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Lou F, Ren Z, Tang Y, Han Z. Full-length transcriptome reveals the circularly polarized light response-related molecular genetic characteristics of Oratosquilla oratoria. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101183. [PMID: 38141370 DOI: 10.1016/j.cbd.2023.101183] [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: 10/25/2023] [Revised: 12/16/2023] [Accepted: 12/16/2023] [Indexed: 12/25/2023]
Abstract
The mantis shrimp is the only animal that can recognize circularly polarized light (CPL), but its molecular genetic characteristics are unclear. Multi-tissue level full-length (FL) transcriptome sequencing of Oratosquilla oratoria, a representative widely distributed mantis shrimp, was performed in the present study. We used comparative transcriptomics to explore the critical genes of O. oratoria selected by CPL and the GNβ gene associated with CPL signal transduction was hypothesized to be positively selected. Furthermore, the FL transcriptomes of O. oratoria compound eyes under five light conditions were sequenced and used to detect alternative splicing (AS). The ASs associated with CPL recognition mainly occurred in the LWS, ARR and TRPC regions. The number of FL transcripts with AS events and annotation information also provided evidence that O. oratoria could recognize LCPL. Additionally, 51 sequences belonging to the LWS, UV and Peropsin gene families were identified based on conserved 7tm domains. The LWS, UV and Peropsin opsins have similar 3D structures with seven domains across the cell membrane and conserved KSLRTPSN, DRY, and QAKK motifs. In conclusion, these results are undoubtedly valuable for perfecting the vision theory of O. oratoria and other mantis shrimp.
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Affiliation(s)
- Fangrui Lou
- School of Ocean, Yantai University, Yantai 264003, Shandong, China.
| | - Zhongjie Ren
- School of Ocean, Yantai University, Yantai 264003, Shandong, China
| | - Yongzheng Tang
- School of Ocean, Yantai University, Yantai 264003, Shandong, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China.
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Xiong Z, Yin H, Wang N, Han G, Gao Y. Chromosome-level genome assembly of navel orange cv. Gannanzao (Citrus sinensis Osbeck cv. Gannanzao). G3 (BETHESDA, MD.) 2024; 14:jkad268. [PMID: 38001056 PMCID: PMC10849316 DOI: 10.1093/g3journal/jkad268] [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: 08/08/2023] [Revised: 08/08/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Navel orange cv. Gannanzao is a variant of the navel orange cv. Newhall (Citrus sinensis Osbeck cv. Newhall) that exhibits an earlier maturation, making it commercially valuable. However, the mechanisms underlying its early maturation remain obscure. To address this question, we conducted genome sequencing and de novo assembly of navel orange cv. Gannanzao. The assembled genome sequence is 334.57 Mb in length with a GC content of 31.48%. It comprises 318 contigs (N50 = 3.23 Mb) and 187 scaffolds (N50 = 31.86 Mb). The Benchmarking Universal Single-Copy Orthologs test demonstrates 94.6% completeness. The annotation revealed 23,037 gene models, 164.95 Mb of repetitive sequences, and 2,554 noncoding RNAs. A comparative analysis identified 323 fruit ripening-related genes in navel orange cv. Gannanzao genome, while navel orange cv. Newhall genome contained 345 such genes. These genes were organized into 320 orthologous gene families, with 30.3% of them exhibiting differences in gene copy numbers between the 2 genomes. Additionally, we identified 15 fruit ripening-related genes that have undergone adaptive evolution, suggesting their potential role in advancing fruit maturation in navel orange cv. Gannanzao. Whole-genome sequencing and annotation of navel orange cv. Gannanzao provides a valuable resource to unravel the early maturation mechanism of citrus and enriches the genomic resources for citrus research.
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Affiliation(s)
- Zhiwei Xiong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Hui Yin
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL 33850, USA
| | - Guanzhu Han
- College of Life Sciences, Nanjing Normal University, Jiangsu 210098, China
| | - Yuxia Gao
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
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Kong L, Chen J, Dong K, Shafik K, Xu W. Genomic analysis of Colletotrichum camelliae responsible for tea brown blight disease. BMC Genomics 2023; 24:528. [PMID: 37674131 PMCID: PMC10483846 DOI: 10.1186/s12864-023-09598-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Colletotrichum camelliae, one of the most important phytopathogenic fungi infecting tea plants (Camellia sinensis), causes brown blight disease resulting in significant economic losses in yield of some sensitive cultivated tea varieties. To better understand its phytopathogenic mechanism, the genetic information is worth being resolved. RESULTS Here, a high-quality genomic sequence of C. camelliae (strain LT-3-1) was sequenced using PacBio RSII sequencing platform, one of the most advanced Three-generation sequencing platforms and assembled. The result showed that the fungal genomic sequence is 67.74 Mb in size (with the N50 contig 5.6 Mb in size) containing 14,849 putative genes, of which about 95.27% were annotated. The data revealed a large class of genomic clusters potentially related to fungal pathogenicity. Based on the Pathogen Host Interactions database, a total of 1698 genes (11.44% of the total ones) were annotated, containing 541 genes related to plant cell wall hydrolases which is remarkably higher than those of most species of Colletotrichum and others considered to be hemibiotrophic and necrotrophic fungi. It's likely that the increase in cell wall-degrading enzymes reflects a crucial adaptive characteristic for infecting tea plants. CONCLUSION Considering that C. camelliae has a specific host range and unique morphological and biological traits that distinguish it from other species of the genus Colletotrichum, characterization of the fungal genome will improve our understanding of the fungus and its phytopathogenic mechanism as well.
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Affiliation(s)
- Linghong Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Jiao Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Kaili Dong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Karim Shafik
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
- Department of plant pathology, Faculty of Agriculture, Alexandria University, Alexandria, 21526, Egypt
| | - Wenxing Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China.
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China.
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Gao Y, Xu J, Li Z, Zhang Y, Riera N, Xiong Z, Ouyang Z, Liu X, Lu Z, Seymour D, Zhong B, Wang N. Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. iScience 2023; 26:106024. [PMID: 36824272 PMCID: PMC9941208 DOI: 10.1016/j.isci.2023.106024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered immune disease. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. We first developed a phased diploid assembly of Citrus sinensis 'Newhall' genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 accessions for genome-wide association mapping of the HLB response. Genes determinants for HLB pathogenicity were associated with host immune response, ROS production, and antioxidants. Overall, this study has provided a significant resource of citrus genomic data and identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity.
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Affiliation(s)
- Yuxia Gao
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhilong Li
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Nadia Riera
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhiwei Xiong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhigang Ouyang
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Xinjun Liu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhanjun Lu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | | | - Balian Zhong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
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Zhang Y, Lou F, Chen J, Han Z, Yang T, Gao T, Song N. Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1002-1013. [PMID: 36083383 DOI: 10.1007/s10126-022-10163-7] [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: 05/18/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
As a newly described Sillaginidae species, Chinese sillago (Sillago sinica) needs a better understanding of gene annotation information. In this study, we reported the first full-length transcriptome data of S. sinica using the PacBio isoform sequencing Iso-seq and a description of transcriptome structure analysis. A total of 454,979 high-quality full-length transcripts were obtained by single-molecule real-time (SMRT) sequencing, which was corrected by Illumina sequencing data. After that, 66,948 non-redundant full-length transcripts were generated after mapping to the reference genome of S. sinica, including 49 fusion isoforms and 9,250 novel isoforms. 63,459 isoforms were successfully annotated by one of the Nr, Nt, SwissProt, Pfam, KOG, GO, and KEGG databases. Additionally, 30,987 alternative polyadenylation (APA) sites, 451,867 alternative splicing (AS) events, 21,928 long non-coding RNAs (lncRNAs) and 12,911 transcription factors (TFs) were identified. The full-length transcripts of S. sinica would provide a precious resource for characterizing the transcriptome of S. sinica and for the further study of gene function and regulatory mechanism of this species.
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Affiliation(s)
- Yuan Zhang
- Fishery College, Ocean University of China, Qingdao, 266003, China
| | - Fangrui Lou
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianyan Yang
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Na Song
- Fishery College, Ocean University of China, Qingdao, 266003, China.
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Jiang J, Huo J, Zhang Y, Xu Y, Zhao C, Miao J. SMRT sequencing of the full-length transcriptome of Gekko gecko. PLoS One 2022; 17:e0264499. [PMID: 35213661 PMCID: PMC8880673 DOI: 10.1371/journal.pone.0264499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
Tokay Gecko (Gekko gecko) is a rare and endangered medicinal animal in China. Its dry body has been used as an anti-asthmatic agent for two thousand years. To date, the genome and transcriptome of this species remain poorly understood. Here, we adopted single molecule real-time (SMRT) sequencing to obtain full-length transcriptome data and characterized the transcriptome structure. We identified 882,273 circular consensus (CCS) reads, including 746,317 full-length nonchimeric (FLNC) reads. The transcript cluster analysis revealed 212,964 consensus sequences, including 203,994 high-quality isoforms. In total, 111,372 of 117,888 transcripts were successfully annotated against eight databases (Nr, eggNOG, Swiss-Prot, GO, COG, KOG, Pfam and KEGG). Furthermore, 23,877 alternative splicing events, 169,128 simple sequence repeats (SSRs), 10,437 lncRNAs and 7,932 transcription factors were predicted across all transcripts. To our knowledge, this report is the first to document the G. gecko transcriptome using SMRT sequencing. The full-length transcript data might accelerate transcriptome research and lay the foundation for further research on G. gecko.
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Affiliation(s)
- Jianping Jiang
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
- * E-mail: (JM); (JJ)
| | - Juan Huo
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Yueyun Zhang
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Yongli Xu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Chengjian Zhao
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
| | - Jianhua Miao
- Guangxi Botanical Garden of Medicinal Plants, Nanning, Guangxi, China
- * E-mail: (JM); (JJ)
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Sarmiento ME, Chin KL, Lau NS, Aziah I, Norazmi MN, Acosta A, Ismail N, Yaacob NS. Mitochondrial DNA sequence of the horseshoe crab Tachypleus gigas. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1710-1714. [PMID: 34104748 PMCID: PMC8158250 DOI: 10.1080/23802359.2021.1930213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This paper reports on the complete mitochondrial (mt) genome of a horseshoe crab, Tachypleus gigas (T. gigas), in Kuala Kemaman, Terengganu, Malaysia. Whole-genome sequencing of hemocyte DNA was performed with Illumina HiSeq system and the generated reads were de novo assembled with ABySS 2.1.5 and reassembled using mitoZ against Carcinoscorpius rotundicauda and Limulus polyphemus, resulting in a contig of 15 Kb. Phylogenetic analysis of the assembled mt genome suggests that the Tachypleus gigas is closely related to Tachypleus tridentatus than to Carcinoscorpius rotundicauda.
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Affiliation(s)
- Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Nyok Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Ismail Aziah
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Noraznawati Ismail
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
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Takahashi S, Oshige M, Katsura S. DNA Manipulation and Single-Molecule Imaging. Molecules 2021; 26:1050. [PMID: 33671359 PMCID: PMC7922115 DOI: 10.3390/molecules26041050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan;
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
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