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Zhao N, Ding X, Tian C, Wang S, Xie S, Zou H, Liu H, Chen J, Lian Liang X, Huang L. Transcriptional landscape of sweetpotato root tip development at the single-cell level. BMC PLANT BIOLOGY 2024; 24:952. [PMID: 39394068 DOI: 10.1186/s12870-024-05574-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 09/05/2024] [Indexed: 10/13/2024]
Abstract
Single-cell transcriptome sequencing (scRNA-seq) is a powerful tool for describing the transcriptome dynamics of plant development but has not yet been utilized to analyze the tissue ontology of sweetpotato. This study established a stable method for isolating single protoplast cells for scRNA-seq to reveal the cell heterogeneity of sweetpotato root tip meristems at the single-cell level. The study analyzed 12,172 single cells and 27,355 genes in the root tips of the sweetpotato variety Guangshu 87, which were distributed into 15 cell clusters. Pseudo-time analysis showed that there were transitional cells in the apical development trajectory of mature cell types from stem cell niches. Furthermore, we identified novel development regulators of sweetpotato tubers via trajectory analysis. The transcription factor IbGATA4 was highly expressed in the adventitious roots during the development of sweetpotato root tips, where it may regulate the development of sweetpotato root tips. In addition, significant differences were observed in the transcriptional profiles of cell types between sweetpotato, Arabidopsis thaliana, and maize. This study mapped the single-cell transcriptome of sweetpotato root tips, laying a foundation for studying the types, functions, differentiation, and development of sweetpotato root tip cells.
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Affiliation(s)
- Nan Zhao
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510000, Guangdong, China
| | - Xiawei Ding
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China
- College of Agriculture, South China Agricultural University, Guangzhou, 510000, Guangdong, China
| | - CaiHuan Tian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shixin Wang
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510000, Guangdong, China
| | - Shuyan Xie
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China
| | - Hongda Zou
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China
| | - Hao Liu
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China
| | - Jingyi Chen
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China
| | - Xue Lian Liang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510000, Guangdong, China.
| | - Lifei Huang
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510000, Guangdong, China.
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Wang R, Lan Z, Luo Y, Deng Z. The complete Chloroplast genome of Stachys geobombycis and comparative analysis with related Stachys species. Sci Rep 2024; 14:8523. [PMID: 38609472 PMCID: PMC11014926 DOI: 10.1038/s41598-024-59132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Herb genomics, at the forefront of traditional Chinese medicine research, combines genomics with traditional practices, facilitating the scientific validation of ancient remedies. This integration enhances public understanding of traditional Chinese medicine's efficacy and broadens its scope in modern healthcare. Stachys species encompass annual or perennial herbs or small shrubs, exhibiting simple petiolate or sessile leaves. Despite their wide-ranging applications across various fields, molecular data have been lacking, hindering the precise identification and taxonomic elucidation of Stachys species. To address this gap, we assembled the complete chloroplast (CP) genome of Stachys geobombycis and conducted reannotation and comparative analysis of seven additional species within the Stachys genus. The findings demonstrate that the CP genomes of these species exhibit quadripartite structures, with lengths ranging from 14,523 to 150,599 bp. Overall, the genome structure remains relatively conserved, hosting 131 annotated genes, including 87 protein coding genes, 36 tRNA genes, and 8 rRNA genes. Additionally, 78 to 98 SSRs and long repeat sequences were detected , and notably, 6 highly variable regions were identified as potential molecular markers in the CP genome through sequence alignment. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Stachys as a member of Stachydeae tribe. Overall, this comprehensive bioinformatics study of Stachys CP genomes lays the groundwork for phylogenetic classification, plant identification, genetic engineering, evolutionary studies, and breeding research concerning medicinal plants within the Stachys genus.
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Affiliation(s)
- Ru Wang
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
| | - Zheng Lan
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yongjian Luo
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China
- Central South University of Forestry and Technology, Key Laboratory of Forestry Biotechnology of Hunan Province, Changsha, 410000, China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, 445000, China.
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Mu F, Zheng H, Zhao Q, Zhu M, Dong T, Kai L, Li Z. Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato. BMC PLANT BIOLOGY 2024; 24:193. [PMID: 38493089 PMCID: PMC10944623 DOI: 10.1186/s12870-024-04824-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/14/2024] [Indexed: 03/18/2024]
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.
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Affiliation(s)
- Fangfang Mu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Hao Zheng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Qiaorui Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China.
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Kim TH, Kim S, Park W, Woo KS, Lee K, Chung MN, Lee YH, Lee HU, Lee KH, Nam SS, Jo H, Lee JD. Genome-wide association study to identify novel loci and genes for Fusarium root rot resistance in sweet potato using genotyping-by-sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1251157. [PMID: 37860237 PMCID: PMC10584150 DOI: 10.3389/fpls.2023.1251157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Fusarium root rot, caused by Fusarium solani, is a major post-harvest disease in sweet potatoes (Ipomoea batatas (L.) Lam.). An effective strategy for controlling this disease is the development of resistant varieties. In this study, a genome-wide association study (GWAS) was conducted on 96 sweet potato genotypes to identify novel candidate loci and dissect the genetic basis of Fusarium root rot resistance. Genotyping was performed using genotyping-by-sequencing (GBS), and 44,255 SNPs were identified after filtering. The genotypes (n = 96) were evaluated through resistance tests in 2021 and 2022, separately and combined. The GWAS identified two significant SNP markers (LG3_22903756 and LG4_2449919) on chromosomes 3 and 4 associated with Fusarium root rot resistance, respectively. Lesion length showed significant differences between homozygous A and G alleles of LG3_22903756, which can potentially be used to develop molecular markers for selecting accessions resistant to Fusarium root rot. Expression analysis of 11 putative genes flanking the significant SNPs revealed the alteration in the expression of nine genes, indicating their possible involvement in Fusarium root rot resistance. The results of this study will aid in the marker-assisted selection and functional analysis of candidate genes for Fusarium root rot resistance in sweet potatoes.
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Affiliation(s)
- Tae Hwa Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sujung Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Won Park
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Koan Sik Woo
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Keunpyo Lee
- International Technology Cooperation Center, Technology Cooperation Bureau, Rural Development Administration, Jeonju, Republic of Korea
| | - Mi Nam Chung
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Young Hoon Lee
- Planning and Coordination Division, National Institute of Crop Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Hyeong-Un Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Kyo Hwui Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Sang-Sik Nam
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea
| | - Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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Li M, Zhou Y, Li K, Guo H. Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1731. [PMID: 37111954 PMCID: PMC10140993 DOI: 10.3390/plants12081731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.
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Affiliation(s)
- Maoxing Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Yuanping Zhou
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Kaifeng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Huachun Guo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
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6
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Genome-Wide Identification and Expression Analysis of the Xyloglucan Endotransglucosylase/Hydrolase Gene Family in Sweet Potato [ Ipomoea batatas (L.) Lam]. Int J Mol Sci 2023; 24:ijms24010775. [PMID: 36614218 PMCID: PMC9820959 DOI: 10.3390/ijms24010775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
The xyloglucan endotransglucosylase/hydrolase (XET/XEH, also named XTH) family is a multigene family, the function of which plays a significant role in cell-wall rebuilding and stress tolerance in plants. However, the specific traits of the XTH gene family members and their expression pattern in different tissues and under stress have not been carried out in sweet potato. Thirty-six XTH genes were identified in I. batatas, all of which had conserved structures (Glyco_hydro_16). Based on Neighbor-Joining phylogenetic analysis the IbXTHs can be divided into three subfamilies-the I/II, IIIA, and IIIB subfamilies, which were unevenly distributed on 13 chromosomes, with the exception of Chr9 and Chr15. Multiple cis-acting regions related to growth and development, as well as stress responses, may be found in the IbXTH gene promoters. The segmental duplication occurrences greatly aided the evolution of IbXTHs. The results of a collinearity analysis showed that the XTH genes of sweet potato shared evolutionary history with three additional species, including A. thaliana, G. max, and O. sativa. Additionally, based on the transcriptome sequencing data, the results revealed that the IbXTHs have different expression patterns in leaves, stems, the root body (RB), the distal end (DE), the root stock (RS), the proximal end (PE), the initiative storage root (ISR), and the fibrous root (FR), and many of them are well expressed in the roots. Differentially expressed gene (DEG) analysis of FRs after hormone treatment of the roots indicated that IbXTH28 and IbXTH30 are up-regulated under salicylic acid (SA) treatment but down-regulated under methyl jasmonate (MeJA) treatment. Attentionally, there were only two genes showing down-regulation under the cold and drought treatment. Collectively, all of the findings suggested that genes from the XTH family are crucial for root specificity. This study could provide a theoretical basis for further research on the molecular function of sweet potato XTH genes.
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Tayşi N, Kaymaz Y, Ateş D, Sari H, Toker C, Tanyolaç MB. Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris. Sci Rep 2022; 12:15068. [PMID: 36064865 PMCID: PMC9445179 DOI: 10.1038/s41598-022-17877-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/02/2022] [Indexed: 12/05/2022] Open
Abstract
Lens is a member of the Papilionoideae subfamily of Fabaceae and is generally used as a source of vegetable protein as part of human diets in many regions worldwide. Chloroplast (cp) genomes are highly active genetic components of plants and can be utilized as molecular markers for various purposes. As one of the wild lentil species, the Lens ervoides cp genome has been sequenced for the first time in this study using next-generation sequencing. The de novo assembly of the cp genome resulted in a single 122,722 bp sequence as two separate coexisting structural haplotypes with similar lengths. Results indicated that the cp genome of L. ervoides belongs to the inverted repeat lacking clade. Several noteworthy divergences within the coding regions were observed in ndhB, ndhF, rbcL, rpoC2, and ycf2 genes. Analysis of relative synonymous codon usage showed that certain genes, psbN, psaI, psbI, psbE, psbK, petD, and ndhC, preferred using biased codons more often and therefore might have elevated expression and translation efficiencies. Overall, this study exhibited the divergence level between the wild-type and cultured lentil cp genomes and pointed to certain regions that can be utilized as distinction markers for various goals.
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Affiliation(s)
- Nurbanu Tayşi
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Yasin Kaymaz
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Duygu Ateş
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - M Bahattin Tanyolaç
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey.
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Li M, Chen L, Lang T, Qu H, Zhang C, Feng J, Pu Z, Peng M, Lin H. Genome-Wide Identification and Expression Analysis of Expansin Gene Family in the Storage Root Development of Diploid Wild Sweetpotato Ipomoea trifida. Genes (Basel) 2022; 13:genes13061043. [PMID: 35741805 PMCID: PMC9222398 DOI: 10.3390/genes13061043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Expansins play important roles in root growth and development, but investigation of the expansin gene family has not yet been reported in Ipomoea trifida, and little is known regarding storage root (SR) development. In this work, we identified a total of 37 expansins (ItrEXPs) in our previously reported SR-forming I. trifida strain Y22 genome, which included 23 ItrEXPAs, 4 ItrEXPBs, 2 ItrEXLAs and 8 ItrEXLBs. The phylogenetic relationship, genome localization, subcellular localization, gene and protein structure, promoter cis-regulating elements, and protein interaction network were systematically analyzed to reveal the possible roles of ItrEXPs in the SR development of I. trifida. The gene expression profiling in Y22 SR development revealed that ItrEXPAs and ItrEXLBs were down-regulated, and ItrEXPBs were up-regulated while ItrEXLAs were not obviously changed during the critical period of SR expansion, and might be beneficial to SR development. Combining the tissue-specific expression in young SR transverse sections of Y22 and sweetpotato tissue, we deduced that ItrEXLB05, ItrEXLB07 and ItrEXLB08 might be the key genes for initial SR formation and enlargement, and ItrEXLA02 might be the key gene for root growth and development. This work provides new insights into the functions of the expansin gene family members in I. trifida, especially for EXLA and EXLB subfamilies genes in SR development.
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Affiliation(s)
- Ming Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; (T.L.); (H.Q.); (C.Z.); (J.F.); (Z.P.)
| | - Lianfu Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Tao Lang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; (T.L.); (H.Q.); (C.Z.); (J.F.); (Z.P.)
| | - Huijuan Qu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; (T.L.); (H.Q.); (C.Z.); (J.F.); (Z.P.)
| | - Cong Zhang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; (T.L.); (H.Q.); (C.Z.); (J.F.); (Z.P.)
| | - Junyan Feng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; (T.L.); (H.Q.); (C.Z.); (J.F.); (Z.P.)
| | - Zhigang Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; (T.L.); (H.Q.); (C.Z.); (J.F.); (Z.P.)
| | - Meifang Peng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; (T.L.); (H.Q.); (C.Z.); (J.F.); (Z.P.)
- Correspondence: (M.P.); (H.L.)
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
- Correspondence: (M.P.); (H.L.)
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Yang Z, Ni Y, Lin Z, Yang L, Chen G, Nijiati N, Hu Y, Chen X. De novo assembly of the complete mitochondrial genome of sweet potato (Ipomoea batatas [L.] Lam) revealed the existence of homologous conformations generated by the repeat-mediated recombination. BMC PLANT BIOLOGY 2022; 22:285. [PMID: 35681138 PMCID: PMC9185937 DOI: 10.1186/s12870-022-03665-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 05/27/2023]
Abstract
Sweet potato (Ipomoea batatas [L.] Lam) is an important food crop, an excellent fodder crop, and a new type of industrial raw material crop. The lack of genomic resources could affect the process of industrialization of sweet potato. Few detailed reports have been completed on the mitochondrial genome of sweet potato. In this research, we sequenced and assembled the mitochondrial genome of sweet potato and investigated its substructure. The mitochondrial genome of sweet potato is 270,304 bp with 23 unique core genes and 12 variable genes. We detected 279 pairs of repeat sequences and found that three pairs of direct repeats could mediate the homologous recombination into four independent circular molecules. We identified 70 SSRs in the whole mitochondrial genome of sweet potato. The longest dispersed repeat in mitochondrial genome was a palindromic repeat with a length of 915 bp. The homologous fragments between the chloroplast and mitochondrial genome account for 7.35% of the mitochondrial genome. We also predicted 597 RNA editing sites and found that the rps3 gene was edited 54 times, which occurred most frequently. This study further demonstrates the existence of multiple conformations in sweet potato mitochondrial genomes and provides a theoretical basis for the evolution of higher plants and cytoplasmic male sterility breeding.
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Affiliation(s)
- Zhijian Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Ni
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zebin Lin
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Liubin Yang
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Guotai Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Nuerla Nijiati
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Yunzhuo Hu
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
| | - Xuanyang Chen
- Key Laboratory of Crop Biotechnology, Fujian Agriculture and Forestry University, Fujian Province Universities, Fuzhou, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fuzhou, Fujian China
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Obata N, Tabuchi H, Kurihara M, Yamamoto E, Shirasawa K, Monden Y. Mapping of Nematode Resistance in Hexaploid Sweetpotato Using an Next-Generation Sequencing-Based Association Study. FRONTIERS IN PLANT SCIENCE 2022; 13:858747. [PMID: 35371138 PMCID: PMC8972059 DOI: 10.3389/fpls.2022.858747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The southern root-knot nematode (SRKN; Meloidogyne incognita) is a typical parasitic nematode that affects sweetpotato [Ipomoea batatas (L.) Lam.], causing a significant decrease in crop yield and commercial value. In Japan, the SRKN is classified into 10 races: SP1-SP5, SP6-1, SP6-2, and SP7-SP9, with the dominant race differing according to the cultivation area. Soil insecticides have previously been used to reduce the soil density of SRKNs; however, this practice is both costly and labor intensive. Therefore, the development of SRKN-resistant sweetpotato lines and cultivars is necessary. However, due to the complexity of polyploid inheritance and the highly heterogeneous genomic composition of sweetpotato, genetic information and research for this species are significantly lacking compared to those for other major diploid crop species. In this study, we utilized the recently developed genome-wide association approach, which uses multiple-dose markers to assess autopolyploid species. We performed an association analysis to investigate resistance toward SRKN-SP2, which is the major race in areas with high sweetpotato production in Japan. The segregation ratio of resistant and susceptible lines in the F1 mapping population derived from the resistant "J-Red" and susceptible "Choshu" cultivars was fitted to 1: 3, suggesting that resistance to SP2 may be regulated by two loci present in the simplex. By aligning the double digest restriction-site associated DNA sequencing reads to the published Ipomoea trifida reference sequence, 46,982 single nucleotide polymorphisms (SNPs) were identified (sequencing depth > 200). The association study yielded its highest peak on chromosome 7 (Chr07) and second highest peak on chromosome 3 (Chr03), presenting as a single-dose in both loci. Selective DNA markers were developed to screen for resistant plants using the SNPs identified on Chr03 and Chr07. Our results showed that SRKN-SP2-resistant plants were selected with a probability of approximately 70% when combining the two selective DNA markers. This study serves as a model for the identification of genomic regions that control agricultural traits and the elucidation of their effects, and is expected to greatly advance marker-assisted breeding and association studies in polyploid crop species.
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Affiliation(s)
- Nozomi Obata
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Hiroaki Tabuchi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Miyu Kurihara
- Faculty of Agriculture, Okayama University, Okayama, Japan
| | - Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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11
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Arisha MH, Ahmad MQ, Tang W, Liu Y, Yan H, Kou M, Wang X, Zhang Y, Li Q. RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato. Sci Rep 2020; 10:12573. [PMID: 32724138 PMCID: PMC7387466 DOI: 10.1038/s41598-020-69232-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 07/02/2020] [Indexed: 11/09/2022] Open
Abstract
Purple-fleshed sweet potato (PFSP) is an important food crop, as it is a rich source of nutrients and anthocyanin pigments. Drought has become a major threat to sustainable sweetpotato production, resulting in huge yield losses. Therefore, the present study was conducted to identify drought stress-responsive genes using next-generation (NGS) and third-generation sequencing (TGS) techniques. Five cDNA libraries were constructed from seedling leaf segments treated with a 30% solution of polyethylene glycol (PEG-6000) for 0, 1, 6, 12, and 48 h for second-generation sequencing. Leaf samples taken from upper third of sweet potato seedlings after 1, 6, 12, and 48 h of drought stress were used for the construction of cDNA libraries for third-generation sequencing; however, leaf samples from untreated plants were collected as controls. A total of 184,259,679 clean reads were obtained using second and third-generation sequencing and then assembled into 17,508 unigenes with an average length of 1,783 base pairs. Out of 17,508 unigenes, 642 (3.6%) unigenes failed to hit any homologs in any databases, which might be considered novel genes. A total of 2, 920, 1578, and 2,418 up-regulated unigenes and 3,834, 2,131, and 3,337 down-regulated unigenes from 1 h, 6 h, 12 h, and 48 h library were identified, respectively in drought stress versus control. In addition, after 6, 12, and 48 h of drought stress, 540 up-regulated unigenes, 486 down-regulated unigenes and 414 significantly differentially expressed unigenes were detected. It was found that several gene families including Basic Helix-loop-helix (bHLH), basic leucine zipper (bZIP), Cystein2/Histidine2 (C2H2), C3H, Ethylene-responsive transcription factor (ERF), Homo domain-leucine zipper (HD-ZIP), MYB, NAC (NAM, ATAF1/2, and CUC2), Thiol specific antioxidant and WRKY showed responses to drought stress. In total, 17,472 simple sequence repeats and 510,617 single nucleotide polymorphisms were identified based on transcriptome sequencing of the PFSP. About 96.55% of the obtained sequences are not available online in sweet potato genomics resources. Therefore, it will enrich annotated sweet potato gene sequences and enhance understanding of the mechanisms of drought tolerance through genetic manipulation. Moreover, it represents a sequence resource for genetic and genomic studies of sweet potato.
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Affiliation(s)
- Mohamed Hamed Arisha
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China. .,Department of Horticulture, Faculty of Agriculture, Zagazig University, Sharkia, 44511, Egypt.
| | - Muhammad Qadir Ahmad
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China.,Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 60000, Pakistan
| | - Wei Tang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Yaju Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Hui Yan
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Meng Kou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Qiang Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Key Laboratory of Biology and Genetic Breeding of Sweetpotato/Ministry of Agriculture and Rural Affairs/Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China.
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12
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Sasai R, Tabuchi H, Shirasawa K, Kishimoto K, Sato S, Okada Y, Kuramoto A, Kobayashi A, Isobe S, Tahara M, Monden Y. Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. DNA Res 2020; 26:399-409. [PMID: 31377774 PMCID: PMC6796513 DOI: 10.1093/dnares/dsz018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022] Open
Abstract
The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.
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Affiliation(s)
- Rumi Sasai
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Hiroaki Tabuchi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | | | - Kazuki Kishimoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Shusei Sato
- Graduate School of Life Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yoshihiro Okada
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | - Akihide Kuramoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, Japan
| | - Akira Kobayashi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
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13
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Feng J, Zhao S, Li M, Zhang C, Qu H, Li Q, Li J, Lin Y, Pu Z. Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq. Genomics 2019; 112:1978-1987. [PMID: 31756427 DOI: 10.1016/j.ygeno.2019.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 11/29/2022]
Abstract
Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in >100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded >128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.
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Affiliation(s)
- Junyan Feng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China.
| | - Shan Zhao
- Center of Analysis and Testing, Sichuan Academy of Agricultural Sciences, 610066, China
| | - Ming Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Cong Zhang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Huijuan Qu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Qing Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Jianwei Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Yang Lin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Zhigang Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China.
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14
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Ding N, Cui H, Miao Y, Tang J, Cao Q, Luo Y. Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato. PeerJ 2019; 7:e7933. [PMID: 31741783 PMCID: PMC6859871 DOI: 10.7717/peerj.7933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither a complete reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid crop are available, which in turn impedes progress in research studies in I. batatas functional genomics and molecular breeding. METHODS In this study, we sequenced full-length transcriptomes in I. batatas and its diploid ancestor I. trifida by single-molecule real-time sequencing and Illumina second-generation sequencing technologies. With the generated datasets, we conducted comprehensive intraspecific and interspecific sequence analyses and experimental characterization. RESULTS A total of 53,861/51,184 high-quality long-read transcripts were obtained, which covered about 10,439/10,452 loci in the I. batatas/I. trifida genome. These datasets enabled us to predict open reading frames successfully in 96.83%/96.82% of transcripts and identify 34,963/33,637 full-length cDNA sequences, 1,401/1,457 transcription factors, 25,315/27,090 simple sequence repeats, 1,656/1,389 long non-coding RNAs, and 5,251/8,901 alternative splicing events. Approximately, 32.34%/38.54% of transcripts and 46.22%/51.18% multi-exon transcripts underwent alternative splicing in I. batatas/I. trifida. Moreover, we validated one alternative splicing event in each of 10 genes and identified tuberous-root-specific expressed isoforms from a starch-branching enzyme, an alpha-glucan phosphorylase, a neutral invertase, and several ABC transporters. Overall, the collection and analysis of large-scale long-read transcripts generated in this study will serve as a valuable resource for the I. batatas research community, which may accelerate the progress in its structural, functional, and comparative genomics studies.
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Affiliation(s)
- Na Ding
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Huihui Cui
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jun Tang
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences, Xuzhou, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Xuzhou, Jiangsu, China
| | - Qinghe Cao
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences, Xuzhou, Jiangsu, China
- Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Xuzhou, Jiangsu, China
| | - Yonghai Luo
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
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15
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Li M, Yang S, Xu W, Pu Z, Feng J, Wang Z, Zhang C, Peng M, Du C, Lin F, Wei C, Qiao S, Zou H, Zhang L, Li Y, Yang H, Liao A, Song W, Zhang Z, Li J, Wang K, Zhang Y, Lin H, Zhang J, Tan W. The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development. BMC PLANT BIOLOGY 2019; 19:119. [PMID: 30935381 PMCID: PMC6444543 DOI: 10.1186/s12870-019-1708-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/11/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. RESULTS Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. CONCLUSIONS We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.
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Affiliation(s)
- Ming Li
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Songtao Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Wei Xu
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Zhigang Pu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Junyan Feng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Zhangying Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong People’s Republic of China
| | - Cong Zhang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Meifang Peng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, NJ 07043 USA
| | - Feng Lin
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Changhe Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Shuai Qiao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Hongda Zou
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong People’s Republic of China
| | - Lei Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Yan Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Huan Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Anzhong Liao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Wei Song
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Ji Li
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Yizheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Jinbo Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Wenfang Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
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Liu Y, Yu Y, Sun J, Cao Q, Tang Z, Liu M, Xu T, Ma D, Li Z, Sun J. Root-zone-specific sensitivity of K+-and Ca2+-permeable channels to H2O2 determines ion homeostasis in salinized diploid and hexaploid Ipomoea trifida. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1389-1405. [PMID: 30689932 PMCID: PMC6382330 DOI: 10.1093/jxb/ery461] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/11/2018] [Accepted: 12/19/2018] [Indexed: 05/13/2023]
Abstract
Polyploids generally possess superior K+/Na+ homeostasis under saline conditions compared with their diploid progenitors. In this study, we identified the physiological mechanisms involved in the ploidy-related mediation of K+/Na+ homeostasis in the roots of diploid (2x) and hexaploid (6x; autohexaploid) Ipomoea trifida, which is the closest relative of cultivated sweet potato. Results showed that 6x I. trifida retained more K+ and accumulated less Na+ in the root and leaf tissues under salt stress than 2x I. trifida. Compared with its 2x ancestor, 6x I. trifida efficiently prevents K+ efflux from the meristem root zone under salt stress through its plasma membrane (PM) K+-permeable channels, which have low sensitivity to H2O2. Moreover, 6x I. trifida efficiently excludes Na+ from the elongation and mature root zones under salt stress because of the high sensitivity of PM Ca2+-permeable channels to H2O2. Our results suggest the root-zone-specific sensitivity to H2O2 of PM K+- and Ca2+-permeable channels in the co-ordinated control of K+/Na+ homeostasis in salinized 2x and 6x I. trifida. This work provides new insights into the improved maintenance of K+/Na+ homeostasis of polyploids under salt stress.
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Affiliation(s)
- Yang Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Yicheng Yu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jianying Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Qinghe Cao
- Sweet Potato Research Institute (CAAS), Jiangsu Xuzhou Sweet Potato Research Institute, MOA Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Xuzhou, Jiangsu, China
| | - Zhonghou Tang
- Sweet Potato Research Institute (CAAS), Jiangsu Xuzhou Sweet Potato Research Institute, MOA Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Xuzhou, Jiangsu, China
| | - Meiyan Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Daifu Ma
- Sweet Potato Research Institute (CAAS), Jiangsu Xuzhou Sweet Potato Research Institute, MOA Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Xuzhou, Jiangsu, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- Correspondence: or
| | - Jian Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- Correspondence: or
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17
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage root crops. BMC Genomics 2018; 19:124. [PMID: 29415650 PMCID: PMC5803842 DOI: 10.1186/s12864-018-4502-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/28/2018] [Indexed: 11/21/2022] Open
Abstract
Background Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and root growth. Storage tubers and root crops are important sustenance food crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage root crops as well. Results Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage root crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage root crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and root tissues of these five storage root crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage root crops exhibited differential accumulation patterns in leaf and storage root tissues. Conclusions Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage root crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in root crops. Electronic supplementary material The online version of this article (10.1186/s12864-018-4502-7) contains supplementary material, which is available to authorized users.
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Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, Voytas DF, Zhong Z, Chen Y, Ren Q, Li Q, Kirkland ER, Zhang Y, Qi Y. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. NATURE PLANTS 2017; 3:688-689. [PMID: 28628131 DOI: 10.1038/s41477-017-0001-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This corrects the article DOI: 10.1038/nplants.2017.18.
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Katayama K, Kobayashi A, Sakai T, Kuranouchi T, Kai Y. Recent progress in sweetpotato breeding and cultivars for diverse applications in Japan. BREEDING SCIENCE 2017; 67:3-14. [PMID: 28465663 PMCID: PMC5407919 DOI: 10.1270/jsbbs.16129] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/19/2016] [Indexed: 05/07/2023]
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) is an outcrossing hexaploid that is cultivated in the tropics and warm-temperate regions of the world. Sweetpotato has played an important role as a famine-relief crop during its long history and has recently been reevaluated as a health-promoting food. In Japan, sweetpotato is used for a wide range of applications, such as table use, processed foods, and alcohol and starch production, and two groups at National Agriculture Research Organization (NARO) undertake the breeding of cultivars for these applications. Sweetpotato breeders utilize breeding processes such as grafting for flower induction and the identification of incompatibility groups before crossing to conquer problems peculiar to sweetpotato. For table use, new cultivars with high sugar content were released recently and have become popular among Japanese consumers. New cultivars with high anthocyanin or β-carotene content were released for processed foods and use as colorants. As raw materials, new cultivars with high alcohol yield were released for the production of shochu spirits. In addition, new cultivars with high starch yield and a cultivar containing starch with excellent cold-storage ability were released for starch production. This review deals with recent progress in sweetpotato breeding and cultivars for diverse applications in Japan.
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Affiliation(s)
- Kenji Katayama
- Division of Field Crop Research, Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Corresponding author (e-mail: )
| | - Akira Kobayashi
- Division of Upland Farming Research, Kyushu Okinawa Agricultural Research Center, NARO,
6651-2 Yokoichi, Miyakonojo, Miyazaki 885-0091,
Japan
| | - Tetsufumi Sakai
- Division of Upland Farming Research, Kyushu Okinawa Agricultural Research Center, NARO,
6651-2 Yokoichi, Miyakonojo, Miyazaki 885-0091,
Japan
| | - Toshikazu Kuranouchi
- Division of Field Crop Research, Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Yumi Kai
- Division of Upland Farming Research, Kyushu Okinawa Agricultural Research Center, NARO,
6651-2 Yokoichi, Miyakonojo, Miyazaki 885-0091,
Japan
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Tanaka M, Ishiguro K, Oki T, Okuno S. Functional components in sweetpotato and their genetic improvement. BREEDING SCIENCE 2017; 67:52-61. [PMID: 28465668 PMCID: PMC5407917 DOI: 10.1270/jsbbs.16125] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/08/2016] [Indexed: 05/13/2023]
Abstract
In addition to the nutritionally important components such as starches, vitamins and minerals, storage roots and leaves of sweetpotato (Ipomoea batatas) contains several components with health-promoting functions. Of these, the functionalities of carotenoids, anthocyanins and caffeoylquinic acids have been well established by in vitro and in vivo experiments. Several sweetpotato cultivars containing high levels of these components have been developed in Japan; e.g., 'Ayamurasaki', which has high amounts of anthocyanin in its storage roots. To further improve the content and also to change the composition of these functional components, the identification of the genes involved in their biosynthesis and genetic modification of the biosynthetic pathway has been attempted. In this review, we summarize the present status of the research and breeding for these functional components, and we discuss the future prospects for improving sweetpotato functionality.
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Affiliation(s)
- Masaru Tanaka
- Division of Upland Farming Research, Kyushu Okinawa Agricultural Research Center, NARO,
Yokoichi 6651-2, Miyakonojo, Miyazaki 885-0091,
Japan
- Corresponding author (e-mail: )
| | - Koji Ishiguro
- Division of Field Crop Research and Development, Hokkaido Agricultural Research Center, NARO,
Shinsei Minami 9-4, Memuro, Kasai, Hokkaido 082-0081,
Japan
| | - Tomoyuki Oki
- Crop Development and Agribusiness Research Division, Kyushu Okinawa Agricultural Research Center, NARO,
Suya 2421, Koshi, Kumamoto 861-1192,
Japan
| | - Shigenori Okuno
- Crop Development and Agribusiness Research Division, Kyushu Okinawa Agricultural Research Center, NARO,
Suya 2421, Koshi, Kumamoto 861-1192,
Japan
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