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Kim J, Park Y, Moon S, Seo JA, Moon J, Park H, Choi BY, Raveendar S, Kim CW, Chung JW, Shim D. A comprehensive analysis integrating phenotypic assessment uncovering thornless cultivar lineages in Aralia elata. Genomics 2024; 116:110824. [PMID: 38485062 DOI: 10.1016/j.ygeno.2024.110824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Aralia elata is an Araliaceae woody plant species found in Northeastern Asia. To understand how genetic pools are distributed for A.elata clones, we were to analyze the population structure of A.elata cultivars and identify how these are correlated with thorn-related phenotype which determines the utility of A.elata. We found that the de novo assembled genome of 'Yeongchun' shared major genomic compartments with the public A.elata genome assembled from the wild-type from China. To identify the population structure of the 32 Korean and Japanese cultivars, we identified 44 SSR markers and revealed three main sub-clusters using ΔK analysis with one isolated cultivar. Machine-learning based clustering with thorn-related phenotype correlated moderately with population structure based on SSR analysis suggested multi-layered genetic regulation of thorn-related phenotypes. Thus, we revealed genetic lineage of A.elata and uncovered isolated cultivar which can provide new genetic material for further breeding.
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Affiliation(s)
- Jaewook Kim
- Department of Biological Science, Chungnam National University, Daejeon 34134, Republic of Korea; Department of Biology Education, Korea National University of Education, Cheongju 28173, Republic of Korea
| | - Yunmi Park
- Special Forest Resources Division, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Suyun Moon
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ji-Ae Seo
- Special Forest Resources Division, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Jisook Moon
- Department of Biological Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyeonseon Park
- Department of Biological Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Bae Young Choi
- Department of Biological Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Sebastin Raveendar
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Cheol-Woo Kim
- Special Forest Resources Division, National Institute of Forest Science, Suwon 16631, Republic of Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Donghwan Shim
- Department of Biological Science, Chungnam National University, Daejeon 34134, Republic of Korea; Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea.
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Lee IH, Choi BY, Kim DS, Han H, Kim YH, Shim D. Temporal transcriptome profiling of Pinus densiflora infected with pine wood nematode reveals genetically programmed changes upon pine wilt disease. Phytopathology 2024. [PMID: 38451552 DOI: 10.1094/phyto-10-23-0397-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Pine, an evergreen conifer, is widely distributed worldwide. It is economically, scientifically, and ecologically important. However, pine wilt disease (PWD) induced by the pine wood nematode (PWN) adversely affects pine trees. Many studies have been conducted on PWN and their beetle vectors to prevent the spread of PWD. However, studies providing a comprehensive understanding of the pine tree transcriptome in response to PWN infection are lacking. Here, we performed temporal profiling of the pine tree transcriptome using PWD-infected red pine trees, Pinus densiflora, inoculated with PWN by RNA-sequencing. Our analysis revealed that defense-responsive genes involved in cell wall modification, jasmonic acid signaling, and phenylpropanoid-related processes were significantly enriched 2 weeks after PWD infection. Furthermore, some WRKY-type and MYB-type transcription factors were upregulated 2 weeks after PWD, suggesting that these transcription factors might be responsible for the genome-wide reprogramming of defense-responsive genes in the early PWD stage. Our comprehensive transcriptome analysis will assist in developing PWD resistant pine trees, and identifying genes to diagnose PWD at the early stage of infection, during which large-scale phenotypic changes are absent in PWD-infected pine trees.
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Affiliation(s)
- Il Hwan Lee
- National Institute of Forest Science, 65585, Dongdaemun-gu, Seoul, Korea (the Republic of);
| | - Bae Young Choi
- Chungnam National University, 26715, Biological Sciences, Daejeon, Korea (the Republic of);
| | - Dong Soo Kim
- National Institute of Forest Science, 65585, Dongdaemun-gu, Seoul, Korea (the Republic of);
| | - Hyelim Han
- National Institute of Forest Science, 65585, Dongdaemun-gu, Seoul, Korea (the Republic of);
| | - Yun-Hee Kim
- Gyeongsang National University, 26720, Jinju, Gyeongsangnam-do, Korea (the Republic of);
| | - Donghwan Shim
- Chungnam National University, 26715, Biological Sciences, 99 Daehak-ro, Daejeon, Korea (the Republic of), 34134;
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Kang HI, Kim IS, Shim D, Kang KS, Cheon KS. Genomic selection for growth characteristics in Korean red pine ( Pinus densiflora Seibold & Zucc.). Front Plant Sci 2024; 15:1285094. [PMID: 38322820 PMCID: PMC10844423 DOI: 10.3389/fpls.2024.1285094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/05/2024] [Indexed: 02/08/2024]
Abstract
Traditionally, selective breeding has been used to improve tree growth. However, traditional selection methods are time-consuming and limit annual genetic gain. Genomic selection (GS) offers an alternative to progeny testing by estimating the genotype-based breeding values of individuals based on genomic information using molecular markers. In the present study, we introduced GS to an open-pollinated breeding population of Korean red pine (Pinus densiflora), which is in high demand in South Korea, to shorten the breeding cycle. We compared the prediction accuracies of GS for growth characteristics (diameter at breast height [DBH], height, straightness, and volume) in Korean red pines under various conditions (marker set, model, and training set) and evaluated the selection efficiency of GS compared to traditional selection methods. Training the GS model to include individuals from various environments using genomic best linear unbiased prediction (GBLUP) and markers with a minor allele frequency larger than 0.05 was effective. The optimized model had an accuracy of 0.164-0.498 and a predictive ability of 0.018-0.441. The predictive ability of GBLUP against that of additive best linear unbiased prediction (ABLUP) was 0.86-5.10, and against the square root of heritability was 0.19-0.76, indicating that GS for Korean red pine was as efficient as in previous studies on forest trees. Moreover, the response to GS was higher than that to traditional selection regarding the annual genetic gain. Therefore, we conclude that the trained GS model is more effective than the traditional breeding methods for Korean red pines. We anticipate that the next generation of trees selected by GS will lay the foundation for the accelerated breeding of Korean red pine.
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Affiliation(s)
- Hye-In Kang
- Division of Tree Improvement and Biotechnology, Department of Forest Bio-resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - In Sik Kim
- Division of Tree Improvement and Biotechnology, Department of Forest Bio-resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Kyu-Suk Kang
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyeong-Seong Cheon
- Division of Tree Improvement and Biotechnology, Department of Forest Bio-resources, National Institute of Forest Science, Suwon, Republic of Korea
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Sung YW, Kim J, Yang JW, Shim D, Kim YH. Transcriptome-Based Comparative Expression Profiling of Sweet Potato during a Compatible Response with Root-Knot Nematode Meloidogyne incognita Infection. Genes (Basel) 2023; 14:2074. [PMID: 38003017 PMCID: PMC10671793 DOI: 10.3390/genes14112074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
M. incognita, a root-knot nematode (RKN), infects the roots of several important food crops, including sweet potato (Ipomoea batatas Lam.), and severely reduces yields. However, the molecular mechanisms underlying infection remain unclear. Previously, we investigated differential responses to RKN invasion in susceptible and resistant sweet potato cultivars through RNA-seq-based transcriptome analysis. In this study, gene expression similarities and differences were examined in RKN-susceptible sweet potato cultivars during the compatible response to RKN infection. Three susceptible cultivars investigated in previous research were used: Dahomi (DHM), Shinhwangmi (SHM), and Yulmi (YM). Of the three cultivars, YM had the highest number of genes with altered expression in response to infection. YM was also the cultivar with the highest susceptibility to RKN. Comparisons among cultivars identified genes that were regulated in more than one cultivar upon infection. Pairwise comparisons revealed that YM and DHM shared the most regulated genes, whereas YM and SHM shared the lowest number of regulated genes. Five genes were up-regulated, and two were down-regulated, in all three cultivars. Among these, four genes were highly up-regulated in all cultivars: germin-like protein, anthranilate synthase α subunit, isocitrate lyase, and uncharacterized protein. Genes were also identified that were uniquely regulated in each cultivar in response to infection, suggesting that susceptible cultivars respond to infection through shared and cultivar-specific pathways. Our findings expand the understanding of the compatible response to RKN invasion in sweet potato roots and provide useful information for further research on RKN defense mechanisms.
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Affiliation(s)
- Yeon Woo Sung
- Department of Biology Education, IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jung-Wook Yang
- Department of Crop Cultivation & Environment, Research National Institute of Crop Science, RDA, Suwon 16429, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
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Park HS, Jo IH, Raveendar S, Kim NH, Gil J, Shim D, Kim C, Yu JK, So YS, Chung JW. A chromosome-level genome assembly of Korean mint (Agastache rugosa). Sci Data 2023; 10:792. [PMID: 37949898 PMCID: PMC10638305 DOI: 10.1038/s41597-023-02714-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Agastache rugosa, also known as Korean mint, is a perennial plant from the Lamiaceae family that is traditionally used for various ailments and contains antioxidant and antibacterial phenolic compounds. Molecular breeding of A. rugosa can enhance secondary metabolite production and improve agricultural traits, but progress in this field has been delayed due to the lack of chromosome-scale genome information. Herein, we constructed a chromosome-level reference genome using Nanopore sequencing and Hi-C technology, resulting in a final genome assembly with a scaffold N50 of 52.15 Mbp and a total size of 410.67 Mbp. Nine pseudochromosomes accounted for 89.1% of the predicted genome. The BUSCO analysis indicated a high level of completeness in the assembly. Repeat annotation revealed 561,061 repeat elements, accounting for 61.65% of the genome, with Copia and Gypsy long terminal repeats being the most abundant. A total of 26,430 protein-coding genes were predicted, with an average length of 1,184 bp. The availability of this chromosome-scale genome will advance our understanding of A. rugosa's genetic makeup and its potential applications in various industries.
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Affiliation(s)
- Hyun-Seung Park
- Department of Integrative Biological Sciences and Industry, Convergence Research Center for Natural Products, Sejong University, Seoul, 05006, Korea
| | - Ick Hyun Jo
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, South Korea
| | - Sebastin Raveendar
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | | | - Jinsu Gil
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Changsoo Kim
- Department of Crop Sciences, Chungnam National University, Daejeon, South Korea
| | - Ju-Kyung Yu
- Department of Crop Science, Chungbuk National University, Cheongju, South Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, South Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea.
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Jeon J, Rahman MM, Yang HW, Kim J, Gam HJ, Song JY, Jeong SW, Kim JI, Choi MG, Shin DH, Choi G, Shim D, Jung JH, Lee IJ, Jeon JS, Park YI. Modulation of warm temperature-sensitive growth using a phytochrome B dark reversion variant, phyB[G515E], in Arabidopsis and rice. J Adv Res 2023:S2090-1232(23)00324-7. [PMID: 37926145 DOI: 10.1016/j.jare.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/19/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023] Open
Abstract
INTRODUCTION Ambient temperature-induced hypocotyl elongation in Arabidopsis seedlings is sensed by the epidermis-localized phytochrome B (phyB) and transduced into auxin biosynthesis via a basic helix-loop-helix transcription factor, phytochrome-interacting factor 4 (PIF4). Once synthesized, auxin travels down from the cotyledons to the hypocotyl, triggering hypocotyl cell elongation. Thus, the phyB-PIF4 module involved in thermosensing and signal transduction is a potential genetic target for engineering warm temperature-insensitive plants. OBJECTIVES This study aims to manipulate warm temperature-induced elongation of plants at the post-translational level using phyB variants with dark reversion, the expression of which is subjected to heat stress. METHODS The thermosensitive growth response of Arabidopsis was manipulated by expressing the single amino acid substitution variant of phyB (phyB[G515E]), which exhibited a lower dark reversion rate than wild-type phyB. Other variants with slow (phyB[G564E]) or rapid (phyB[S584F]) dark reversion or light insensitivity (phyB[G767R]) were also included in this study for comparison. Warming-induced transient expression of phyB variants was achieved using heat shock-inducible promoters. Arabidopsis PHYB[G515E] and PHYB[G564E] were also constitutively expressed in rice in an attempt to manipulate the heat sensitivity of a monocotyledonous plant species. RESULTS At an elevated temperature, Arabidopsis seedlings transiently expressing PHYB[G515E] under the control of a heat shock-inducible promoter exhibited shorter hypocotyls than those expressing PHYB and other PHYB variant genes. This warm temperature-insensitive growth was related to the lowered PIF4 and auxin responses. In addition, transgenic rice seedlings expressing Arabidopsis PHYB[G515E] and PHYB[G564E] showed warm temperature-insensitive shoot growth. CONCLUSION Transient expression of phyB variants with altered dark reversion rates could serve as an effective optogenetic technique for manipulating PIF4-auxin-mediated thermomorphogenic responses in plants.
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Affiliation(s)
- Jin Jeon
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Md Mizanor Rahman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ho-Jun Gam
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ji Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seok Won Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeong-Il Kim
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Myoung-Goo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Dong-Ho Shin
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jae-Hoon Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
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Choi BY, Park H, Kim J, Wang S, Lee J, Lee Y, Shim D. BLZ8 activates a plastidial peroxiredoxin and a ferredoxin to protect Chlamydomonas reinhardtii against oxidative stress. Plant Biol (Stuttg) 2023; 25:915-923. [PMID: 37338124 DOI: 10.1111/plb.13552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Reactive oxygen species (ROS) cause damage to various cellular processes in almost all organisms, in particular photosynthetic organisms that depend on the electron transfer chain for CO2 fixation. However, the detoxifying process to mitigate ROS damage has not been studied intensively in microalgae. Here, we characterized the ROS detoxifying role of a bZIP transcription factor, BLZ8, in Chlamydomonas reinhardtii. To identify downstream targets of BLZ8, we carried out comparative genome-wide transcriptomic profiling of BLZ8 OX and its parental CC-4533 under oxidative stress conditions. Luciferase reporter activity assays and RT-qPCR were performed to test whether BLZ8 regulates downstream genes. We performed an in silico functional gene network analysis and an in vivo immunoprecipitation assay to identify the interaction between downstream targets of BLZ8. Comparative transcriptomic analysis and RT-qPCR revealed that overexpression of BLZ8 increased the expression levels of plastid peroxiredoxin1 (PRX1) and ferredoxin-5 (FDX5) under oxidative stress conditions. BLZ8 alone could activate the transcriptional activity of FDX5 and required bZIP2 to activate transcriptional activity of PRX1. Functional gene network analysis using FDX5 and PRX1 orthologs in A. thaliana suggested that these two genes were functionally associated. Indeed, our immunoprecipitation assay revealed the physical interaction between PRX1 and FDX5. Furthermore, the complemented strain, fdx5 (FDX5), recovered growth retardation of the fdx5 mutant under oxidative stress conditions, indicating that FDX5 contributes to oxidative stress tolerance. These results suggest that BLZ8 activates PRX1 and FDX5 expression, resulting in the detoxification of ROS to confer oxidative stress tolerance in microalgae.
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Affiliation(s)
- B Y Choi
- Department of Biological Sciences, Chungnam National University, Daejeon, Korea
| | - H Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Korea
| | - J Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, Korea
| | - S Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Suzhou, China
| | - J Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Suzhou, China
| | - Y Lee
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - D Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, Korea
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Korea
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Kim J, Yun Y, Huh J, Um Y, Shim D. Comparative transcriptome analysis on wild-simulated ginseng of different age revealed possible mechanism of ginsenoside accumulation. Plant Physiol Biochem 2023; 201:107870. [PMID: 37442050 DOI: 10.1016/j.plaphy.2023.107870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Panax ginseng is one of the most famous pharmaceutical plants in Asia. Ginseng plants grown in mountain have longer longevity which ensures higher accumulation of ginsenoside components than those grown in farms. However, wild-simulated ginseng over certain age cannot be easily distinguished in morphology. To identify transcriptomic mechanism of ginsenoside accumulation in older wild-simulated ginseng without large phenotype change, we performed comparative transcriptome analysis for leaf, shoot, and root tissues of 7-yr-old and 13yr-old wild-simulated ginseng. Of 559 differentially expressed genes (DEGs) in comparison between 7-yr-old and 13yr-old wild-simulated ginseng, 280 leaf-, 103 shoot-, and 164 root-mainly expressing genes were found to be changed in transcript level according to age. Functional analysis revealed that pentose-phosphate shunt and abscisic acid responsive genes were up-regulated in leaf tissues of 7-yr-old ginseng while defense responsive genes were up-regulated in root tissues of 13-yr-old ginseng. Quantitative real-time PCR revealed that jasmonic acid responsive genes, ERDL6, and some UGTs were up-regulated in 13-yr-old ginseng in higher order lateral root tissues. These data suggest that bacterial stimulation in mountain region can enhance the expression of several genes which might support minor ginsenoside biosynthesis.
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Affiliation(s)
- Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yeongbae Yun
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju, Gyeongbuk 36040, Republic of Korea
| | - Jeonghoon Huh
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju, Gyeongbuk 36040, Republic of Korea
| | - Yurry Um
- Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju, Gyeongbuk 36040, Republic of Korea.
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea; Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea.
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Kim J, Park MJ, Shim D, Ryoo R. De novo genome assembly of the bioluminescent mushroom Omphalotus guepiniiformis reveals an Omphalotus-specific lineage of the luciferase gene block. Genomics 2022; 114:110514. [PMID: 36332840 DOI: 10.1016/j.ygeno.2022.110514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/04/2022] [Accepted: 10/23/2022] [Indexed: 11/05/2022]
Abstract
Omphalotus guepiniiformis, a bioluminescent mushroom species, is a source of the potentially valuable anticancer chemical. To provide genome information, we de novo assembled the high-quality O. guepiniiformis genome using two Next-Generation sequencing techniques, PacBio and Illumina sequencing. Our draft O. guepiniiformis genome comprises 42.5 Mbp of sequence with only 80 contigs and an N50 sequence length of over 1 Mbp. There were 15,554 predicted coding genes, and 7693 genes were functionally annotated with Gene Ontology terms. We performed a genomic study focusing on mushroom bioluminescent pathway cluster genes by comparing 17 luminescent and 23 non-luminescent Agaricales species belonging to 23 genera. Synteny analysis of genomic regions near the luminescent pathway cluster genes inferred that the Omphalotus lineage was genus-specific. In summary, our de novo assembled O. guepiniiformis genome provides significant biological insights into this organism, including the evolution of the luciferase gene block, and forms the basis for future analyses.
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Affiliation(s)
- Jaewook Kim
- Department of Biological Sciences, Chungnam National University, 34134 Daejeon, Republic of Korea
| | - Mi-Jeong Park
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, 16631 Suwon, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, 34134 Daejeon, Republic of Korea.
| | - Rhim Ryoo
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, 16631 Suwon, Republic of Korea.
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Hong J, Geem KR, Kim J, Jo IH, Yang TJ, Shim D, Ryu H. Prolonged Exposure to High Temperature Inhibits Shoot Primary and Root Secondary Growth in Panax ginseng. Int J Mol Sci 2022; 23:ijms231911647. [PMID: 36232949 PMCID: PMC9569605 DOI: 10.3390/ijms231911647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
High temperature is one of the most significant abiotic stresses reducing crop yield and quality by inhibiting plant growth and development. Global warming has recently increased the frequency of heat waves, which negatively impacts agricultural fields. Despite numerous studies on heat stress responses and signal transduction in model plant species, the molecular mechanism underlying thermomorphogenesis in Panax ginseng remains largely unknown. Here, we investigated the high temperature response of ginseng at the phenotypic and molecular levels. Both the primary shoot growth and secondary root growth of ginseng plants were significantly reduced at high temperature. Histological analysis revealed that these decreases in shoot and root growth were caused by decreases in cell elongation and cambium stem cell activity, respectively. Analysis of P. ginseng RNA-seq data revealed that heat-stress-repressed stem and root growth is closely related to changes in photosynthesis, cell wall organization, cell wall loosening, and abscisic acid (ABA) and jasmonic acid (JA) signaling. Reduction in both the light and dark reactions of photosynthesis resulted in defects in starch granule development in the storage parenchymal cells of the main tap root. Thus, by combining bioinformatics and histological analyses, we show that high temperature signaling pathways are integrated with crucial biological processes that repress stem and root growth in ginseng, providing novel insight into the heat stress response mechanism of P. ginseng.
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Affiliation(s)
- Jeongeui Hong
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Rok Geem
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Korea
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
- Correspondence: (D.S.); (H.R.); Tel.: +82-42-821-6279 (D.S.); +82-43-261-2293 (H.R.); Fax: +82-42-822-9690 (D.S.); +82-43-260-2298 (H.R.)
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Korea
- Correspondence: (D.S.); (H.R.); Tel.: +82-42-821-6279 (D.S.); +82-43-261-2293 (H.R.); Fax: +82-42-822-9690 (D.S.); +82-43-260-2298 (H.R.)
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11
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Lee J, Chen H, Lee G, Emonet A, Kim S, Shim D, Lee Y. MSD2-mediated ROS metabolism fine-tunes the timing of floral organ abscission in Arabidopsis. New Phytol 2022; 235:2466-2480. [PMID: 35689444 PMCID: PMC9543660 DOI: 10.1111/nph.18303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/27/2022] [Indexed: 06/14/2023]
Abstract
The timely removal of end-of-purpose flowering organs is as essential for reproduction and plant survival as timely flowering. Despite much progress in understanding the molecular mechanisms of floral organ abscission, little is known about how various environmental factors are integrated into developmental programmes that determine the timing of abscission. Here, we investigated whether reactive oxygen species (ROS), mediators of various stress-related signalling pathways, are involved in determining the timing of abscission and, if so, how they are integrated with the developmental pathway in Arabidopsis thaliana. MSD2, encoding a secretory manganese superoxide dismutase, was preferentially expressed in the abscission zone of flowers, and floral organ abscission was accelerated by the accumulation of ROS in msd2 mutants. The expression of the genes encoding the receptor-like kinase HAESA (HAE) and its cognate peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), the key signalling components of abscission, was accelerated in msd2 mutants, suggesting that MSD2 acts upstream of IDA-HAE. Further transcriptome and pharmacological analyses revealed that abscisic acid and nitric oxide facilitate abscission by regulating the expression of IDA and HAE during MSD2-mediated signalling. These results suggest that MSD2-dependent ROS metabolism is an important regulatory point integrating environmental stimuli into the developmental programme leading to abscission.
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Affiliation(s)
- Jinsu Lee
- Research Institute of Basic SciencesSeoul National UniversitySeoul08826Korea
- Research Centre for Plant PlasticitySeoul National UniversitySeoul08826Korea
| | - Huize Chen
- Research Institute of Basic SciencesSeoul National UniversitySeoul08826Korea
- Higher Education Key Laboratory of Plant Molecular and Environmental Stress Response in Shanxi ProvinceShanxi Normal UniversityTaiyuan030000ShanxiChina
| | - Gisuk Lee
- Department of Biological SciencesKorea Advanced Institute for Science and TechnologyDaejeon34141Korea
| | - Aurélia Emonet
- Department of Plant Molecular BiologyUniversity of Lausanne1015LausanneSwitzerland
| | - Sang‐Gyu Kim
- Department of Biological SciencesKorea Advanced Institute for Science and TechnologyDaejeon34141Korea
| | - Donghwan Shim
- Department of Biological SciencesChungnam National UniversityDaejeon34134Korea
| | - Yuree Lee
- Research Centre for Plant PlasticitySeoul National UniversitySeoul08826Korea
- School of Biological SciencesSeoul National UniversitySeoul08826Korea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoul08826Korea
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12
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Choi BY, Shim D, Kong F, Auroy P, Lee Y, Li-Beisson Y, Lee Y, Yamaoka Y. The Chlamydomonas transcription factor MYB1 mediates lipid accumulation under nitrogen depletion. New Phytol 2022; 235:595-610. [PMID: 35383411 DOI: 10.1111/nph.18141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Microalgae accumulate high levels of oil under stress, but the underlying biosynthetic pathways are not fully understood. We sought to identify key regulators of lipid metabolism under stress conditions. We found that the Chlamydomonas reinhardtii gene encoding the MYB-type transcription factor MYB1 is highly induced under stress conditions. Two myb1 mutants accumulated less total fatty acids and storage lipids than their parental strain upon nitrogen (N) depletion. Transcriptome analysis revealed that genes involved in lipid metabolism are highly enriched in the wild-type but not in the myb1-1 mutant after 4 h of N depletion. Among these genes were several involved in the transport of fatty acids from the chloroplast to the endoplasmic reticulum (ER): acyl-ACP thioesterase (FAT1), Fatty Acid EXporters (FAX1, FAX2), and long-chain acyl-CoA synthetase1 (LACS1). Furthermore, overexpression of FAT1 in the chloroplast increased lipid production. These results suggest that, upon N depletion, MYB1 promotes lipid accumulation by facilitating fatty acid transport from the chloroplast to the ER. This study identifies MYB1 as an important positive regulator of lipid accumulation in C. reinhardtii upon N depletion, adding another player to the established regulators of this process, including NITROGEN RESPONSE REGULATOR 1 (NRR1) and TRIACYLGLYCEROL ACCUMULATION REGULATOR 1 (TAR1).
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Affiliation(s)
- Bae Young Choi
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Fantao Kong
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Pascaline Auroy
- CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, Aix Marseille Université, CEA Cadarache, Saint Paul-Lez-Durance, 13108, France
| | - Yuree Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Yonghua Li-Beisson
- CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, Aix Marseille Université, CEA Cadarache, Saint Paul-Lez-Durance, 13108, France
| | - Youngsook Lee
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Yasuyo Yamaoka
- Division of Biotechnology, The Catholic University of Korea, Bucheon, 420-743, Korea
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13
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Geem KR, Kim J, Bae W, Jee MG, Yu J, Jang I, Lee DY, Hong CP, Shim D, Ryu H. Nitrate enhances the secondary growth of storage roots in Panax ginseng. J Ginseng Res 2022; 47:469-478. [DOI: 10.1016/j.jgr.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
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14
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Kim K, Choi BY, Kang J, Shim D, Martinoia E, Lee Y. Arabidopsis ABCG27 plays an essential role in flower and leaf development by modulating abscisic acid content. Physiol Plant 2022; 174:e13734. [PMID: 35699652 DOI: 10.1111/ppl.13734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Abscisic acid (ABA) is a phytohormone that mediates stress responses and regulates plant development. Several ATP-binding cassette (ABC) transporters in the G subfamily of ABC (ABCG) proteins have been reported to transport ABA. We investigated whether there are any other ABCG proteins that mediate plant developmental processes regulated by ABA in Arabidopsis (Arabidopsis thaliana). The ABCG27 gene was upregulated in response to exogenous ABA treatment. The abcg27 knockout mutant exhibited two developmental defects: epinastic leaves and abnormally long pistils, which reduced fertility and silique length. ABCG27 expression was induced threefold when flower buds were exposed to exogenous ABA, and the promoter of ABCG27 had two ABA-responsive elements. ABA content in the pistil and true leaves were increased in the abcg27 knockout mutant. Detached abcg27 pistils exposed to exogenous ABA grew longer than those of the wild-type control. ABCG27 fused to GFP localized to the plasma membrane when expressed in Arabidopsis mesophyll protoplasts. A transcriptome analysis of the pistils and true leaves of the wild type and abcg27 knockout mutant revealed that the expression of organ development-related genes changed in the knockout mutant. In particular, the expression of trans-acting small interference (ta-si) RNA processing enzyme genes, which regulate flower and leaf development, was low in the knockout mutant. Together, these results suggest that ABCG27 most likely function as an ABA transporter at the plasma membrane, modulating ABA levels and thereby regulating the development of the pistils and leaves under normal, non-stressed conditions.
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Affiliation(s)
- Kyungyoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Bae Young Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Joohyun Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Youngsook Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
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15
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Ahn JY, Kim J, Yang JY, Lee HJ, Kim S, Cho KS, Lee SH, Kim JH, Lee TH, Hur Y, Shim D. Comparative Transcriptome Analysis between Two Potato Cultivars in Tuber Induction to Reveal Associated Genes with Anthocyanin Accumulation. Int J Mol Sci 2022; 23:ijms23073681. [PMID: 35409041 PMCID: PMC8998591 DOI: 10.3390/ijms23073681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
Anthocyanins are generally accumulated within a few layers, including the epidermal cells of leaves and stems in plants. Solanum tuberosum cv. ‘Jayoung’ (hereafter, JY) is known to accumulate anthocyanin both in inner tissues and skins. We discovered that anthocyanin accumulation in the inner tissues of JY was almost diminished (more than 95% was decreased) in tuber induction condition. To investigate the transcriptomic mechanism of anthocyanin accumulation in JY flesh, which can be modulated by growth condition, we performed mRNA sequencing with white-colored flesh tissue of Solanum tuberosum cv. ‘Atlantic’ (hereafter, ‘Daeseo’, DS) grown under canonical growth conditions, a JY flesh sample grown under canonical growth conditions, and a JY flesh sample grown under tuber induction conditions. We could identify 36 common DEGs (differentially expressed genes) in JY flesh from canonical growth conditions that showed JY-specifically increased or decreased expression level. These genes were enriched with flavonoid biosynthetic process terms in GO analysis, as well as gene set enrichment analysis (GSEA) analysis. Further in silico analysis on expression levels of anthocyanin biosynthetic genes including rate-limiting genes such as StCHS and StCHI followed by RT-PCR and qRT-PCR analysis showed a strong positive correlation with the observed phenotypes. Finally, we identified StWRKY44 from 36 common DEGs as a possible regulator of anthocyanin accumulation, which was further supported by network analysis. In conclusion, we identified StWRKY44 as a putative regulator of tuber-induction-dependent anthocyanin accumulation.
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Affiliation(s)
- Ju Young Ahn
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Ju Yeon Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Hyun Ju Lee
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Soyun Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Kwang-Soo Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Admin-istration, Pyeongchang 25342, Korea;
| | - Sang-Ho Lee
- Department of Biomedical Engineering, Mokwon University, Daejeon 35349, Korea;
| | - Jin-Hyun Kim
- Division of Genomics, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (J.-H.K.); (T.-H.L.)
| | - Tae-Ho Lee
- Division of Genomics, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (J.-H.K.); (T.-H.L.)
| | - Yoonkang Hur
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
- Correspondence: (Y.H.); (D.S.)
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
- Correspondence: (Y.H.); (D.S.)
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16
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Choi BY, Kim H, Shim D, Jang S, Yamaoka Y, Shin S, Yamano T, Kajikawa M, Jin E, Fukuzawa H, Lee Y. The Chlamydomonas bZIP transcription factor BLZ8 confers oxidative stress tolerance by inducing the carbon-concentrating mechanism. Plant Cell 2022; 34:910-926. [PMID: 34893905 PMCID: PMC8824676 DOI: 10.1093/plcell/koab293] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/28/2021] [Indexed: 05/19/2023]
Abstract
Photosynthetic organisms are exposed to various environmental sources of oxidative stress. Land plants have diverse mechanisms to withstand oxidative stress, but how microalgae do so remains unclear. Here, we characterized the Chlamydomonas reinhardtii basic leucine zipper (bZIP) transcription factor BLZ8, which is highly induced by oxidative stress. Oxidative stress tolerance increased with increasing BLZ8 expression levels. BLZ8 regulated the expression of genes likely involved in the carbon-concentrating mechanism (CCM): HIGH-LIGHT ACTIVATED 3 (HLA3), CARBONIC ANHYDRASE 7 (CAH7), and CARBONIC ANHYDRASE 8 (CAH8). BLZ8 expression increased the photosynthetic affinity for inorganic carbon under alkaline stress conditions, suggesting that BLZ8 induces the CCM. BLZ8 expression also increased the photosynthetic linear electron transfer rate, reducing the excitation pressure of the photosynthetic electron transport chain and in turn suppressing reactive oxygen species (ROS) production under oxidative stress conditions. A carbonic anhydrase inhibitor, ethoxzolamide, abolished the enhanced tolerance to alkaline stress conferred by BLZ8 overexpression. BLZ8 directly regulated the expression of the three target genes and required bZIP2 as a dimerization partner in activating CAH8 and HLA3. Our results suggest that a CCM-mediated increase in the CO2 supply for photosynthesis is critical to minimize oxidative damage in microalgae, since slow gas diffusion in aqueous environments limits CO2 availability for photosynthesis, which can trigger ROS formation.
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Affiliation(s)
| | | | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134 Korea
| | - Sunghoon Jang
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | | | - Seungjun Shin
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | | | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul 133-791, South Korea
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Jo IH, Han S, Shim D, Ryu H, Hyun TK, Lee Y, Kim D, So YS, Chung JW. Complete Chloroplast Genome of the Inverted Repeat-Lacking Species Vicia bungei and Development of Polymorphic Simple Sequence Repeat Markers. Front Plant Sci 2022; 13:891783. [PMID: 35651765 PMCID: PMC9149428 DOI: 10.3389/fpls.2022.891783] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Vicia bungei is an economically important forage crop in South Korea and China. Although detailed genetic and genomic data can improve population genetic studies, conservation efforts, and improved breeding of crops, few such data are available for Vicia species in general and none at all for V. bungei. Therefore, the main objectives of this study were to sequence, assemble, and annotate V. bungei chloroplast genome and to identify simple sequence repeats (SSRs) as polymorphic genetic markers. RESULTS The whole-genome sequence of V. bungei was generated using an Illumina MiSeq platform. De novo assembly of complete chloroplast genome sequences was performed for the low-coverage sequence using CLC Genome Assembler with a 200-600-bp overlap size. Vicia bungei chloroplast genome was 130,796-bp long. The genome lacked an inverted repeat unit and thus resembled those of species in the inverted repeat-lacking clade within Fabaceae. Genome annotation using Dual OrganellarGenoMe Annotator (DOGMA) identified 107 genes, comprising 75 protein-coding, 28 transfer RNA, and 4 ribosomal RNA genes. In total, 432 SSRs were detected in V. bungei chloroplast genome, including 64 mononucleotides, 14 dinucleotides, 5 trinucleotides, 4 tetranucleotides, 233 pentanucleotides, 90 hexanucleotides, and 14 complex repeated motifs. These were used to develop 232 novel chloroplast SSR markers, 39 of which were chosen at random to test amplification and genetic diversity in Vicia species (20 accessions from seven species). The unweighted pair group method with arithmetic mean cluster analysis identified seven clusters at the interspecies level and intraspecific differences within clusters. CONCLUSION The complete chloroplast genome sequence of V. bungei was determined. This reference genome should facilitate chloroplast resequencing and future searches for additional genetic markers using population samples. The novel chloroplast genome resources and SSR markers will greatly contribute to the conservation of the genus Vicia and facilitate genetic and evolutionary studies of this genus and of other higher plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, South Korea
| | - Seahee Han
- Division of Botany, Honam National Institute of Biological Resources, Mokpo, South Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, South Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | - Daeil Kim
- Department of Horticulture, Chungbuk National University, Cheongju, South Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, South Korea
- *Correspondence: Yoon-Sup So,
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
- Jong-Wook Chung,
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18
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An H, Lee HY, Shim D, Choi SH, Cho H, Hyun TK, Jo IH, Chung JW. Development of CAPS Markers for Evaluation of Genetic Diversity and Population Structure in the Germplasm of Button Mushroom ( Agaricus bisporus). J Fungi (Basel) 2021; 7:375. [PMID: 34064696 PMCID: PMC8151297 DOI: 10.3390/jof7050375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/24/2023] Open
Abstract
Agaricus bisporus is a globally cultivated mushroom with high economic value. Despite its widespread cultivation, commercial button mushroom strains have little genetic diversity and discrimination of strains for identification and breeding purposes is challenging. Molecular markers suitable for diversity analyses of germplasms with similar genotypes and discrimination between accessions are needed to support the development of new varieties. To develop cleaved amplified polymorphic sequences (CAPs) markers, single nucleotide polymorphism (SNP) mining was performed based on the A. bisporus genome and resequencing data. A total of 70 sets of CAPs markers were developed and applied to 41 A. bisporus accessions for diversity, multivariate, and population structure analyses. Of the 70 SNPs, 62.85% (44/70) were transitions (G/A or C/T) and 37.15% (26/70) were transversions (A/C, A/T, C/G, or G/T). The number of alleles per locus was 1 or 2 (average = 1.9), and expected heterozygosity and gene diversity were 0.0-0.499 (mean = 0.265) and 0.0-0.9367 (mean = 0.3599), respectively. Multivariate and cluster analyses of accessions produced similar groups, with F-statistic values of 0.134 and 0.153 for distance-based and model-based groups, respectively. A minimum set of 10 markers optimized for accession identification were selected based on high index of genetic diversity (GD, range 0.299-0.499) and major allele frequency (MAF, range 0.524-0.817). The CAPS markers can be used to evaluate genetic diversity and population structure and will facilitate the management of emerging genetic resources.
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Affiliation(s)
- Hyejin An
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.A.); (H.C.); (T.K.H.)
| | - Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea;
| | - Donghwan Shim
- Department of Biological Science, Chungnam National University, Daejeon 34134, Korea;
| | - Seong Ho Choi
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea;
| | - Hyunwoo Cho
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.A.); (H.C.); (T.K.H.)
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.A.); (H.C.); (T.K.H.)
| | - Ick-Hyun Jo
- National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.A.); (H.C.); (T.K.H.)
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19
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Lee IH, Kim HS, Nam KJ, Lee KL, Yang JW, Kwak SS, Lee JJ, Shim D, Kim YH. The Defense Response Involved in Sweetpotato Resistance to Root-Knot Nematode Meloidogyne incognita: Comparison of Root Transcriptomes of Resistant and Susceptible Sweetpotato Cultivars With Respect to Induced and Constitutive Defense Responses. Front Plant Sci 2021; 12:671677. [PMID: 34025707 PMCID: PMC8131533 DOI: 10.3389/fpls.2021.671677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/13/2021] [Indexed: 05/08/2023]
Abstract
Sweetpotato (Ipomoea batatas [L.] Lam) is an economically important, nutrient- and pigment-rich root vegetable used as both food and feed. Root-knot nematode (RKN), Meloidogyne incognita, causes major yield losses in sweetpotato and other crops worldwide. The identification of genes and mechanisms responsible for resistance to RKN will facilitate the development of RKN resistant cultivars not only in sweetpotato but also in other crops. In this study, we performed RNA-seq analysis of RKN resistant cultivars (RCs; Danjami, Pungwonmi and Juhwangmi) and susceptible cultivars (SCs; Dahomi, Shinhwangmi and Yulmi) of sweetpotato infected with M. incognita to examine the induced and constitutive defense response-related transcriptional changes. During induced defense, genes related to defense and secondary metabolites were induced in SCs, whereas those related to receptor protein kinase signaling and protein phosphorylation were induced in RCs. In the uninfected control, genes involved in proteolysis and biotic stimuli showed differential expression levels between RCs and SCs during constitutive defense. Additionally, genes related to redox regulation, lipid and cell wall metabolism, protease inhibitor and proteases were putatively identified as RKN defense-related genes. The root transcriptome of SCs was also analyzed under uninfected conditions, and several potential candidate genes were identified. Overall, our data provide key insights into the transcriptional changes in sweetpotato genes that occur during induced and constitutive defense responses against RKN infection.
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Affiliation(s)
- Il-Hwan Lee
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, South Korea
| | - Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Ki Jung Nam
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, South Korea
| | - Kang-Lok Lee
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, South Korea
| | - Jung-Wook Yang
- Department of Crop Cultivation & Environment, Research National Institute of Crop Science, Rural Development Administration, Suwon, South Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Jeung Joo Lee
- Department of Plant Medicine, IALS, Gyeongsang National University, Jinju, South Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Yun-Hee Kim
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, South Korea
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Kim H, Shim D, Moon S, Lee J, Bae W, Choi H, Kim K, Ryu H. Transcriptional network regulation of the brassinosteroid signaling pathway by the BES1-TPL-HDA19 co-repressor complex. Planta 2019; 250:1371-1377. [PMID: 31280329 DOI: 10.1007/s00425-019-03233-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/03/2019] [Indexed: 05/26/2023]
Abstract
The brassinosteroid-related BES1 and BZR1 transcription factors dynamically modulate downstream gene networks via the TPL-HDA19 co-repressor complex in BR-signaling pathways in Arabidopsis thaliana. Brassinosteroids (BRs) are plant steroid hormones that are essential for diverse growth and developmental processes across the whole life cycle of plants. In Arabidopsis thaliana, the BR-related transcription factors BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINAZOLE-RESISTANT 1 (BZR1) regulate a range of global gene expression in response to BR and several external signaling cues; however, the molecular mechanisms by which they mediate the reprogramming of downstream transcription remain unclear. We here report that formation of a protein complex between BES1 and BZR1 and Histone Deacetylase 19 (HDA19) via the conserved ERF-associated amphiphilic repression (EAR) motif proved essential for regulation of BR-signaling-related gene expression. Defects in BR-related functions of BES1 and BZR1 proteins containing a mutated EAR motif were completely rescued by artificial fusion with EAR-repression domain (SRDX), TOPLESS (TPL), or HDA19 proteins. RNA-sequencing analysis of Arabidopsis plants over-expressing bes1-DmEAR or bes1-DmEAR-HDA19 revealed an essential role for HDA19 activity in regulation of BES1/BZR1-mediated BR signaling. In addition to BR-related gene expression, the BES1-HDA19 transcription factor complex was important for abiotic stress-related drought stress tolerance and organ boundary formation. These results suggested that integrating activation of BR-signaling pathways with the formation of the protein complex containing BES1/BZR1 and TPL-HDA19 via the EAR motif was important in fine-tuning BR-related gene networks in plants.
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Affiliation(s)
- Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Donghwan Shim
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyunmo Choi
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Kyunghwan Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Kim MH, Cho JS, Jeon HW, Sangsawang K, Shim D, Choi YI, Park EJ, Lee H, Ko JH. Wood Transcriptome Profiling Identifies Critical Pathway Genes of Secondary Wall Biosynthesis and Novel Regulators for Vascular Cambium Development in Populus. Genes (Basel) 2019; 10:E690. [PMID: 31500311 PMCID: PMC6770981 DOI: 10.3390/genes10090690] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022] Open
Abstract
Wood, the most abundant biomass on Earth, is composed of secondary xylem differentiated from vascular cambium. However, the underlying molecular mechanisms of wood formation remain largely unclear. To gain insight into wood formation, we performed a series of wood-forming tissue-specific transcriptome analyses from a hybrid poplar (Populus alba × P. glandulosa, clone BH) using RNA-seq. Together with shoot apex and leaf tissue, cambium and xylem tissues were isolated from vertical stem segments representing a gradient of secondary growth developmental stages (i.e., immature, intermediate, and mature stem). In a comparative transcriptome analysis of the 'developing xylem' and 'leaf' tissue, we could identify critical players catalyzing each biosynthetic step of secondary wall components (e.g., cellulose, xylan, and lignin). Several candidate genes involved in the initiation of vascular cambium formation were found via a co-expression network analysis using abundantly expressed genes in the 'intermediate stem-derived cambium' tissue. We found that transgenic Arabidopsis plants overexpressing the PtrHAM4-1, a GRAS family transcription factor, resulted in a significant increase of vascular cambium development. This phenotype was successfully reproduced in the transgenic poplars overexpressing the PtrHAM4-1. Taken together, our results may serve as a springboard for further research to unravel the molecular mechanism of wood formation, one of the most important biological processes on this planet.
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Affiliation(s)
- Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Korea.
| | - Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Korea.
| | - Hyung-Woo Jeon
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Korea.
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Kanidta Sangsawang
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Korea.
| | - Donghwan Shim
- Korea Forest Research Institute, Suwon 16631, Korea.
| | - Young-Im Choi
- Korea Forest Research Institute, Suwon 16631, Korea.
| | - Eung-Jun Park
- Korea Forest Research Institute, Suwon 16631, Korea.
| | - Hyoshin Lee
- Korea Forest Research Institute, Suwon 16631, Korea.
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Korea.
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22
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Sung YW, Lee IH, Shim D, Lee KL, Nam KJ, Yang JW, Lee JJ, Kwak SS, Kim YH. Transcriptomic changes in sweetpotato peroxidases in response to infection with the root-knot nematode Meloidogyne incognita. Mol Biol Rep 2019; 46:4555-4564. [PMID: 31222458 DOI: 10.1007/s11033-019-04911-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/07/2019] [Indexed: 12/13/2022]
Abstract
A previous transcriptomic analysis of the roots of susceptible and resistant cultivars of sweetpotato (Ipomoea batatas) identified genes that were likely to contribute to protection against infection with the root-knot nematode Meloidogyne incognita. The current study examined the roles of peroxidase genes in sweetpotato defense responses during root-knot nematode infection, using the susceptible (cv. Yulmi) and resistant (cv. Juhwangmi) cultivars. Differentially expressed genes were assigned to gene ontology categories to predict their functional roles and associated biological processes. Comparison with Arabidopsis peroxidases identified a group of genes orthologous to Arabidopsis PEROXIDASE 52 (AtPrx52). An analysis of sweetpotato peroxidase genes determined their roles in protecting plants against root-knot nematode infection and enabled identification of important peroxidases. The interactions involved in sweetpotato resistance to nematode infection are discussed.
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Affiliation(s)
- Yeon Woo Sung
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea.,Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, Republic of Korea
| | - Il Hwan Lee
- Department of Forest Bio-resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Donghwan Shim
- Department of Forest Bio-resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Kang-Lok Lee
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Ki Jung Nam
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jung-Wook Yang
- National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
| | - Jeung Joo Lee
- Department of Plant Medicine, IALS, Gyeongsang National University, Jinju, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
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Lee J, Han S, Lee HY, Jeong B, Heo TY, Hyun TK, Kim K, Je BI, Lee H, Shim D, Park SJ, Ryu H. Brassinosteroids facilitate xylem differentiation and wood formation in tomato. Planta 2019; 249:1391-1403. [PMID: 30673841 DOI: 10.1007/s00425-019-03094-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
BR signaling pathways facilitate xylem differentiation and wood formation by fine tuning SlBZR1/SlBZR2-mediated gene expression networks involved in plant secondary growth. Brassinosteroid (BR) signaling and BR crosstalk with diverse signaling cues are involved in the pleiotropic regulation of plant growth and development. Recent studies reported the critical roles of BR biosynthesis and signaling in vascular bundle development and plant secondary growth; however, the molecular bases of these roles are unclear. Here, we performed comparative physiological and anatomical analyses of shoot morphological growth in a cultivated wild-type tomato (Solanum lycopersicum cv. BGA) and a BR biosynthetic mutant [Micro Tom (MT)]. We observed that the canonical BR signaling pathway was essential for xylem differentiation and sequential wood formation by facilitating plant secondary growth. The gradual retardation of xylem development phenotypes during shoot vegetative growth in the BR-deficient MT tomato mutant recovered completely in response to exogenous BR treatment or genetic complementation of the BR biosynthetic DWARF (D) gene. By contrast, overexpression of the tomato Glycogen synthase kinase 3 (SlGSK3) or CRISPR-Cas9 (CR)-mediated knockout of the tomato Brassinosteroid-insensitive 1 (SlBRI1) impaired BR signaling and resulted in severely defective xylem differentiation and secondary growth. Genetic modulation of the transcriptional activity of the tomato Brassinazole-resistant 1/2 (SlBZR1/SlBZR2) confirmed the positive roles of BR signaling pathways for xylem differentiation and secondary growth. Our data indicate that BR signaling pathways directly promote xylem differentiation and wood formation by canonical BR-activated SlBZR1/SlBZR2.
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Affiliation(s)
- Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Seahee Han
- National Agrobiodiversity Center, National Academy of Agricultural Science RDA, Jeonju, 54875, Republic of Korea
| | - Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Bomi Jeong
- Department of Information and Statistics, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Tae-Young Heo
- Department of Information and Statistics, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Kyunghwan Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Byoung Il Je
- Department of Horticultural Bioscience, College of Natural Resource and Life Science, Pusan National University, Miryang, 50467, Republic of Korea
| | - Horim Lee
- Department of Biotechnology, Duksung Women's University, Seoul, 01369, Republic of Korea
| | - Donghwan Shim
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Soon Ju Park
- Division of Biological Sciences, Research Institute for Basic Science, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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24
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Lee IH, Shim D, Jeong JC, Sung YW, Nam KJ, Yang JW, Ha J, Lee JJ, Kim YH. Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-resistant and susceptible sweetpotato cultivars. Planta 2019; 249:431-444. [PMID: 30232599 DOI: 10.1007/s00425-018-3001-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/29/2018] [Indexed: 05/17/2023]
Abstract
Transcriptome analysis was performed on the roots of susceptible and resistant sweetpotato cultivars infected with the major root-knot nematode species Meloidogyne incognita. In addition, we identified a transcription factor-mediated defense signaling pathway that might function in sweetpotato-nematode interactions. Root-knot nematodes (RKNs, Meloidogyne spp.) are important sedentary endoparasites of many agricultural crop plants that significantly reduce production in field-grown sweetpotato. To date, no studies involving gene expression profiling in sweetpotato during RKN infection have been reported. Therefore, in the present study, transcriptome analysis was performed on the roots of susceptible (cv. Yulmi) and resistant (cv. Juhwangmi) sweetpotato cultivars infected with the widespread, major RKN species Meloidogyne incognita. Using the Illumina HiSeq 2000 platform, we generated 455,295,628 pair-end reads from the fibrous roots of both cultivars, which were assembled into 74,733 transcripts. A number of common and unique genes were differentially expressed in susceptible vs. resistant cultivars as a result of RKN infection. We assigned the differentially expressed genes into gene ontology categories and used MapMan annotation to predict their functional roles and associated biological processes. The candidate genes including hormonal signaling-related transcription factors and pathogenesis-related genes that could contribute to protection against RKN infection in sweetpotato roots were identified and sweetpotato-nematode interactions involved in resistance are discussed.
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Affiliation(s)
- Il Hwan Lee
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Jea Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Yeon Woo Sung
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Ki Jung Nam
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jung-Wook Yang
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Joon Ha
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju, Republic of Korea
| | - Jeung Joo Lee
- Department of Plant Medicine, IALS, Gyeongsang National University, Jinju, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
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25
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Lee J, Shim D, Moon S, Kim H, Bae W, Kim K, Kim YH, Rhee SK, Hong CP, Hong SY, Lee YJ, Sung J, Ryu H. Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato. Plant Physiol Biochem 2018; 127:553-560. [PMID: 29723826 DOI: 10.1016/j.plaphy.2018.04.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 05/03/2023]
Abstract
Brassinosteroids (BRs) are plant steroid hormones that play crucial roles in a range of growth and developmental processes. Although BR signal transduction and biosynthetic pathways have been well characterized in model plants, their biological roles in an important crop, tomato (Solanum lycopersicum), remain unknown. Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using physiological and transcriptomic approaches. The cultivated tomato showed higher tolerance to drought and osmotic stresses than the MT tomato. However, BR-defective phenotypes of MT, including plant growth and stomatal closure defects, were completely recovered by application of exogenous BR or complementation with a SlDWARF gene. Using genome-wide transcriptome analysis, 619 significantly differentially expressed genes (DEGs) were identified between WT and MT plants. Several DEGs were linked to known signaling networks, including those related to biotic/abiotic stress responses, lignification, cell wall development, and hormone responses. Consistent with the higher susceptibility of MT to drought stress, several gene sets involved in responses to drought and osmotic stress were differentially regulated between the WT and MT tomato plants. Our data suggest that BR signaling pathways are involved in mediating the response to abiotic stress via fine-tuning of abiotic stress-related gene networks in tomato plants.
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Affiliation(s)
- Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Republic of Korea.
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Kyunghwan Kim
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Yang-Hoon Kim
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Chang Pyo Hong
- TheragenEtex Bio Institute, Suwon 16229, Republic of Korea.
| | - Suk-Young Hong
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Ye-Jin Lee
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Jwakyung Sung
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
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26
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Choi I, Subramanian P, Shim D, Oh BJ, Hahn BS. RNA-Seq of Plant-Parasitic Nematode Meloidogyne incognita at Various Stages of Its Development. Front Genet 2017; 8:190. [PMID: 29230237 PMCID: PMC5711784 DOI: 10.3389/fgene.2017.00190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/14/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Inchan Choi
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Parthiban Subramanian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, South Korea
| | - Byung-Ju Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Bum-Soo Hahn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
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27
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Moon S, Lee HY, Shim D, Kim M, Ka KH, Ryoo R, Ko HG, Koo CD, Chung JW, Ryu H. Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes. Mycobiology 2017; 45:105-109. [PMID: 28781544 PMCID: PMC5541145 DOI: 10.5941/myco.2017.45.2.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/03/2017] [Accepted: 06/12/2017] [Indexed: 05/15/2023]
Abstract
Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.
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Affiliation(s)
- Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
| | - Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Donghwan Shim
- Division of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Korea
| | - Myungkil Kim
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Kang-Hyeon Ka
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Rhim Ryoo
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Han-Gyu Ko
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju 12653, Korea
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
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28
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Lee HY, Moon S, Shim D, Hong CP, Lee Y, Koo CD, Chung JW, Ryu H. Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars. Genes (Basel) 2017; 8:genes8040109. [PMID: 28338645 PMCID: PMC5406856 DOI: 10.3390/genes8040109] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/28/2017] [Accepted: 03/21/2017] [Indexed: 11/16/2022] Open
Abstract
The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2-11; the observed and expected heterozygosity were 0.00-1.00 and 0.10-0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Korea.
| | | | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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Lane T, Best T, Zembower N, Davitt J, Henry N, Xu Y, Koch J, Liang H, McGraw J, Schuster S, Shim D, Coggeshall MV, Carlson JE, Staton ME. The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. BMC Genomics 2016; 17:702. [PMID: 27589953 PMCID: PMC5009568 DOI: 10.1186/s12864-016-3052-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/27/2016] [Indexed: 11/25/2022] Open
Abstract
Background To develop a set of transcriptome sequences to support research on environmental stress responses in green ash (Fraxinus pennsylvanica), we undertook deep RNA sequencing of green ash tissues under various stress treatments. The treatments, including emerald ash borer (EAB) feeding, heat, drought, cold and ozone, were selected to mimic the increasing threats of climate change and invasive pests faced by green ash across its native habitat. Results We report the generation and assembly of RNA sequences from 55 green ash samples into 107,611 putative unique transcripts (PUTs). 52,899 open reading frames were identified. Functional annotation of the PUTs by comparison to the Uniprot protein database identified matches for 63 % of transcripts and for 98 % of transcripts with ORFs. Further functional annotation identified conserved protein domains and assigned gene ontology terms to the PUTs. Examination of transcript expression across different RNA libraries revealed that expression patterns clustered based on tissues regardless of stress treatment. The transcripts from stress treatments were further examined to identify differential expression. Tens to hundreds of differentially expressed PUTs were identified for each stress treatment. A set of 109 PUTs were found to be consistently up or down regulated across three or more different stress treatments, representing basal stress response candidate genes in green ash. In addition, 1956 simple sequence repeats were identified in the PUTs, of which we identified 465 high quality DNA markers and designed flanking PCR primers. Conclusions North American native ash trees have suffered extensive mortality due to EAB infestation, creating a need to breed or select for resistant green ash genotypes. Stress from climate change is an additional concern for longevity of native ash populations. The use of genomics could accelerate management efforts. The green ash transcriptome we have developed provides important sequence information, genetic markers and stress-response candidate genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3052-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Lane
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA
| | - Teodora Best
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Nicole Zembower
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jack Davitt
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA
| | - Nathan Henry
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA
| | - Yi Xu
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA.,Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Jennifer Koch
- Northern Research Station, USDA Forest Service, Delaware, OH, 43015, USA
| | - Haiying Liang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - John McGraw
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Stephan Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Donghwan Shim
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark V Coggeshall
- Department of Forestry, University of Missouri, Columbia, MO, 65211, USA
| | - John E Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37966, USA.
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Kim HU, Lee KR, Shim D, Lee JH, Chen GQ, Hwang S. Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens. BMC Genomics 2016; 17:474. [PMID: 27342315 PMCID: PMC4920993 DOI: 10.1186/s12864-016-2805-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/27/2016] [Indexed: 12/02/2022] Open
Abstract
Background Perilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis. Results Perilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses. Conclusions This work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2805-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea.
| | - Kyeong-Ryeol Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | | | - Grace Q Chen
- U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea
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Kim HU, Lee KR, Shim D, Lee JH, Chen GQ, Hwang S. Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens. BMC Genomics 2016; 17:474. [PMID: 27342315 DOI: 10.1186/s12864-016-2805-2800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/27/2016] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Perilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis. RESULTS Perilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses. CONCLUSIONS This work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds.
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Affiliation(s)
- Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea.
| | - Kyeong-Ryeol Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | | | - Grace Q Chen
- U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, 05006, Republic of Korea
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Shim D, Raveendar S, Lee JR, Lee GA, Ro NY, Jeon YA, Cho GT, Lee HS, Ma KH, Chung JW. The complete chloroplast genome of Capsicum frutescens (Solanaceae). Appl Plant Sci 2016; 4:apps1600002. [PMID: 27213127 PMCID: PMC4873274 DOI: 10.3732/apps.1600002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/05/2016] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. METHODS AND RESULTS Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. CONCLUSIONS The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.
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Affiliation(s)
- Donghwan Shim
- Department of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441-350, Republic of Korea
| | - Sebastin Raveendar
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Na-Young Ro
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Young-Ah Jeon
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Ho-Sun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Kyung-Ho Ma
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jong-Wook Chung
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
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Kim RJ, Kim HJ, Shim D, Suh MC. Molecular and biochemical characterizations of the monoacylglycerol lipase gene family of Arabidopsis thaliana. Plant J 2016; 85:758-71. [PMID: 26932457 DOI: 10.1111/tpj.13146] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 05/23/2023]
Abstract
Monoacylglycerol lipase (MAGL) catalyzes the last step of triacylglycerol breakdown, which is the hydrolysis of monoacylglycerol (MAG) to fatty acid and glycerol. Arabidopsis harbors over 270 genes annotated as 'lipase', the largest class of acyl lipid metabolism genes that have not been characterized experimentally. In this study, computational modeling suggested that 16 Arabidopsis putative MAGLs (AtMAGLs) have a three-dimensional structure that is similar to a human MAGL. Heterologous expression and enzyme assays indicated that 11 of the 16 encoded proteins indeed possess MAG lipase activity. Additionally, AtMAGL4 displayed hydrolase activity with lysophosphatidylcholine and lysophosphatidylethanolamine (LPE) substrates and AtMAGL1 and 2 utilized LPE as a substrate. All recombinant AtMAGLs preferred MAG substrates with unsaturated fatty acids over saturated fatty acids and AtMAGL8 exhibited the highest hydrolase activities with MAG containing 20:1 fatty acids. Except for AtMAGL4, -14 and -16, all AtMAGLs showed similar activity with both sn-1 and sn-2 MAG isomers. Spatial, temporal and stress-induced expression of the 16 AtMAGL genes was analyzed by transcriptome analyses. AtMAGL:eYFP fusion proteins provided initial evidence that AtMAGL1, -3, -6, -7, -8, -11, -13, -14 and -16 are targeted to the endoplasmic reticulum and/or Golgi network, AtMAGL10, -12 and -15 to the cytosol and AtMAGL2, -4 and -5 to the chloroplasts. Furthermore, AtMAGL8 was associated with the surface of oil bodies in germinating seeds and leaves accumulating oil bodies. This study provides the broad characterization of one of the least well-understood groups of Arabidopsis lipid-related enzymes and will be useful for better understanding their roles in planta.
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Affiliation(s)
- Ryeo Jin Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
| | - Hae Jin Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
| | - Donghwan Shim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
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Shim D, Park SG, Kim K, Bae W, Lee GW, Ha BS, Ro HS, Kim M, Ryoo R, Rhee SK, Nou IS, Koo CD, Hong CP, Ryu H. Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes. J Biotechnol 2016; 223:24-5. [PMID: 26924240 DOI: 10.1016/j.jbiotec.2016.02.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 12/22/2022]
Abstract
Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1 Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation provides key information about various signaling pathways and secondary metabolites. This genomic information should help establish the molecular genetic markers for MAS/MAB and increase our understanding of the genome structure and function.
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Affiliation(s)
- Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Sin-Gi Park
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Kangmin Kim
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Gir Won Lee
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Byeong-Suk Ha
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Myungkil Kim
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Republic of Korea
| | - Rhim Ryoo
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Republic of Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Republic of Korea
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Chang Pyo Hong
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
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Pang T, Guo L, Shim D, Cannon N, Tang S, Chen J, Xia X, Yin W, Carlson JE. Characterization of the Transcriptome of the Xerophyte Ammopiptanthus mongolicus Leaves under Drought Stress by 454 Pyrosequencing. PLoS One 2015; 10:e0136495. [PMID: 26313687 PMCID: PMC4552034 DOI: 10.1371/journal.pone.0136495] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ammopiptanthus mongolicus (Maxim. Ex Kom.) Cheng f., an endangered ancient legume species, endemic to the Gobi desert in north-western China. As the only evergreen broadleaf shrub in this area, A. mongolicus plays an important role in the region's ecological-environmental stability. Despite the strong potential of A. mongolicus in providing new insights on drought tolerance, sequence information on the species in public databases remains scarce. To both learn about the role of gene expression in drought stress tolerance in A. mongolicus and to expand genomic resources for the species, transcriptome sequencing of stress-treated A. mongolicus plants was performed. RESULTS Using 454 pyrosequencing technology, 8,480 and 7,474 contigs were generated after de novo assembly of RNA sequences from leaves of untreated and drought-treated plants, respectively. After clustering using TGICL and CAP3 programs, a combined assembly of all reads produced a total of 11,357 putative unique transcripts (PUTs). Functional annotation and classification of the transcripts were conducted by aligning the 11,357 PUTs against the public protein databases and nucleotide database (Nt). Between control and drought-treated plants, 1,620 differentially expressed genes (DEGs) were identified, of which 1,106 were up-regulated and 514 were down-regulated. The differential expression of twenty candidate genes in metabolic pathways and transcription factors families related to stress-response were confirmed by quantitative real-time PCR. Representatives of several large gene families, such as WRKY and P5CS, were identified and verified in A. mongolicus for the first time. CONCLUSIONS The additional transcriptome resources, gene expression profiles, functional annotations, and candidate genes provide a more comprehensive understanding of the stress response pathways in xeric-adapted plant species such as A. mongolicus.
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Affiliation(s)
- Tao Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Lili Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
- College of Agricultural, Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Donghwan Shim
- The Schatz Center for Tree Molecular Genetics, Department Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441–350, Korea
| | - Nathaniel Cannon
- The Schatz Center for Tree Molecular Genetics, Department Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sha Tang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Jinhuan Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Key Laboratory for Silviculture and Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - John E. Carlson
- The Schatz Center for Tree Molecular Genetics, Department Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, United States of America
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Raveendar S, Na YW, Lee JR, Shim D, Ma KH, Lee SY, Chung JW. The complete chloroplast genome of Capsicum annuum var. glabriusculum using Illumina sequencing. Molecules 2015; 20:13080-8. [PMID: 26205052 PMCID: PMC6332240 DOI: 10.3390/molecules200713080] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/06/2015] [Accepted: 07/16/2015] [Indexed: 11/17/2022] Open
Abstract
Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC; SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants.
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Affiliation(s)
- Sebastin Raveendar
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Young-Wang Na
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441-350, Korea.
| | - Kyung-Ho Ma
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Sok-Young Lee
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jong-Wook Chung
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
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Shim D, Ko JH, Kim WC, Wang Q, Keathley DE, Han KH. A molecular framework for seasonal growth-dormancy regulation in perennial plants. Hortic Res 2014; 1:14059. [PMID: 26504555 PMCID: PMC4591672 DOI: 10.1038/hortres.2014.59] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 09/25/2014] [Accepted: 10/16/2014] [Indexed: 05/03/2023]
Abstract
The timing of the onset and release of dormancy impacts the survival, productivity and spatial distribution of temperate horticultural and forestry perennials and is mediated by at least three main regulatory programs involving signal perception and processing by phytochromes (PHYs) and PHY-interacting transcription factors (PIFs). PIF4 functions as a key regulator of plant growth in response to both external and internal signals. In poplar, the expression of PIF4 and PIF3-LIKE1 is upregulated in response to short days, while PHYA and PHYB are not regulated at the transcriptional level. Integration of light and environmental signals is achieved by gating the expression and transcriptional activity of PIF4. During this annual cycle, auxin promotes the degradation of Aux/IAA transcriptional repressors through the SKP-Cullin-F-boxTIR1 complex, relieving the repression of auxin-responsive genes by allowing auxin response factors (ARFs) to activate the transcription of auxin-responsive genes involved in growth responses. Analyses of transcriptome changes during dormancy transitions have identified MADS-box transcription factors associated with endodormancy induction. Previous studies show that poplar dormancy-associated MADS-box (DAM) genes PtMADS7 and PtMADS21 are differentially regulated during the growth-dormancy cycle. Endodormancy may be regulated by internal factors, which are specifically localized in buds. PtMADS7/PtMADS21 may function as an internal regulator in poplar. The control of flowering time shares certain regulatory hierarchies with control of the dormancy/growth cycle. However, the particularities of different stages of the dormancy/growth cycle warrant comprehensive approaches to identify the causative genes for the entire cycle. A growing body of knowledge also indicates epigenetic regulation plays a role in these processes in perennial horticultural and forestry plants. The increased knowledge contributes to better understanding of the dormancy process and consequently to precise manipulation of dormancy-related horticultural traits, such as flowering time.
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Affiliation(s)
- Donghwan Shim
- Schatz Center for Tree Molecular Genetics, Pennsylvania State University, University Park, PA16802, USA
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Republic of Korea
| | - Won-Chan Kim
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Department of Forestry, Michigan State University, East Lansing, MI 48824, USA
| | - Qijun Wang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Konjac Research Center, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Daniel E Keathley
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Kyung-Hwan Han
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Department of Forestry, Michigan State University, East Lansing, MI 48824, USA
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Shim D, Kim S, Choi YI, Song WY, Park J, Youk ES, Jeong SC, Martinoia E, Noh EW, Lee Y. Transgenic poplar trees expressing yeast cadmium factor 1 exhibit the characteristics necessary for the phytoremediation of mine tailing soil. Chemosphere 2013; 90:1478-86. [PMID: 23062827 DOI: 10.1016/j.chemosphere.2012.09.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 09/09/2012] [Accepted: 09/10/2012] [Indexed: 05/18/2023]
Abstract
Genetic engineering of plants for phytoremediation is thought to be possible based on results using model plants expressing genes involved in heavy metal resistance, which improve the plant's tolerance of heavy metals and accumulation capacity. The next step of progress in this technology requires the genetic engineering of plants that produce large amounts of biomass and the testing of these transgenic plants in contaminated soils. Thus, we transformed a sterile line of poplar Populus alba X P. tremula var. glandulosa with a heavy metal resistance gene, ScYCF1 (yeast cadmium factor 1), which encodes a transporter that sequesters toxic metal(loid)s into the vacuoles of budding yeast, and tested these transgenic plants in soil taken from a closed mine site contaminated with multiple toxic metal(loid)s under greenhouse and field conditions. The YCF1-expressing transgenic poplar plants exhibited enhanced growth, reduced toxicity symptoms, and increased Cd content in the aerial tissue compared to the non-transgenic plants. Furthermore, the plants accumulated increased amounts of Cd, Zn, and Pb in the root, because they could establish an extensive root system in mine tailing soil. These results suggest that the generation of YCF1-expressing transgenic poplar represents the first step towards producing plants for phytoremediation. The YCF1-expressing poplar may be useful for phytostabilization and phytoattenuation, especially in highly contaminated regions, where wild-type plants cannot survive.
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Affiliation(s)
- Donghwan Shim
- POSTECH-UZH Global Research Laboratory, Division of Integrative Biology and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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Jung SR, Seo JB, Shim D, Hille B, Koh DS. Actin cytoskeleton controls movement of intracellular organelles in pancreatic duct epithelial cells. Cell Calcium 2012; 51:459-69. [PMID: 22579052 DOI: 10.1016/j.ceca.2012.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 04/06/2012] [Accepted: 04/09/2012] [Indexed: 12/01/2022]
Abstract
In most eukaryotic cells, microtubules and filamentous actin (F-actin) provide tracks on which intracellular organelles move using molecular motors. Here we report that cytoplasmic movement of both mitochondria and lysosomes is slowed by F-actin meshwork formation in pancreatic duct epithelial cells (PDEC). Mitochondria and lysosomes were labeled with fluorescent Mitotracker Red CMXRos and Lysotracker Red DND-99, respectively, and their movements were monitored using epi-fluorescence and confocal microscopy. Mitochondria and lysosomes moving actively at rest stopped rapidly within several seconds after an intracellular Ca(2+) rise induced by activation of P2Y(2) purinergic receptors. The 'freezing' of the organelles was inhibited by blocking the Ca(2+) rise or by pretreatment with latrunculin B, an inhibitor of F-actin formation. Indeed, this freezing effect on the organelles was accompanied by the formation of F-actin in the whole cytoplasm as stained with Alexa 488-phalloidin in fixed PDEC. For real-time monitoring of F-actin formation in live cells, we expressed sGFP-fimbrin actin binding domain2 (fABD2) in PDEC. Rapid recruitment of the fluorescent probe near the nucleus and lysosomes suggested dense F-actin formation around intracellular structures. The development of F-actin paralleled that of organelle freezing. We conclude that rapid Ca(2+)-dependent F-actin formation physically restrains intracellular organelles and reduces their mobility non-selectively in PDEC.
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Affiliation(s)
- Seung-Ryoung Jung
- Department of Physiology and Biophysics, University of Washington, Seattle, 98195, United States
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Suh G, Hong J, Shim D, Kim D, Choi Y. P2.35 A novel mutation of CLCN1(G276C) with variable phenotype of Thomsen disease in a Korean family. Neuromuscul Disord 2010. [DOI: 10.1016/j.nmd.2010.07.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Schilter HC, Pereira ATM, Eschenazi PD, Fernandes A, Shim D, Sousa ALS, Teixeira MM, Negrão-Corrêa D. Regulation of immune responses to Strongyloides venezuelensis challenge after primary infection with different larvae doses. Parasite Immunol 2010; 32:184-92. [PMID: 20398181 DOI: 10.1111/j.1365-3024.2009.01176.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nematode infections are generally followed by high rates of reinfection, leading to elevated prevalence in endemic areas. Therefore, the effective control of nematode infections depends on understanding the induction and regulation of protective mechanisms. However, most experimental models for protective immune response against nematodes use high parasite exposure, not always reflecting what occurs naturally in human populations. In this study, we tested whether infecting mice with different Strongyloides venezuelensis larvae loads would affect protective responses against reinfection. Interestingly, we found that a previous infection with 10-500 larvae conferred high rate of protection against reinfection with S. venezuelensis in mice, by destroying large numbers of migrating larvae. However, low-dose priming did not abolish adult worm maturation, as detected in high-dose primed group. Results also indicated that a previous low-dose infection delayed the development of cellular infiltrate, while a high inoculum rapidly induced these inflammatory features. Cytokine production by splenocyte cultures of challenge infected mice demonstrated that low-dose priming had increased production of IL-4 and IFN-gamma, while high-dose induced IL-4 production but not IFN-gamma. Our data support the hypothesis that low-dose nematode infection does not induce a polarized type-2 immune response, allowing adult worm survival.
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Affiliation(s)
- H C Schilter
- Department of Parasitology, Biological Science Institute of the Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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Shim D, Hwang JU, Lee J, Lee S, Choi Y, An G, Martinoia E, Lee Y. Orthologs of the class A4 heat shock transcription factor HsfA4a confer cadmium tolerance in wheat and rice. Plant Cell 2009; 21:4031-43. [PMID: 20028842 PMCID: PMC2814514 DOI: 10.1105/tpc.109.066902] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 11/16/2009] [Accepted: 11/30/2009] [Indexed: 05/18/2023]
Abstract
Cadmium (Cd) is a widespread soil pollutant; thus, the underlying molecular controls of plant Cd tolerance are of substantial interest. A screen for wheat (Triticum aestivum) genes that confer Cd tolerance to a Cd hypersensitive yeast strain identified Heat shock transcription factor A4a (HsfA4a). Ta HsfA4a is most similar to the class A4 Hsfs from monocots. The most closely related rice (Oryza sativa) homolog, Os HsfA4a, conferred Cd tolerance in yeast, as did Ta HsfA4a, but the second most closely related rice homolog, Os HsfA4d, did not. Cd tolerance was enhanced in rice plants expressing Ta HsfA4a and decreased in rice plants with knocked-down expression of Os HsfA4a. An analysis of the functional domain using chimeric proteins constructed from Ta HsfA4a and Os HsfA4d revealed that the DNA binding domain (DBD) of HsfA4a is critical for Cd tolerance, and within the DBD, Ala-31 and Leu-42 are important for Cd tolerance. Moreover, Ta HsfA4a-mediated Cd resistance in yeast requires metallothionein (MT). In the roots of wheat and rice, Cd stress caused increases in HsfA4a expression, together the MT genes. Our findings thus suggest that HsfA4a of wheat and rice confers Cd tolerance by upregulating MT gene expression in planta.
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Affiliation(s)
- Donghwan Shim
- POSTECH-UZH Global Research Laboratory, Division of Integrative Biology and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Jae-Ung Hwang
- POSTECH-UZH Global Research Laboratory, Division of Integrative Biology and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Joohyun Lee
- POSTECH-UZH Global Research Laboratory, Division of Integrative Biology and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Sichul Lee
- Division of Molecular and Life Science, Biotechnology Research Center, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yunjung Choi
- POSTECH-UZH Global Research Laboratory, Division of Integrative Biology and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Gynheung An
- Division of Molecular and Life Science, Biotechnology Research Center, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Enrico Martinoia
- POSTECH-UZH Global Research Laboratory, Division of Integrative Biology and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, Korea
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Youngsook Lee
- POSTECH-UZH Global Research Laboratory, Division of Integrative Biology and Biotechnology, Pohang University of Science and Technology, Pohang, 790-784, Korea
- Address correspondence to
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Kim YY, Kim DY, Shim D, Song WY, Lee J, Schroeder JI, Kim S, Moran N, Lee Y. Expression of the novel wheat gene TM20 confers enhanced cadmium tolerance to bakers' yeast. J Biol Chem 2008; 283:15893-902. [PMID: 18411273 DOI: 10.1074/jbc.m708947200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cadmium causes the generation of reactive oxygen species, which in turn causes cell damage. We isolated a novel gene from a wheat root cDNA library, which conferred Cd(II)-specific tolerance when expressed in yeast (Saccharomyces cerevisiae). The gene, which we called TaTM20, for Triticum aestivum transmembrane 20, encodes a putative hydrophobic polypeptide of 889 amino acids, containing 20 transmembrane domains arranged as a 5-fold internal repeating unit of 4 transmembrane domains each. Expression of TaTM20 in yeast cells stimulated Cd(II) efflux resulting in a decrease in the content of yeast intracellular cadmium. TaTM20-induced Cd(II) tolerance was maintained in yeast even under conditions of reduced GSH. These results demonstrate that TaTM20 enhances Cd(II) tolerance in yeast through the stimulation of Cd(II) efflux from the cell, partially independent of GSH. Treatment of wheat seedlings with Cd(II) induced their expression of TaTM20, decreasing subsequent root Cd(II) accumulation and suggesting a possible role for TaTM20 in Cd(II) tolerance in wheat.
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Affiliation(s)
- Yu-Young Kim
- POSTECH-UZH Cooperative Laboratory, Division of Molecular Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
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Vogel GL, Shim D, Schumacher GE, Carey CM, Chow LC, Takagi S. Salivary Fluoride from Fluoride Dentifrices or Rinses after Use of a Calcium Pre-Rinse or Calcium Dentifrice. Caries Res 2006; 40:449-54. [PMID: 16946616 DOI: 10.1159/000094293] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 11/30/2005] [Indexed: 11/19/2022] Open
Abstract
The low concentration of available calcium (Ca) in oral fluids limits the formation of Ca-mediated fluoride deposits that maintain oral fluoride (F) after a topical F treatment. The purpose of this study was to examine if a high concentration of Ca would increase salivary F when used before a F rinse or dentifrice. We found that a Ca pre-rinse (150 mmol/l Ca lactate) or Ca dentifrice (0.084 g Ca glycerolphosphate per gram dentifrice) used immediately before a 60 s 228-ppm F rinse (12 mmol/l NaF) produced a 4.6x or 3.6x increase (p < 0.05) respectively in the 1 h salivary F concentrations over the F rinse alone. Reducing the post-Ca F rinse to 10 s still produced a significant 2.2x increase in salivary F compared to the 60 s F rinse alone. Used with a conventional 1,100 ppm F (i.e. 1,100 microg F per gram) NaF dentifrice (Crest), the above Ca pre-rinse increased 1 h salivary F levels by 2.3x over the F dentifrice alone. However, a F rinse given before a Ca rinse produced no increase in 1 h salivary F concentrations. Although the persistence of these increases requires further study, these results suggest that a moderately high concentration of Ca given shortly before a F rinse or F dentifrice may increase the cariostatic effect of the F product.
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Affiliation(s)
- G L Vogel
- American Dental Association Foundation, Paffenbarger Research Center, Gaithersburg, MD 20899-8546, USA.
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Abstract
Endostatin is a tumor-derived angiogenesis inhibitor, and the endogenous 20 kDa carboxyl-terminal fragment of collagen XVIII. In addition to inhibiting angiogenesis,endostatin inhibits tumor growth and the induction of apoptosis in several endothelial cell types. However, the mechanisms that regulate endostatin-induced apoptotic cell death are unclear. Here, we investigated apoptotic cell death and the underlying regulatory mechanisms elicited of endostatin in human umbilical vein endothelial cells (HUVECs). Endostatin was found to induce typical apoptotic features, such as, chromatin condensation and DNA fragmentation in these cells. Thus, as the phosphoinositide 3-OH kinase (PI3K)/protein kinase B (PKB) signaling pathway has been shown to prevent apoptosis in various cell types, we investigated whether this pathway could protect cells against endostatin induced apoptosis. It was found that the inhibition of PI3K/PKB significantly increased endostatin-induced apoptosis, and that endostatininduced cell death is physiologically linked to PKB-mediated cell survival through caspase-8.
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Affiliation(s)
- Hee Young Kang
- Division of Life Sciences, Chungbuk National University, Cheongju, 361-763, Korea
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Shim D, Kang HY, Jeon BW, Kang SS, Chang SI, Kim HY. Protein kinase B inhibits apoptosis induced by actinomycin D in ECV304 cells through phosphorylation of caspase 8. Arch Biochem Biophys 2004; 425:214-20. [PMID: 15111130 DOI: 10.1016/j.abb.2004.03.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Revised: 03/17/2004] [Indexed: 10/26/2022]
Abstract
Actinomycin D (act-D) anchors itself into DNA-base pairs by intercalation and thereby inhibits mRNA synthesis. It has been well established that act-D elicits apoptosis in various cell types involving endothelial cells. However, the regulatory mechanisms of actinomycin D-induced apoptotic cell death still remain unclear. Here, we investigated apoptotic cell death and its underlying regulatory mechanisms elicited by actinomycin D in ECV304. Act-D induced typical apoptotic features including chromatin condensation and translocation of phosphatidylserine. Since the phosphoinositide 3-OH kinase (PI3K)/protein kinase B (PKB) signaling pathway has been shown to prevent apoptosis in various cell types, it was of interest to determine if this pathway could protect against apoptosis induced by act-D. Inhibition of PI3K/PKB significantly increased act-D-induced apoptosis. Moreover, act-D-induced cell death was physiologically linked to PKB-mediated cell survival through caspase-8. These results suggest that cross-talk between the PKB and caspase-8 pathways may regulate the balance between cell survival and cell death in ECV304.
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Affiliation(s)
- Donghwan Shim
- Division of Life Sciences, Chungbuk National University, Cheongju 361-763, Republic of Korea
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Song WY, Martinoia E, Lee J, Kim D, Kim DY, Vogt E, Shim D, Choi KS, Hwang I, Lee Y. A novel family of cys-rich membrane proteins mediates cadmium resistance in Arabidopsis. Plant Physiol 2004; 135:1027-39. [PMID: 15181212 PMCID: PMC514137 DOI: 10.1104/pp.103.037739] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 02/13/2004] [Accepted: 02/19/2004] [Indexed: 05/20/2023]
Abstract
Cadmium (Cd) is a widespread pollutant that is toxic to plant growth. However, only a few genes that contribute to Cd resistance in plants have been identified. To identify additional Cd(II) resistance genes, we screened an Arabidopsis cDNA library using a yeast (Saccharomyces cerevisiae) expression system employing the Cd(II)-sensitive yeast mutant ycf1. This screening process yielded a small Cys-rich membrane protein (Arabidopsis plant cadmium resistance, AtPcrs). Database searches revealed that there are nine close homologs in Arabidopsis. Homologs were also found in other plants. Four of the five homologs that were tested also increased resistance to Cd(II) when expressed in ycf1. AtPcr1 localizes at the plasma membrane in both yeast and Arabidopsis. Arabidopsis plants overexpressing AtPcr1 exhibited increased Cd(II) resistance, whereas antisense plants that showed reduced AtPcr1 expression were more sensitive to Cd(II). AtPcr1 overexpression reduced Cd uptake by yeast cells and also reduced the Cd contents of both yeast and Arabidopsis protoplasts treated with Cd. Thus, it appears that the Pcr family members may play an important role in the Cd resistance of plants.
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Affiliation(s)
- Won-Yong Song
- National Research Laboratory of Phytoremediation, Division of Molecular Life Science, POSTECH, Pohang, 790-784, Korea
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Lee J, Shim D, Song WY, Hwang I, Lee Y. Arabidopsis metallothioneins 2a and 3 enhance resistance to cadmium when expressed in Vicia faba guard cells. Plant Mol Biol 2004; 54:805-15. [PMID: 15604653 DOI: 10.1007/s11103-004-0190-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The Arabidopsis metallothionein genes AtMT1 and AtMT2 confer Cd(II) resistance to Cd(II)-sensitive yeast, but it has not been directly shown whether they or other metallothioneins provide the same protection to plants. We tested whether AtMT2a and AtMT3 can confer Cd(II) resistance to plant cells by introducing GFP- or RFP-fused forms into guard cells of Vicia faba by biolistic bombardment. AtMT2a and AtMT3 protected guard cell chloroplasts from degradation upon exposure to Cd(II), an effect that was confirmed using an FDA assay to test the viability of the exposed guard cells. AtMT2a- and AtMT3-GFP were localized in the cytoplasm both before and after treatment of V. faba guard cells or Arabidopsis protoplasts with Cd(II), and the levels of reactive oxygen species were lower in transformed guard cells than in non-transformed cells after Cd(II)-treatment. These results suggest that the Cd(II)-detoxification mechanism of AtMT2a and AtMT3 may not include sequestration into vacuoles or other organelles, but does involve reduction of the level of reactive oxygen species in Cd(II)-treated cells. Increased expression of AtMT2a and AtMT3 was observed in Arabidopsis seedlings exposed to Cd(II). Together, these data support a role for the metallothioneins AtMT2a and AtMT3 in Cd(II) resistance in intact plant cells.
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Affiliation(s)
- Joohyun Lee
- National Research Laboratory of Phytoremediation, Division of Molecular Life Sciences, Pohang University of Science and Technology, Korea
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George JC, Shim D, Bucuvalas JC, Immerman E, Manning PB, Pearl JM, Beekman RH. Cost-effectiveness of coarctation repair strategies: endovascular stenting versus surgery. Pediatr Cardiol 2003; 24:544-7. [PMID: 12881774 DOI: 10.1007/s00246-003-0496-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The cost-effectiveness of stent (ST) implantation for the repair of coarctation of the aorta (CoA) is not documented in the medical literature. Inflation-adjusted hospital costs for ST implantation and for surgical (SU) repair were obtained using the HBOC Cost Accounting System software and evaluated for all patients 5 years of age or older who underwent elective treatment of CoA between July 1997 and June 2001. The average age of the ST group (n = 10) to 9.5 +/- 3.5 years for the SU group (n = 12) (p > 0.10). The ST group had one failure due to inability to cross the CoA (failure rate, 10%). Successful repair was accomplished in all other ST cases and in all SU cases, with no residual systolic gradients at 1-year follow-up. Hospital length of stay for the ST group was 0.8 +/- 1.2 days compared to 3.5 +/- 0.5 days for the SU group (p < 0.001). The mean inflation-adjusted cost for the ST group was dollar 7,148 +/- 2,984 versus dollar 11,769 +/- 3,702 for the SU group (p < 0.005). By intention to treat analysis, the cost of repair in the ST-first group was dollar 8,325 +/- 3,354 given the 10% failure rate (p < 0.04 vs the SU only group). Sensitivity analysis demonstrates that cost of repair is lower with the ST-first strategy compared to SU only until the failure rate of ST implantation exceeds 39%. Repair of CoA using an endovascular stent strategy is cost-effective compared to conventional surgical repair.
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Affiliation(s)
- J C George
- The Heart Center, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
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Affiliation(s)
- D Shim
- The Heart Center, Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.
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