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Bae EK, Choi H, Choi JW, Lee H, Kim SG, Ko JH, Choi YI. Efficient knockout of the phytoene desaturase gene in a hybrid poplar (Populus alba × Populus glandulosa) using the CRISPR/Cas9 system with a single gRNA. Transgenic Res 2021; 30:837-849. [PMID: 34259977 DOI: 10.1007/s11248-021-00272-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/18/2021] [Indexed: 10/20/2022]
Abstract
The CRISPR/Cas9 system has been used for genome editing in several plant species; however, there are few reports on its use in trees. Here, CRISPR/Cas9 was used to mutate a target gene in Populus alba × Populus glandulosa hybrid poplars. The hybrid poplar is routinely used in molecular biological studies due to the well-established Agrobacterium-mediated transformation method. A single guide RNA (sgRNA) with reported high mutation efficiency in other popular species was designed with a protospacer adjacent motif sequence for the phytoene desaturase 1 (PagPDS1) gene. The pHSE/Cas9-PagPDS1 sgRNA vector was delivered into hybrid poplar cells using Agrobacterium-mediated transformation. The transgenic plants were propagated and classified them into three groups according to their phenotypes. Among a total of 110 lines of transgenic hybrid poplars, 82 lines showed either an albino or a pale green phenotype, indicating around 74.5% phenotypic mutation efficiency of the PagPDS1 gene. The albino phenotypes were observed when the CRISPR/Cas9-mediated mutations in both PagPDS1 alleles in the transgenic plants. There was no off-target modification of the PagPDS2 gene, which has a potential sgRNA target sequence with two mismatches. The results confirmed that the sgRNA can specifically edit PagPDS1 rather than PagPDS2, indicating that CRISPR/Cas9-mediated genome editing can effectively induce target mutations in the hybrid poplar. This technique will be useful to improve tree quality in hybrid poplars (P. alba × P. glandulosa); for example, by enhancing biomass or stress tolerance.
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Affiliation(s)
- Eun-Kyung Bae
- Forest Bioresources Department, National Institute of Forest Science, 39 Onjeong-ro, Gwonseon-gu, Suwon, 16631, Korea
| | - Hyunmo Choi
- Forest Biomaterials Research Center, National Institute of Forest Science, 672 Jinju-daero, Jinju, 52817, Korea
| | - Ji Won Choi
- Forest Bioresources Department, National Institute of Forest Science, 39 Onjeong-ro, Gwonseon-gu, Suwon, 16631, Korea
| | - Hyoshin Lee
- Forest Bioresources Department, National Institute of Forest Science, 39 Onjeong-ro, Gwonseon-gu, Suwon, 16631, Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Korea
| | - Jae-Heung Ko
- Plant and Environmental New Resources, Kyung Hee University, 1732 Deongyeong-daero, Giheung-gu, Yongin, 17104, Korea
| | - Young-Im Choi
- Forest Bioresources Department, National Institute of Forest Science, 39 Onjeong-ro, Gwonseon-gu, Suwon, 16631, Korea.
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A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers. Int J Genomics 2021; 2021:6652508. [PMID: 34212028 PMCID: PMC8208876 DOI: 10.1155/2021/6652508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/20/2022] Open
Abstract
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
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Park J, Xi H, Kim Y. The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana. Int J Genomics 2020; 2020:3236461. [PMID: 32964010 PMCID: PMC7492873 DOI: 10.1155/2020/3236461] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 01/18/2023] Open
Abstract
Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Inc., 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, 301 Room, 670, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
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Kim HJ, Hwang JY, Park KJ, Park HC, Kang HE, Park J, Sohn HJ. The complete mitochondrial genome of Cervus canadensis (Erxleben, 1777), as a model species of Chronic Wasting Disease (CWD). Mitochondrial DNA B Resour 2020; 5:2621-2623. [PMID: 33457884 PMCID: PMC7782213 DOI: 10.1080/23802359.2020.1780983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/06/2020] [Indexed: 11/16/2022] Open
Abstract
Cervus canadensis (Erxleben, 1777) has been used as a model species of Chronic Wasting Disease (CWD). We completed the mitochondrial genome of C. canadensis, susceptible to the CWD. Its length is 16,428 bp, identical to the previous mitochondrial genome of C. canadensis nannodes, and 37 genes (13 protein-coding genes, two rRNAs, and 22 tRNAs) were identified. It may reflect the extreme decrease of tule elk population in 1870s and CWD is not related to genetic elements on mitochondrial genome. Phylogenetic trees show that our mitochondrial genome is clustered with the previously sequenced mitochondrial genome of C. canadensis nannodes .
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Affiliation(s)
- Hyo-Jin Kim
- Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency (APQA), OIE Reference Laboratory for CWD, Gimcheon, Korea
| | - Ji-Yong Hwang
- Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency (APQA), OIE Reference Laboratory for CWD, Gimcheon, Korea
| | - Kyung-Je Park
- Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency (APQA), OIE Reference Laboratory for CWD, Gimcheon, Korea
| | - Hoo-Chang Park
- Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency (APQA), OIE Reference Laboratory for CWD, Gimcheon, Korea
| | - Hae-Eun Kang
- Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency (APQA), OIE Reference Laboratory for CWD, Gimcheon, Korea
| | - Jongsun Park
- InfoBoss Inc, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Hyun-Joo Sohn
- Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency (APQA), OIE Reference Laboratory for CWD, Gimcheon, Korea
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Park J, Kim Y, Xi H, Heo KI, Min J, Woo J, Lee D, Seo Y, Kim YH. The complete chloroplast genomes of two cold hardness coffee trees, Coffea arabica L. (Rubiaceae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1715883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Kyoung-In Heo
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Juhyeon Min
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongwook Woo
- Stronghold Technology, Inc, Seoul, Republic of Korea
| | - Dukgou Lee
- Stronghold Technology, Inc, Seoul, Republic of Korea
| | - Youmi Seo
- Stronghold Technology, Inc, Seoul, Republic of Korea
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Kwon W, Kim Y, Park J. The complete mitochondrial genome of Dumortiera hirsuta (Sw.) Nees (Dumortieraceae, Marchantiophyta). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1596767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Woochan Kwon
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Park J, Kim Y, Xi H. The complete chloroplast genome sequence of male individual of Korean endemic willow, Salix koriyanagi Kimura ex Goerz (Salicaceae). MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1602012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Hong Xi
- InfoBoss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
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Kwon W, Min J, Xi H, Park J. The complete chloroplast genome of Riccia fluitans L. (Ricciaceae, Marchantiophyta). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1613193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Woochan Kwon
- InfoBoss Co., Ltd., Seoul, Gangnam-gu, Republic of Korea
- InfoBoss Research Center, Seoul, Gangnam-gu, Republic of Korea
| | - Juhyeon Min
- InfoBoss Co., Ltd., Seoul, Gangnam-gu, Republic of Korea
- InfoBoss Research Center, Seoul, Gangnam-gu, Republic of Korea
| | - Hong Xi
- InfoBoss Co., Ltd., Seoul, Gangnam-gu, Republic of Korea
- InfoBoss Research Center, Seoul, Gangnam-gu, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Gangnam-gu, Republic of Korea
- InfoBoss Research Center, Seoul, Gangnam-gu, Republic of Korea
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