a transcriptional network regulate root secondary growth in P. ginseng. These results provide novel insights into the mechanism controlling secondary root growth in P. ginseng.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng

Hong

Kim

Lee

et al. 2021

IJMS

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“…We then determined whether the GA signaling related genes are evolutionarily conserved in P. ginseng genome. To identify GA signaling components, two genomic data obtained from our previous research (Jo et al 2017) and other two groups (Waminal et al 2018;Xu et al 2017) were analyzed. By a blast analysis based on the amino acid sequence of the GA signaling factor of Arabidopsis, it was possible to obtain 14 genes including 4 SLY1s and 10 RGAs in the genome of P. ginseng.…”

Section: Docking Results Of the Ga 3 Interacting With The Pggid1 Proteinsmentioning

confidence: 99%

Functional characterization of gibberellin signaling-related genes in Panax ginseng

et al. 2021

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Gibberellins (GAs) are essential phytohormones for plant growth that influence developmental processes and crop yields. Recent functional genomic analyses of model plants have yielded good characterizations of the canonical GA signaling pathways and related genes. Although Panax ginseng has long been considered to have economic and medicinal importance, functional genomic studies of the GA signaling pathways in this crucial perennial herb plant have been rarely conducted. Here, we identified and performed functional analysis of the GA signaling-related genes, including PgGID1s, PgSLY1s, and PgRGAs. We confirmed that the physiological role of GA signaling components in P. ginseng was evolutionarily conserved. In addition, the important functional domains and amino acid residues for protein interactions among active GA, GID1, SCF SLY1 , and RGA were also functionally conserved. Prediction and comparison of crystallographic structural similarities between PgGID1s and AtGID1a supported their function as GA receptors. Moreover, the subcellular localization and GAdependent promotion of DELLA degradation in P. ginseng was similar to the canonical GA signaling pathways in other plants. Finally, we found that overexpression of PgRGA2 and PgSLY1-1 was sufficient to complement the GA-related phenotypes of atgid1a/c double-and rga quintuple-mutants, respectively. This critical information for these GA signaling genes has the potential to facilitate future genetic engineering and breeding of P. ginseng for increased crop yield and production of useful substances.

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“…S8c,d ). In addition, we identified telomeric repeats using the same approach 31 ; FISH revealed that all of these sequences are localized to all P. ginseng chromosome termini, with an additional interstitial site detected on one chromosome (Supplementary Fig. S8e ).…”

Section: Resultsmentioning

confidence: 99%

Rapid and Efficient FISH using Pre-Labeled Oligomer Probes

Waminal

Pellerin

Kim

et al. 2018

Sci Rep

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Fluorescence in situ hybridization (FISH) is used to visualize the distribution of DNA elements within a genome. Conventional methods for FISH take 1–2 days. Here, we developed a simplified, rapid FISH technique using pre-labeled oligonucleotide probes (PLOPs) and tested the procedure using 18 PLOPs from 45S and 5S rDNA, Arabidopsis-type telomere, and newly-identified Panax ginseng-specific tandem repeats. The 16 developed rDNA PLOPs can be universally applied to plants and animals. The telomere PLOPs can be utilized in most plants with Arabidopsis-type telomeres. The ginseng-specific PLOP can be used to distinguish P. ginseng from related Panax species. Differential labeling of PLOPs allowed us to simultaneously visualize different target loci while reducing the FISH hybridization time from ~16 h to 5 min. PLOP-FISH is efficient, reliable, and rapid, making it ideal for routine analysis, especially of newly sequenced genomes using either universal or specific targets, such as novel tandem repeats identified from whole-genome sequencing data.

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Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in Panax ginseng

Cited by 14 publications

References 33 publications

Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng

Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng

Functional characterization of gibberellin signaling-related genes in Panax ginseng

Rapid and Efficient FISH using Pre-Labeled Oligomer Probes

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