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Geem KR, Lim Y, Hong J, Bae W, Lee J, Han S, Gil J, Cho H, Ryu H. Cytokinin signaling promotes root secondary growth and bud formation in Panax ginseng. J Ginseng Res 2024; 48:220-228. [PMID: 38465220 PMCID: PMC10919999 DOI: 10.1016/j.jgr.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 03/12/2024] Open
Abstract
Background Panax ginseng, one of the valuable perennial medicinal plants, stores numerous pharmacological substrates in its storage roots. Given its perennial growth habit, organ regeneration occurs each year, and cambium stem cell activity is necessary for secondary growth and storage root formation. Cytokinin (CK) is a phytohormone involved in the maintenance of meristematic cells for the development of storage organs; however, its physiological role in storage-root secondary growth remains unknown. Methods Exogenous CK was repeatedly applied to P. ginseng, and morphological and histological changes were observed. RNA-seq analysis was used to elucidate the transcriptional network of CK that regulates P. ginseng growth and development. The HISTIDINE KINASE 3 (PgHK3) and RESPONSE REGULATOR 2 (PgRR2) genes were cloned in P. ginseng and functionally analyzed in Arabidopsis as a two-component system involved in CK signaling. Results Phenotypic and histological analyses showed that CK increased cambium activity and dormant axillary bud formation in P. ginseng, thus promoting storage-root secondary growth and bud formation. The evolutionarily conserved two-component signaling pathways in P. ginseng were sufficient to restore CK signaling in the Arabidopsis ahk2/3 double mutant and rescue its growth defects. Finally, RNA-seq analysis of CK-treated P. ginseng roots revealed that plant-type cell wall biogenesis-related genes are tightly connected with mitotic cell division, cytokinesis, and auxin signaling to regulate CK-mediated P. ginseng development. Conclusion Overall, we identified the CK signaling-related two-component systems and their physiological role in P. ginseng. This scientific information has the potential to significantly improve the field-cultivation and biotechnology-based breeding of ginseng.
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Affiliation(s)
- Kyoung Rok Geem
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Yookyung Lim
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jeongeui Hong
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Republic of Korea
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jinsu Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Soeun Han
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jinsu Gil
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyunwoo Cho
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Republic of Korea
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Tan K, Dong Y, Tan K, Lim LS, Waiho K, Chen J, Xu P, Kwan KY. siRNA Silencing of FpVtg Induces Ovarian Cell Apoptosis in Redtail Prawn, Fenneropenaeus penicillatus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1176-1190. [PMID: 38010485 DOI: 10.1007/s10126-023-10269-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Inadequate gonadal maturation and poor spawning performance increasingly threaten the sustainability of shrimp aquaculture. Unraveling the mechanisms regulating ovarian development and maturation hence is critical to address industry challenges. Vitellogenin (Vtg), a precursor of yolk protein found in the hepatopancreas and ovary of shrimp, plays a key role in facilitating shrimp's oocyte maturation and embryonic development after oviposition. This study found that FpVtg was specifically expressed in F. penicillatus hepatopancreas and ovary. FpVtg was localized predominantly in the oocyte cytoplasm and distributed uniformly in the hepatopancreas tissue. Silencing FpVtg led to apoptosis in both hepatopancreas and ovary tissues. Furthermore, FpVtg depletion upregulated the expression of ovarian peritrophin 1, ovarian peritrophin 2, serine proteinase inhibitor 6, and juvenile hormone esterase-like carboxylesterase 1, while downregulated that of vitellogenin, delta-9 desaturase, and insulin-like receptor. KEGG pathway analysis implicated such as PI3K-AKT signaling, RNA transport, ECM-receptor interaction, hippo signaling, oocyte meiosis, and apoptosis were enriched and involved in ovarian development. These findings have provided insights into the FpVtg's reproductive role and the associated regulatory genes and pathways in F. penicillatus. This knowledge can contribute to establishing strategies to improve the breeding and aquaculture production of F. penicillatus by elucidating its vitellogenesis regulation in redtail prawn and other penaeid species. Further characterization of the implicated pathways and genes will clarify the intricacies underlying ovarian maturation.
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Affiliation(s)
- Kianann Tan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China
| | - Yaxin Dong
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China
| | - Karsoon Tan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China
| | - Leong-Seng Lim
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu City, Sabah, Malaysia
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus City, 21030, Terengganu, Malaysia
| | - Jing Chen
- Zhejiang Institute of Freshwater Fisheries, Huzhou City, 313001, China
| | - Peng Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China.
| | - Kit Yue Kwan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China.
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Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng. Int J Mol Sci 2021; 22:ijms22168694. [PMID: 34445398 PMCID: PMC8395461 DOI: 10.3390/ijms22168694] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
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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Zhang D, Li W, Chen ZJ, Wei FG, Liu YL, Gao LZ. SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng. Sci Rep 2020; 10:15310. [PMID: 32943706 PMCID: PMC7499265 DOI: 10.1038/s41598-020-72291-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/19/2020] [Indexed: 02/08/2023] Open
Abstract
Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.
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Affiliation(s)
- Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Zhong-Jian Chen
- Wenshan Sanqi Institute of Science and Technology, Wenshan University, Wenshan, 663000, China
| | - Fu-Gang Wei
- Wenshan Miaoxiang Notoginseng Industral Co., LTD, Wenshan, 663000, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China. .,Plant Germplasm and Genomics Center, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204, China.
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Zhou M, Yang G, Sun G, Guo Z, Gong X, Pan Y. Resolving complicated relationships of the Panax bipinnatifidus complex in southwestern China by RAD-seq data. Mol Phylogenet Evol 2020; 149:106851. [PMID: 32438045 DOI: 10.1016/j.ympev.2020.106851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 11/26/2022]
Abstract
The P. binpinnatifidus complex included most of the Panax species distributed in Sino-Himalaya regions except for P. pseudoginseng, P. stipuleanatus and P. notoginseng. However, the delimitation and identification of these taxa within the species complex are very difficult due to the existence of morphological intermediates, and their evolutionary relationships remain unresolved despite several studies have been carried out based on traditional DNA markers. The taxonomic uncertainty hinders the identification, conservation and exploration of these wild populations of Panax. To study this species complex, we employed ddRAD-seq data of these taxa from 18 different localities of southwestern China, using two RAD analysis pipelines, STACKS and pyRAD. Based on the results of phylogenetic analysis, the species complex was divided into four clades with high supports, which largely agreed with morphologically described species. Two clades, corresponding to P. vietnamensis and P. zingiberensis, respectively, were sister groups, indicating that these two species had a closer genetic relationship; the third clade was consisted of samples with bamboo-like rhizomes named as P. wangianus clade, and the fourth one with moniliform rhizomes was named as P. bipinnatifidus clade. The population genetic structure analysis and D-statistics test showed the localized admixture among these species, which indicated that introgression had occurred among the related lineages continuously distributed in southeastern Yunnan and adjacent regions.
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Affiliation(s)
- Mingmei Zhou
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqian Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guiling Sun
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Henan 475001, China
| | - Zhenhua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xun Gong
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yuezhi Pan
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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Zhang X, Zhou J, Li L, Huang W, Ahmad HI, Li H, Jiang H, Chen J. Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon ( Acipenser schrenckii). Front Zool 2020; 17:11. [PMID: 32308726 PMCID: PMC7147073 DOI: 10.1186/s12983-020-00355-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii. RESULTS A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3028), and completely different KEGG pathways were significantly enriched between the ovary-biased and testis-biased DEUs. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50% (30/60) genes of those showed significantly differential expression in testes and ovaries. Among these, the Amh and Gsdf with testis-biased expression, and the Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii, respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity in early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4339 predicted transcript factors (TFs) were also respectively identified, which were all significantly associated with the early gametogenesis of A. schrenckii. CONCLUSIONS Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage, which could provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.
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Affiliation(s)
- Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Wenzhong Huang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Hafiz Ishfaq Ahmad
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Huiming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260 Guangdong China
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Till 2018: a survey of biomolecular sequences in genus Panax. J Ginseng Res 2020; 44:33-43. [PMID: 32095095 PMCID: PMC7033366 DOI: 10.1016/j.jgr.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.
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Kim N, Jayakodi M, Lee S, Choi B, Jang W, Lee J, Kim HH, Waminal NE, Lakshmanan M, van Nguyen B, Lee YS, Park H, Koo HJ, Park JY, Perumal S, Joh HJ, Lee H, Kim J, Kim IS, Kim K, Koduru L, Kang KB, Sung SH, Yu Y, Park DS, Choi D, Seo E, Kim S, Kim Y, Hyun DY, Park Y, Kim C, Lee T, Kim HU, Soh MS, Lee Y, In JG, Kim H, Kim Y, Yang D, Wing RA, Lee D, Paterson AH, Yang T. Genome and evolution of the shade-requiring medicinal herb Panax ginseng. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1904-1917. [PMID: 29604169 PMCID: PMC6181221 DOI: 10.1111/pbi.12926] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/19/2018] [Accepted: 03/18/2018] [Indexed: 05/19/2023]
Abstract
Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.
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Affiliation(s)
- Nam‐Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sang‐Choon Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | | | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hyun Hee Kim
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoulKorea
| | - Nomar E. Waminal
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoulKorea
| | - Meiyappan Lakshmanan
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR)Singapore CitySingapore
| | - Binh van Nguyen
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hyun‐Seung Park
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hyun Jo Koo
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hana Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Jinkyung Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - In Seo Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Lokanand Koduru
- School of Chemical EngineeringSungkyunkwan UniversityJangan‐gu, Suwon, Gyeonggi‐doKorea
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical ScienceSeoul National UniversitySeoulKorea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical ScienceSeoul National UniversitySeoulKorea
| | - Yeisoo Yu
- Phyzen Genomics InstituteSeongnamGyeonggi‐doKorea
| | - Daniel S. Park
- Department of Organismic and Evolutionary BiologyHarvard University HerbariaCambridgeMAUSA
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Young‐Chang Kim
- Planning and Coordination DivisionNIHS, RDAWanju‐gunJeollabuk‐doKorea
| | - Dong Yun Hyun
- Ginseng Research DivisionNational Institute of Horticultural & Herbal Science, RDAEumseongChungcheongbuk‐doKorea
| | - Youn‐Il Park
- Department of Biological SciencesChungnam National UniversityDaejeonKorea
| | - Changsoo Kim
- Department of Crop ScienceChungnam National UniversityDaejeonKorea
| | - Tae‐Ho Lee
- Genomics DivisionNational Institute of Agricultural SciencesJeonjuJeollabuk‐doKorea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource EngineeringPlant Engineering Research InstituteSejong UniversitySeoulKorea
| | - Moon Soo Soh
- Division of Integrative Bioscience and BiotechnologySejong UniversitySeoulKorea
| | - Yi Lee
- Department of Industrial Plant Science & TechnologyChungbuk National UniversityCheongjuChungcheongbuk‐doKorea
| | - Jun Gyo In
- Laboratory of Resource and AnalysisR&D HeadquartersKorea Ginseng CorporationDaejeonKorea
| | - Heui‐Soo Kim
- Department of Biological SciencesCollege of Natural SciencesPusan National UniversityBusanKorea
| | - Yong‐Min Kim
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
| | - Deok‐Chun Yang
- Graduate School of Biotechnology and Ginseng BankKyung Hee UniversityYonginGyeonggi‐doKorea
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesThe University of ArizonaTucsonAZUSA
| | - Dong‐Yup Lee
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR)Singapore CitySingapore
- School of Chemical EngineeringSungkyunkwan UniversityJangan‐gu, Suwon, Gyeonggi‐doKorea
| | - Andrew H. Paterson
- Plant Genome Mapping LaboratoryCollege of Agricultural and Environmental Sciences and Franklin College of Arts and SciencesUniversity of GeorgiaAthensGAUSA
| | - Tae‐Jin Yang
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
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Jung I, Kang H, Kim JU, Chang H, Kim S, Jung W. The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. BMC SYSTEMS BIOLOGY 2018; 12:27. [PMID: 29560829 PMCID: PMC5861484 DOI: 10.1186/s12918-018-0548-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss. Despite of its importance as a traditional medicine, biological mechanisms of ginseng has not been well studied and even the genome sequence of ginseng is yet to be determined due to its complex genome structure. Thus, it is challenging to investigate the molecular biology mechanisms at the transcript level. RESULTS To investigate how ginseng responds to the high ambient temperature environment, we performed high throughput RNA sequencing and implemented a bioinformatics pipeline for the integrated analysis of small-RNA and mRNA-seq data without a reference genome. By performing reverse transcriptase (RT) PCR and sanger sequencing of transcripts that were assembled using our pipeline, we validated that their sequences were expressed in our samples. Furthermore, to investigate the interaction between genes and non-coding small RNAs and their regulation status under the high ambient temperature, we identified potential gene regulatory miRNAs. As a result, 100,672 contigs with significant expression level were identified and 6 known, 214 conserved and 60 potential novel miRNAs were predicted to be expressed under the high ambient temperature. CONCLUSION Collectively, we have found that development, flowering and temperature responsive genes were induced under high ambient temperature, whereas photosynthesis related genes were repressed. Functional miRNAs were down-regulated under the high ambient temperature. Among them are miR156 and miR396 that target flowering (SPL6/9) and growth regulating genes (GRF) respectively.
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Affiliation(s)
- Inuk Jung
- Bioinformatics Institute, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Hyejin Kang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Jang Uk Kim
- National Institute of Horticultural and Herbal Science, Ginseng Research Division, RDA, Eumsung-gun, Chungbuk, Republic of Korea
| | - Hyeonsook Chang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Sun Kim
- Bioinformatics Institute, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea.,Department of Computer Science and Engineering, Seoul National University, Gwanak-Gu, Seoul, Republic of Korea
| | - Woosuk Jung
- Department of Applied Bioscience, Konkuk University, Gwangjin-Gu, Seoul, Republic of Korea.
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Jo IH, Lee J, Hong CE, Lee DJ, Bae W, Park SG, Ahn YJ, Kim YC, Kim JU, Lee JW, Hyun DY, Rhee SK, Hong CP, Bang KH, Ryu H. Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes (Basel) 2017; 8:E228. [PMID: 28914759 PMCID: PMC5615361 DOI: 10.3390/genes8090228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chi Eun Hong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | | | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Young Chang Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jang Uk Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jung Woo Lee
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Dong Yun Hyun
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea.
| | | | - Kyong Hwan Bang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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Lee J, Waminal NE, Choi HI, Perumal S, Lee SC, Nguyen VB, Jang W, Kim NH, Gao LZ, Yang TJ. Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax. Sci Rep 2017; 7:9045. [PMID: 28831052 PMCID: PMC5567358 DOI: 10.1038/s41598-017-08194-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8-4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39-52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23-35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.
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Affiliation(s)
- Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Van Binh Nguyen
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea.
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12
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Cytohistological study of the leaf structures of Panax ginseng Meyer and Panax quinquefolius L. J Ginseng Res 2016; 41:463-468. [PMID: 29021692 PMCID: PMC5628331 DOI: 10.1016/j.jgr.2016.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 12/11/2022] Open
Abstract
Background Both Panax ginseng Meyer and Panax quinquefolius are obligate shade-loving plants whose natural habitats are broadleaved forests of Eastern Asia and North America. Panax species are easily damaged by photoinhibition when they are exposed to high temperatures or insufficient shade. In this study, a cytohistological study of the leaf structures of two of the most well-known Panax species was performed to better understand the physiological processes that limit photosynthesis. Methods Leaves of ginseng plants grown in soil and hydroponic culture were sectioned for analysis. Leaf structures of both Panax species were observed using a light microscope, scanning electron microscope, and transmission electron microscope. Results The mesostructure of both P. ginseng and P. quinquefolius frequently had one layer of noncylindrical palisade cells and three or four layers of spongy parenchymal cells. P. quinquefolius contained a similar number of stomata in the abaxial leaf surface but more tightly appressed enlarged grana stacks than P. ginseng contained. The adaxial surface of the epidermis in P. quinquefolius showed cuticle ridges with a pattern similar to that of P. ginseng. Conclusion The anatomical leaf structure of both P. ginseng and P. quinquefolius shows that they are typical shade-loving sciophytes. Slight differences in chloroplast structure suggests that the two different species can be authenticated using transmission electron microscopy images, and light-resistant cultivar breeding can be performed via controlling photosynthesis efficiency.
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13
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Liu Y, Peng R, Liu F, Wang X, Cui X, Zhou Z, Wang C, Cai X, Wang Y, Lin Z, Wang K. A Gossypium BAC clone contains key repeat components distinguishing sub-genome of allotetraploidy cottons. Mol Cytogenet 2016; 9:27. [PMID: 27006694 PMCID: PMC4802715 DOI: 10.1186/s13039-016-0235-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/14/2016] [Indexed: 11/23/2022] Open
Abstract
Background Dissecting genome organization is indispensable for further functional and applied studies. As genome sequences data shown, cotton genomes contain more than 60 % repetitive sequences, so study on repetitive sequences composition, structure, and distribution is the key step to dissect cotton genome. Results In this study, a bacterial artificial chromosome (BAC) clone enriched in repetitive sequences, was discovered initiatively by fluorescence in situ hybridization (FISH). FISHing with allotetraploidy cotton as target DNA, dispersed signals on most regions of all A sub-genome chromosomes, and only middle regions of all D sub-genome chromosomes were detected. Further FISHing with other cotton species bearing A or D genome as target DNA, specific signals were viewed. After BAC sequencing and bioinformational analysis, 129 repeat elements, size about 57,172 bp were found, accounting for more than 62 % of the BAC sequence (91,238 bp). Among them, a type of long terminal repeat-retrotransposon (LTR-RT), LTR/Gypsy was the key element causing the specific FISH results. Using the fragments of BAC matching with the identified Gypsy-like LTR as probes, the BAC-57I23-like FISH signals were reappeared. Running BLASTN, the fragments had good match with all chromosomes of G. arboreum (A2) genome and A sub-genome of G. hirsutum (AD1), and had relatively inferior match with all chromosomes of D sub-genome of AD1, but had little match with the chromosomes of G. raimondii (D5) genome, which was consistent with the FISH results. Conclusion A repeats-enriched cytogenetic marker to identify A and D sub-genomes of Gossypium was discovered by FISH. Combined sequences analysis with FISH verification, the assembly quality of repetitive sequences in the allotetraploidy cotton draft genome was assessed, and better chromosome belonging was verified. We also found the genomic distribution of the identified Gypsy-LTR-RT was similar to the distribution of heterochromatin. The expansion of this type of Gypsy-LTR-RT in heterochromatic regions may be one of the major reasons for the size gap between A and D genome. The findings showed here will help to understand the composition, structure, and evolution of cotton genome, and contribute to the further perfection of the draft genomes of cotton.
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Affiliation(s)
- Yuling Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China ; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Renhai Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China ; Anyang Institute of Technology, Anyang, Henan 455000 China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Xinglei Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Chunying Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
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14
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Shi FX, Li MR, Li YL, Jiang P, Zhang C, Pan YZ, Liu B, Xiao HX, Li LF. The impacts of polyploidy, geographic and ecological isolations on the diversification of Panax (Araliaceae). BMC PLANT BIOLOGY 2015; 15:297. [PMID: 26690782 PMCID: PMC4687065 DOI: 10.1186/s12870-015-0669-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/23/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND Panax L. is a medicinally important genus within family Araliaceae, where almost all species are of cultural significance for traditional Chinese medicine. Previous studies suggested two independent origins of the East Asia and North America disjunct distribution of this genus and multiple rounds of whole genome duplications (WGDs) might have occurred during the evolutionary process. RESULTS We employed multiple chloroplast and nuclear markers to investigate the evolution and diversification of Panax. Our phylogenetic analyses confirmed previous observations of the independent origins of disjunct distribution and both ancient and recent WGDs have occurred within Panax. The estimations of divergence time implied that the ancient WGD might have occurred before the establishment of Panax. Thereafter, at least two independent recent WGD events have occurred within Panax, one of which has led to the formation of three geographically isolated tetraploid species P. ginseng, P. japonicus and P. quinquefolius. Population genetic analyses showed that the diploid species P. notoginseng harbored significantly lower nucleotide diversity than those of the two tetraploid species P. ginseng and P. quinquefolius and the three species showed distinct nucleotide variation patterns at exon regions. CONCLUSION Our findings based on the phylogenetic and population genetic analyses, coupled with the species distribution patterns of Panax, suggested that the two rounds of WGD along with the geographic and ecological isolations might have together contributed to the evolution and diversification of this genus.
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Affiliation(s)
- Feng-Xue Shi
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Ming-Rui Li
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Cui Zhang
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
| | - Yue-Zhi Pan
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Hong-Xing Xiao
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China.
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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The Spatial and Temporal Transcriptomic Landscapes of Ginseng, Panax ginseng C. A. Meyer. Sci Rep 2015; 5:18283. [PMID: 26655864 PMCID: PMC4675998 DOI: 10.1038/srep18283] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/12/2015] [Indexed: 11/09/2022] Open
Abstract
Ginseng, including Asian ginseng (Panax ginseng C. A. Meyer) and American ginseng (P. quinquefolius L.), is one of the most important medicinal herbs in Asia and North America, but significantly understudied. This study sequenced and characterized the transcriptomes and expression profiles of genes expressed in 14 tissues and four different aged roots of Asian ginseng. A total of 265.2 million 100-bp clean reads were generated using the high-throughput sequencing platform HiSeq 2000, representing >8.3x of the 3.2-Gb ginseng genome. From the sequences, 248,993 unigenes were assembled for whole plant, 61,912–113,456 unigenes for each tissue and 54,444–65,412 unigenes for different year-old roots. We comprehensively analyzed the unigene sets and gene expression profiles. We found that the number of genes allocated to each functional category is stable across tissues or developmental stages, while the expression profiles of different genes of a gene family or involved in ginsenoside biosynthesis dramatically diversified spatially and temporally. These results provide an overall insight into the spatial and temporal transcriptome dynamics and landscapes of Asian ginseng, and comprehensive resources for advanced research and breeding of ginseng and related species.
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Li MR, Shi FX, Zhou YX, Li YL, Wang XF, Zhang C, Wang XT, Liu B, Xiao HX, Li LF. Genetic and Epigenetic Diversities Shed Light on Domestication of Cultivated Ginseng (Panax ginseng). MOLECULAR PLANT 2015; 8:1612-22. [PMID: 26278367 DOI: 10.1016/j.molp.2015.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 07/20/2015] [Accepted: 07/23/2015] [Indexed: 05/12/2023]
Abstract
Chinese ginseng (Panax ginseng) is a medically important herb within Panax and has crucial cultural values in East Asia. As the symbol of traditional Chinese medicine, Chinese ginseng has been used as a herbal remedy to restore stamina and capacity in East Asia for thousands of years. To address the evolutionary origin and domestication history of cultivated ginseng, we employed multiple molecular approaches to investigate the genetic structures of cultivated and wild ginseng across their distribution ranges in northeastern Asia. Phylogenetic and population genetic analyses revealed that the four cultivated ginseng landraces, COMMON, BIANTIAO, SHIZHU, and GAOLI (also known as Korean ginseng), were not domesticated independently and Fusong Town is likely one of the primary domestication centers. In addition, our results from population genetic and epigenetic analyses demonstrated that cultivated ginseng maintained high levels of genetic and epigenetic diversity, but showed distinct cytosine methylation patterns compared with wild ginseng. The patterns of genetic and epigenetic variation revealed by this study have shed light on the domestication history of cultivated ginseng, which may serve as a framework for future genetic improvements.
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Affiliation(s)
- Ming-Rui Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China; Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Feng-Xue Shi
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China; Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Yu-Xin Zhou
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China; Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China
| | - Xin-Feng Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China; Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Cui Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China; Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Xu-Tong Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China
| | - Hong-Xing Xiao
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China.
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Street, Changchun 130024, China.
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Wang M, Wu B, Chen C, Lu S. Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:256-70. [PMID: 25040236 DOI: 10.1111/jipb.12239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/03/2014] [Indexed: 05/11/2023]
Abstract
Increasing evidence suggests that long non-coding RNAs (lncRNAs) play significant roles in plants. However, little is known about lncRNAs in Panax ginseng C. A. Meyer, an economically significant medicinal plant species. A total of 3,688 mRNA-like non-coding RNAs (mlncRNAs), a class of lncRNAs, were identified in P. ginseng. Approximately 40% of the identified mlncRNAs were processed into small RNAs, implying their regulatory roles via small RNA-mediated mechanisms. Eleven miRNA-generating mlncRNAs also produced siRNAs, suggesting the coordinated production of miRNAs and siRNAs in P. ginseng. The mlncRNA-derived small RNAs might be 21-, 22-, or 24-nt phased and could be generated from both or only one strand of mlncRNAs, or from super long hairpin structures. A full-length mlncRNA, termed MAR (multiple-function-associated mlncRNA), was cloned. It generated the most abundant siRNAs. The MAR siRNAs were predominantly 24-nt and some of them were distributed in a phased pattern. A total of 228 targets were predicted for 71 MAR siRNAs. Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways, suggesting the significance of MAR in P. ginseng. Consistently, MAR was detected in all tissues analyzed and responded to methyl jasmonate (MeJA) treatment. It sheds light on the function of mlncRNAs in plants.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/genetics
- Gene Expression Regulation, Plant
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames/genetics
- Panax/genetics
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Reproducibility of Results
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Affiliation(s)
- Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
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18
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Murthy HN, Georgiev MI, Kim YS, Jeong CS, Kim SJ, Park SY, Paek KY. Ginsenosides: prospective for sustainable biotechnological production. Appl Microbiol Biotechnol 2014; 98:6243-54. [DOI: 10.1007/s00253-014-5801-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 01/06/2023]
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Choi HI, Waminal NE, Park HM, Kim NH, Choi BS, Park M, Choi D, Lim YP, Kwon SJ, Park BS, Kim HH, Yang TJ. Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:906-16. [PMID: 24456463 DOI: 10.1111/tpj.12441] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/07/2014] [Accepted: 01/13/2014] [Indexed: 05/12/2023]
Abstract
Ginseng (Panax ginseng) is a famous medicinal herb, but the composition and structure of its genome are largely unknown. Here we characterized the major repeat components and inspected their distribution in the ginseng genome. By analyzing three repeat-rich bacterial artificial chromosome (BAC) sequences from ginseng, we identified complex insertion patterns of 34 long terminal repeat retrotransposons (LTR-RTs) and 11 LTR-RT derivatives accounting for more than 80% of the BAC sequences. The LTR-RTs were classified into three Ty3/gypsy (PgDel, PgTat and PgAthila) and two Ty1/Copia (PgTork and PgOryco) families. Mapping of 30-Gbp Illumina whole-genome shotgun reads to the BAC sequences revealed that these five LTR-RT families occupy at least 34% of the ginseng genome. The Ty3/Gypsy families were predominant, comprising 74 and 33% of the BAC sequences and the genome, respectively. In particular, the PgDel family accounted for 29% of the genome and presumably played major roles in enlargement of the size of the ginseng genome. Fluorescence in situ hybridization (FISH) revealed that the PgDel1 elements are distributed throughout the chromosomes along dispersed heterochromatic regions except for ribosomal DNA blocks. The intensity of the PgDel2 FISH signals was biased toward 24 out of 48 chromosomes. Unique gene probes showed two pairs of signals with different locations, one pair in subtelomeric regions on PgDel2-rich chromosomes and the other in interstitial regions on PgDel2-poor chromosomes, demonstrating allotetraploidy in ginseng. Our findings promote understanding of the evolution of the ginseng genome and of that of related species in the Araliaceae.
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Affiliation(s)
- Hong-Il Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
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Kim NH, Choi HI, Kim KH, Jang W, Yang TJ. Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag-simple sequence repeat bands in Panax ginseng Meyer. J Ginseng Res 2014; 38:130-5. [PMID: 24748837 PMCID: PMC3986581 DOI: 10.1016/j.jgr.2013.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/30/2013] [Accepted: 12/31/2013] [Indexed: 11/20/2022] Open
Abstract
Background Panax ginseng, the most famous medicinal herb, has a highly duplicated genome structure. However, the genome duplication of P. ginseng has not been characterized at the sequence level. Multiple band patterns have been consistently observed during the development of DNA markers using unique sequences in P. ginseng. Methods We compared the sequences of multiple bands derived from unique expressed sequence tag-simple sequence repeat (EST-SSR) markers to investigate the sequence level genome duplication. Results Reamplification and sequencing of the individual bands revealed that, for each marker, two bands around the expected size were genuine amplicons derived from two paralogous loci. In each case, one of the two bands was polymorphic, showing different allelic forms among nine ginseng cultivars, whereas the other band was usually monomorphic. Sequences derived from the two loci showed a high similarity, including the same primer-binding site, but each locus could be distinguished based on SSR number variations and additional single nucleotide polymorphisms (SNPs) or InDels. A locus-specific marker designed from the SNP site between the paralogous loci produced a single band that also showed clear polymorphism among ginseng cultivars. Conclusion Our data imply that the recent genome duplication has resulted in two highly similar paralogous regions in the ginseng genome. The two paralogous sequences could be differentiated by large SSR number variations and one or two additional SNPs or InDels in every 100 bp of genic region, which can serve as a reliable identifier for each locus.
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Affiliation(s)
- Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hong-Il Choi
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Kyung Hee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, Combes MC, Gavory F, de Kochko A, Kudrna D, Leroy T, Poulain J, Rondeau M, Song X, Wing R, Lashermes P. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution. PLANT MOLECULAR BIOLOGY 2013; 83:177-189. [PMID: 23708951 DOI: 10.1007/s11103-013-0077-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/14/2013] [Indexed: 06/02/2023]
Abstract
Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.
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Affiliation(s)
- Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394, Montpellier Cedex 5, France
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Choi HI, Kim NH, Kim JH, Choi BS, Ahn IO, Lee JS, Yang TJ. Development of Reproducible EST-derived SSR Markers and Assessment of Genetic Diversity in Panax ginseng Cultivars and Related Species. J Ginseng Res 2013; 35:399-412. [PMID: 23717085 PMCID: PMC3659560 DOI: 10.5142/jgr.2011.35.4.399] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/08/2011] [Accepted: 07/29/2011] [Indexed: 11/18/2022] Open
Abstract
Little is known about the genetics or genomics of Panax ginseng. In this study, we developed 70 expressed sequence tag-derived polymorphic simple sequence repeat markers by trials of 140 primer pairs. All of the 70 markers showed reproducible polymorphism among four Panax speciesand 19 of them were polymorphic in six P. ginseng cultivars. These markers segregated 1:2:1 manner of Mendelian inheritance in an F2 population of a cross between two P. ginseng cultivars, 'Yunpoong' and 'Chunpoong', indicating that these are reproducible and inheritable mappable markers. A phylogenetic analysis using the genotype data showed three distinctive groups: a P. ginseng-P. japonicus clade, P. notoginseng and P. quinquefolius, with similarity coefficients of 0.70. P. japonicus was intermingled with P. ginseng cultivars, indicating that both species have similar genetic backgrounds. P. ginseng cultivars were subdivided into three minor groups: an independent cultivar 'Chunpoong', a subgroup with three accessions including two cultivars, 'Gumpoong' and 'Yunpoong' and one landrace 'Hwangsook' and another subgroup with two accessions including one cultivar, 'Gopoong' and one landrace 'Jakyung'. Each primer pair produced 1 to 4 bands, indicating that the ginseng genome has a highly replicated paleopolyploid genome structure.
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Affiliation(s)
- Hong-Il Choi
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National University College of Agriculture and Life Sciences, Seoul 151-921, Korea
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Cação SMB, Silva NV, Domingues DS, Vieira LGE, Diniz LEC, Vinecky F, Alves GSC, Andrade AC, Carpentieri-Pipolo V, Pereira LFP. Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2. Genetica 2013; 141:217-26. [PMID: 23677718 DOI: 10.1007/s10709-013-9720-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
Abstract
Most of the world's coffee production originates from Coffea arabica, an allotetraploid species with low genetic diversity and for which few genomic resources are available. Genomic libraries with large DNA fragment inserts are useful tools for the study of plant genomes, including the production of physical maps, integration studies of physical and genetic maps, genome structure analysis and gene isolation by positional cloning. Here, we report the construction and characterization of a Bacterial Artificial Chromosome (BAC) library from C. arabica Timor Hybrid CIFC 832/2, a parental genotype for several modern coffee cultivars. The BAC library consists of 56,832 clones with an average insert size of 118 kb, which represents a dihaploid genome coverage of five to sixfold. The content of organellar DNA was estimated at 1.04 and 0.5 % for chloroplast and mitochondrial DNA, respectively. The BAC library was screened for the NADPH-dependent mannose-6-phosphate reductase gene (CaM6PR) with markers positioned on four linkage groups of a partial C. arabica genetic map. A mixed approach using PCR and membrane hybridization of BAC pools allowed for the discovery of nine BAC clones with the CaM6PR gene and 53 BAC clones that were anchored to the genetic map with simple sequence repeat markers. This library will be a useful tool for future studies on comparative genomics and the identification of genes and regulatory elements controlling major traits in this economically important crop species.
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Affiliation(s)
- S M B Cação
- Laboratory of Plant Biotechnology, Instituto Agronomico do Paraná, CP 481 Londrina, Paraná 86001-970, Brazil
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Waminal NE, Park HM, Ryu KB, Kim JH, Yang TJ, Kim HH. Karyotype analysis of Panax ginseng C.A.Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution. COMPARATIVE CYTOGENETICS 2012; 6:425-41. [PMID: 24260682 PMCID: PMC3834566 DOI: 10.3897/compcytogen.v6i4.3740] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/26/2012] [Indexed: 05/26/2023]
Abstract
Ginseng has long been considered a valuable plant owing to its medicinal properties; however, genomic information based on chromosome characterization and physical mapping of cytogenetic markers has been very limited. Dual-color FISH karyotype and DAPI banding analyses of Panax ginseng C. A. Meyer, 1843 were conducted using 5S and 45S rDNA probes. The somatic chromosome complement was 2n=48 with lengths from 3.3 μm to 6.3 μm. The karyotype was composed of 12 metacentric, 9 submetacentric, and 3 subtelocentric pairs. The 5S rDNA probe localized to the intercalary region of the short arm of pair 11, while the 45S rDNA was located at the secondary constriction of the subtelocentric satellited chromosome 14. DAPI bands were clearly observed for most chromosomes, with various signal intensities and chromosomal distributions that consequently improved chromosome identification. As a result, all 24 chromosomes could be distinguished and numbers were assigned to each chromosome for the first time. The results presented here will be useful for the on-going ginseng genome sequencing and further molecular-cytogenetic studies and breeding programs of ginseng.
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Affiliation(s)
- Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Korea
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
| | - Hye Mi Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Korea
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
| | - Kwang Bok Ryu
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
- Department of Horticultural Science, Kyungpook National University, Daegu, 702–701, Korea
| | - Joo Hyung Kim
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151–921, Korea
| | - Hyun Hee Kim
- Plant Biotechnology Institute, Department of Life Science, Sahmyook University, Seoul, 139–742, Korea
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High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng. PLoS One 2012; 7:e44385. [PMID: 22962612 PMCID: PMC3433442 DOI: 10.1371/journal.pone.0044385] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 08/03/2012] [Indexed: 12/18/2022] Open
Abstract
microRNAs (miRNAs) play vital regulatory roles in many organisms through direct cleavage of transcripts, translational repression, or chromatin modification. Identification of miRNAs has been carried out in various plant species. However, no information is available for miRNAs from Panax ginseng, an economically significant medicinal plant species. Using the next generation high-throughput sequencing technology, we obtained 13,326,328 small RNA reads from the roots, stems, leaves and flowers of P. ginseng. Analysis of these small RNAs revealed the existence of a large, diverse and highly complicated small RNA population in P. ginseng. We identified 73 conserved miRNAs, which could be grouped into 33 families, and 28 non-conserved ones belonging to 9 families. Characterization of P. ginseng miRNA precursors revealed many features, such as production of two miRNAs from distinct regions of a precursor, clusters of two precursors in a transcript, and generation of miRNAs from both sense and antisense transcripts. It suggests the complexity of miRNA production in P. gingseng. Using a computational approach, we predicted for the conserved and non-conserved miRNA families 99 and 31 target genes, respectively, of which eight were experimentally validated. Among all predicted targets, only about 20% are conserved among various plant species, whereas the others appear to be non-conserved, indicating the diversity of miRNA functions. Consistently, many miRNAs exhibited tissue-specific expression patterns. Moreover, we identified five dehydration- and ten heat-responsive miRNAs and found the existence of a crosstalk among some of the stress-responsive miRNAs. Our results provide the first clue to the elucidation of miRNA functions in P. ginseng.
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Construction of a llama bacterial artificial chromosome library with approximately 9-fold genome equivalent coverage. J Biomed Biotechnol 2012; 2012:371414. [PMID: 22811594 PMCID: PMC3395300 DOI: 10.1155/2012/371414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/21/2012] [Accepted: 06/04/2012] [Indexed: 11/18/2022] Open
Abstract
The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be 2.4 × 109 bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.
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Sharma MK, Sharma R, Cao P, Jenkins J, Bartley LE, Qualls M, Grimwood J, Schmutz J, Rokhsar D, Ronald PC. A genome-wide survey of switchgrass genome structure and organization. PLoS One 2012; 7:e33892. [PMID: 22511929 PMCID: PMC3325252 DOI: 10.1371/journal.pone.0033892] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 02/19/2012] [Indexed: 11/18/2022] Open
Abstract
The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.
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Affiliation(s)
- Manoj K. Sharma
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Rita Sharma
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura E. Bartley
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Morgan Qualls
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, United States of America
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Daniel Rokhsar
- United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- University of California, Berkeley, California, United States of America
| | - Pamela C. Ronald
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
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Ragupathy R, Rathinavelu R, Cloutier S. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics 2011; 12:217. [PMID: 21554714 PMCID: PMC3113786 DOI: 10.1186/1471-2164-12-217] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/09/2011] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. RESULTS The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. CONCLUSION The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.
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Affiliation(s)
- Raja Ragupathy
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada
| | - Rajkumar Rathinavelu
- Genomics & Bioinformatics Division, ITC Research & Development Centre, Bangalore, India
| | - Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada
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Bang KH, Lee JW, Kim YC, Kim DH, Lee EH, Jeung JU. Construction of Genomic DNA Library of Korean Ginseng (Panax ginseng C. A. MEYER) and Development of Sequence-Tagged Sites. Biol Pharm Bull 2010; 33:1579-88. [DOI: 10.1248/bpb.33.1579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kyong-Hwan Bang
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Jei-Wan Lee
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Young-Chang Kim
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Dong-Hwi Kim
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Eung-Ho Lee
- Ginseng Research Division, National Institute of Horticultural & Herbal Science, Korean Rural Development Administration (RDA)
| | - Ji-Ung Jeung
- Rice Research Division, National Institute of Crop Science, Korean Rural Development Administration (RDA)
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Chapus C, Edwards SV. Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird. BMC Genomics 2009; 10 Suppl 2:S8. [PMID: 19607659 PMCID: PMC2966332 DOI: 10.1186/1471-2164-10-s2-s8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. RESULTS From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. CONCLUSION Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.
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Affiliation(s)
- Charles Chapus
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Development and characterization of new microsatellite markers in Panax ginseng (C.A. Meyer) from BAC end sequences. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9924-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cavagnaro PF, Chung SM, Szklarczyk M, Grzebelus D, Senalik D, Atkins AE, Simon PW. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Mol Genet Genomics 2008; 281:273-88. [PMID: 19104839 DOI: 10.1007/s00438-008-0411-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 11/29/2008] [Indexed: 11/29/2022]
Abstract
Carrot is the most economically important member of the Apiaceae family and a major source of provitamin A carotenoids in the human diet. However, carrot molecular resources are relatively underdeveloped, hampering a number of genetic studies. Here, we report on the synthesis and characterization of a bacterial artificial chromosome (BAC) library of carrot. The library is 17.3-fold redundant and consists of 92,160 clones with an average insert size of 121 kb. To provide an overview of the composition and organization of the carrot nuclear genome we generated and analyzed 2,696 BAC-end sequences (BES) from nearly 2,000 BACs, totaling 1.74 Mb of BES. This analysis revealed that 14% of the BES consists of known repetitive elements, with transposable elements representing more than 80% of this fraction. Eleven novel carrot repetitive elements were identified, covering 8.5% of the BES. Analysis of microsatellites showed a comparably low frequency for these elements in the carrot BES. Comparisons of the translated BES with protein databases indicated that approximately 10% of the carrot genome represents coding sequences. Moreover, among eight dicot species used for comparison purposes, carrot BES had highest homology to protein-coding sequences from tomato. This deep-coverage library will aid carrot breeding and genetics.
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Affiliation(s)
- Pablo F Cavagnaro
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
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Liang Y, Zhao S. Progress in understanding of ginsenoside biosynthesis. PLANT BIOLOGY (STUTTGART, GERMANY) 2008; 10:415-21. [PMID: 18557901 DOI: 10.1111/j.1438-8677.2008.00064.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Ginseng is an economically important medicinal plant. The major bioactive ingredients of ginseng are ginsenosides, which are triterpene saponins. Because of difficulties in ginseng cultivation and the low productivity of ginseng cell and tissue culture, it has become important to improve ginsenoside levels by using metabolic engineering based on the biosynthetic pathway of ginsenosides. During the last decade, substantial advances have been made in biosynthesis of ginsenosides. This review is concerned with recent developments in our understanding of the biosynthesis of ginsenosides.
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Affiliation(s)
- Y Liang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China.
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Hong CP, Kwon SJ, Kim JS, Yang TJ, Park BS, Lim YP. Progress in understanding and sequencing the genome of Brassica rapa. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:582837. [PMID: 18288250 PMCID: PMC2233773 DOI: 10.1155/2008/582837] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 11/21/2007] [Indexed: 05/24/2023]
Abstract
Brassica rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day "diploid" Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. rapa gene number compared to that of A. thaliana. Repetitive DNA of B. rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. rapa will offer a new perspective for plant biology and evolution in the context of polyploidization.
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Affiliation(s)
- Chang Pyo Hong
- Department of Horticulture,
College of Agriculture and Life Science,
Chungnam National University,
Daejeon 305764,
South Korea
| | - Soo-Jin Kwon
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Jung Sun Kim
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Tae-Jin Yang
- Department of Plant Science,
College of Agriculture and Life Sciences,
Seoul National University,
Seoul 151921,
South Korea
| | - Beom-Seok Park
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Yong Pyo Lim
- Department of Horticulture,
College of Agriculture and Life Science,
Chungnam National University,
Daejeon 305764,
South Korea
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Lai CWJ, Yu Q, Hou S, Skelton RL, Jones MR, Lewis KLT, Murray J, Eustice M, Guan P, Agbayani R, Moore PH, Ming R, Presting GG. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol Genet Genomics 2006; 276:1-12. [PMID: 16703363 DOI: 10.1007/s00438-006-0122-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2006] [Accepted: 03/22/2006] [Indexed: 02/03/2023]
Abstract
Papaya (Carica papaya L.) is a major tree fruit crop of tropical and subtropical regions with an estimated genome size of 372 Mbp. We present the analysis of 4.7% of the papaya genome based on BAC end sequences (BESs) representing 17 million high-quality bases. Microsatellites discovered in 5,452 BESs and flanking primer sequences are available to papaya breeding programs at http://www.genomics.hawaii.edu/papaya/BES . Sixteen percent of BESs contain plant repeat elements, the vast majority (83.3%) of which are class I retrotransposons. Several novel papaya-specific repeats were identified. Approximately 19.1% of the BESs have homology to Arabidopsis cDNA. Increasing numbers of completely sequenced plant genomes and BES projects enable novel approaches to comparative plant genomics. Paired BESs of Carica, Arabidopsis, Populus, Brassica and Lycopersicon were mapped onto the completed genomes of Arabidopsis and Populus. In general the level of microsynteny was highest between closely related organisms. However, papaya revealed a higher degree of apparent synteny with the more distantly related poplar than with the more closely related Arabidopsis. This, as well as significant colinearity observed between peach and poplar genome sequences, support recent observations of frequent genome rearrangements in the Arabidopsis lineage and suggest that the poplar genome sequence may be more useful for elucidating the papaya and other rosid genomes. These insights will play a critical role in selecting species and sequencing strategies that will optimally represent crop genomes in sequence databases.
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Affiliation(s)
- Chun Wan J Lai
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Agricultural Sciences Building Room 218, Honolulu, HI, 96822, USA
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Stevens MR, Coleman CE, Parkinson SE, Maughan PJ, Zhang HB, Balzotti MR, Kooyman DL, Arumuganathan K, Bonifacio A, Fairbanks DJ, Jellen EN, Stevens JJ. Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:1593-600. [PMID: 16586115 DOI: 10.1007/s00122-006-0266-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 03/07/2006] [Indexed: 05/08/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is adapted to the harsh environments of the Andean Altiplano region. Its seeds have a well-balanced amino acid composition and exceptionally high protein content with respect to human nutrition. Quinoa grain is a staple in the diet of some of the most impoverished people in the world. The plant is an allotetraploid displaying disomic inheritance (2n=4x=36) with a di-haploid genome of 967 Mbp (megabase pair), or 2C=2.01 pg. We constructed two quinoa BAC libraries using BamHI (26,880 clones) and EcoRI (48,000 clones) restriction endonucleases. Cloned inserts in the BamHI library average 113 kb (kilobase) with approximately 2% of the clones lacking inserts, whereas cloned inserts in the EcoRI library average 130 kb and approximately 1% lack inserts. Three plastid genes used as probes of high-density arrayed blots of 73,728 BACs identified approximately 2.8% of the clones as containing plastid DNA inserts. We estimate that the combined quinoa libraries represent at least 9.0 di-haploid nuclear genome equivalents. An average of 12.2 positive clones per probe were identified with 13 quinoa single-copy ESTs as probes of the high-density arrayed blots, suggesting that the estimate of 9.0x coverage of the genome is conservative. Utility of the BAC libraries for gene identification was demonstrated by probing the library with a partial sequence of the 11S globulin seed storage protein gene and identifying multiple positive clones. The presence of the 11S globulin gene in four of the clones was verified by direct comparison with quinoa genomic DNA on a Southern blot. Besides serving as a useful tool for gene identification, the quinoa BAC libraries will be an important resource for physical mapping of the quinoa genome.
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Affiliation(s)
- M R Stevens
- Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84602-5157, USA.
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Frelichowski JE, Palmer MB, Main D, Tomkins JP, Cantrell RG, Stelly DM, Yu J, Kohel RJ, Ulloa M. Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends. Mol Genet Genomics 2006; 275:479-91. [PMID: 16501995 DOI: 10.1007/s00438-006-0106-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 01/14/2006] [Indexed: 10/25/2022]
Abstract
Fine mapping and positional cloning will eventually improve with the anchoring of additional markers derived from genomic clones such as BACs. From 2,603 new BAC-end genomic sequences from Gossypium hirsutum Acala 'Maxxa', 1,316 PCR primer pairs (designated as MUSB) were designed to flank microsatellite or simple sequence repeat motif sequences. Most (1164 or 88%) MUSB primer pairs successfully amplified DNA from three species of cotton with an average of three amplicons per marker and 365 markers (21%) were polymorphic between G. hirsutum and G. barbadense. An interspecific RIL population developed from the above two entries was used to map 433 marker loci and 46 linkage groups with a genetic distance of 2,126.3 cM covering approximately 45% of the cotton genome and an average distance between two loci of 4.9 cM. Based on genome-specific chromosomes identified in G. hirsutum tetraploid (A and D), 56.9% of the coverage was located on the A subgenome while 39.7% was assigned to the D subgenome in the genetic map, suggesting that the A subgenome may be more polymorphic and recombinationally active than originally thought. The linkage groups were assigned to 23 of the 26 chromosomes. This is the first genetic map in which the linkage groups A01 and A02/D03 have been assigned to specific chromosomes. In addition the MUSB-derived markers from BAC-end sequences markers allows fine genetic and QTL mapping of important traits and for the first time provides reconciliation of the genetic and physical maps. Limited QTL analyses suggested that loci on chromosomes 2, 3, 12, 15 and 18 may affect variation in fiber quality traits. The original BAC clones containing the newly mapped MUSB that tag the QTLs provide critical DNA regions for the discovery of gene sequences involved in biological processes such as fiber development and pest resistance in cotton.
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Yap KYL, Chan SY, Weng Chan Y, Sing Lim C. Overview on the Analytical Tools for Quality Control of Natural Product-Based Supplements: A Case Study of Ginseng. Assay Drug Dev Technol 2005; 3:683-99. [PMID: 16438663 DOI: 10.1089/adt.2005.3.683] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The quality of pharmaceutical products like ginseng is important for ensuring consumer safety and efficacy. Many ginseng products sold today are in various formulations such as powder, capsules, tablets, soft-gels, liquid extracts, and tea. This renders ginseng less identifiable by smell, taste, or physical appearance. Furthermore, as ginseng is expensive, adulteration with other cheaper products occurs. Hence quality assurance of ginseng is needed. This paper reviews the major techniques for ascertaining the level of ginsenosides, the primary active ingredients for ginseng, and covers high-performance liquid, gas, and thin-layer chromatographies, infrared and nuclear magnetic resonance spectroscopies, enzyme immunoassays, and other molecular methods. Supporting techniques such as ultraviolet, fluorescence, diode array and evaporative light scattering detections, and mass spectrometry will also be touched upon. This review also discusses the principles and applications of biosensors-in particular fiber optic-based sensors-and their feasibility in ginseng analysis based on preliminary studies. Despite their potential, there is currently no or limited commercial exploitation of fiber optic-based sensors to perform ginseng quality analysis. The opportunity for biosensors to be used for the rapid quality surveillance of ginseng is appealing, but several key issues still need to be addressed before they find widespread applications in the traditional Chinese medicine industry.
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Affiliation(s)
- Kevin Yi-Lwern Yap
- Biosensors Group, Biomedical Engineering Research Centre, Nanyang Technological University, Singapore
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