1
|
Afreen U, Pandey A, Jha SK, Kumar M, Mukhopadhyay K. Comprehensive analysis of hairpin small RNAs involved in resistance and pathogenesis during wheat-Puccinia triticina interactions. PHYSIOLOGIA PLANTARUM 2024; 176:e14516. [PMID: 39223917 DOI: 10.1111/ppl.14516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/13/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Wheat leaf rust, caused by the fungus Puccinia triticina (Pt), severely affects the grain quality and quantity of bread wheat (Triticum aestivum L.). Hairpin small(s)RNAs, like micro(mi)RNAs and their variants [including isomiRNAs (isomiRs) and microRNA-like RNAs (milRNAs)], along with their corresponding target genes, bestow leaf rust disease resistance, development and progression from both interacting species. However, the regulatory networks remain inadequately understood. Thirteen differentially expressed novel miRNAs, including two isomiRs and three milRNAs were discerned from induced reads of wheat sRNA libraries, and a further 5,393 and 1,275 candidate target genes were predicted in wheat and Pt, respectively. Functional annotation divulged that wheat-originated miRNAs/isomiRs were involved in resistance, while Pt-derived milRNAs imparted pathogenesis. The identified milRNAs- Tae-Pt-milR5, Tae-Pt-milR12, and Tae-Pt-milR14b and their cleavage sites on Pt target gene MEP5 were confirmed through degradome library screening, suggesting cross-kingdom translocation of Pt virulent genes in wheat host. Co-expression analysis of miRNAs/isomiRs-target genes provided insights into combating leaf rust disease, while co-expression analysis of milRNAs-target gene pairs reflected the extent of pathogenicity exerted by Pt with varied expression levels at the analyzed time points. The analysis pinpointed leaf rust-responsive candidate hairpin sRNAs- Tae-miR8, Tae-Pt-miR12, Tae-Pt-miR14a, and Tae-Pt-miR14b in wheat and Tae-Pt-milR12 in Pt. This study provides new insights into the hairpin sRNAs involved in the resistance and pathogenesis of wheat and Pt, respectively. Furthermore, crucial hairpin sRNAs and their promising targets for future biotechnological interventions to augment stress resilience have been identified.
Collapse
Affiliation(s)
- Uzma Afreen
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Anjali Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Manish Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Kunal Mukhopadhyay
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| |
Collapse
|
2
|
Nagar DN, Mani K, Braganca JM. Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India. Sci Rep 2024; 14:20214. [PMID: 39215047 PMCID: PMC11364659 DOI: 10.1038/s41598-024-70149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Haloarchaeal cultures were isolated from solar salterns of Goa and Tamil Nadu and designated as BS2, BBK2 and E3. These isolates grew with a characteristic bright orange to pink pigmentation and were capable of growing in media containing upto 25% (w/vol) NaCl. Whole genome sequencing (WGS) of the three haloarchaeal strains BS2, BBK2 and E3 indicated an assembled genomic size of 4.1 Mb, 3.8 Mb and 4 Mb with G + C content of 61.8, 65.6 and 59.8% respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the archaeal isolates belong to Haloarcula, Haloferax and Halogeometricum genera. Haloarcula rubripromontorii BS2 was predicted to have 4292 genes with 4242 CDS regions, 46 tRNAs, 6 rRNAs and 3 misc_RNAs. In case of Haloferax lucentense BBK2,, 3840 genes with 3780 CDS regions were detected along with 52 tRNAs, 5 rRNAs and 3 misc_RNAs. Halogeometricum borinquense E3 contained 4101 genes, 4043 CDS regions, 52 tRNAs, 4 rRNAs, and 2 misc_RNAs. The functional annotation and curation of the haloarchaeal genome, revealed C50 carotenoid biosynthetic genes like phytoene desaturase/carotenoid 3' -4' desaturase (crtI), lycopene elongase (ubiA/lyeJ) and carotenoid biosynthesis membrane protein (cruF) in the three isolates. Whereas crtD (C-3',4' desaturase), crtY (lycopene cyclase) and brp/blh (β-carotene dioxygenase) genes were identified only in BS2.
Collapse
Affiliation(s)
- Devika N Nagar
- Dept of Biological Sciences, Birla Institute of Technology and Science, Pilani, K K Birla Goa Campus, NH 17B Zuarinagar, Goa, 403 726, India
| | - Kabilan Mani
- Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - Judith M Braganca
- Dept of Biological Sciences, Birla Institute of Technology and Science, Pilani, K K Birla Goa Campus, NH 17B Zuarinagar, Goa, 403 726, India.
| |
Collapse
|
3
|
Badhe MR, Das P, Sahoo S, Paul A, Sahoo PK, Reddy RRK, Suryawanshi AR, Nandanpawar PC, Das Mahapatra K, Nagpure NS, Goswami M, Mohanty J. Physiological Responses to Acute Heat Stress in Rohu, Labeo rohita: Insights from Liver Proteomics. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10360-6. [PMID: 39207653 DOI: 10.1007/s10126-024-10360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Heat stress is a major problem in aquaculture species, causing changes in physiology such as decreased feed intake, growth rate, reproduction, and internal cellular damage, thereby affecting fish's health. The effects of an acute heat stress simulating a daily rise and fall in temperature on summer days were evaluated in the liver proteome of rohu (Labeo rohita) fingerlings in the present study. The fish maintained at 30 °C were gradually exposed to a higher temperature of 36 °C at an increment rate of 1 °C per 1.5 h, and after 3 h at that temperature, it was gradually reduced to 30 °C. The liver tissue samples were collected at 5 am, 5 pm, and 5 am the next day from the exposed and control fish. Protein samples were prepared from the liver tissues, and the extracted proteins were compared using 2-dimensional (2D) gel electrophoresis (2DGE) and mass spectrometry (MS) using a MALDI-TOF/TOF mass spectrometer. A total of 44 differentially expressed protein spots were visualized in 2D gel analysis from heat stress exposed fish at three time points, out of which 21 proteins including one hypothetical protein could be identified by MS. The abundance of five selected differentially expressed proteins (DEPs) was validated using qPCR. The majority of DEPs were found to be involved primarily in lipid, protein and energy metabolism, immune system regulation, cytoskeletal stability, and ROS management. The findings of this study would help in the development of strategies to mitigate heat stress in L. rohita.
Collapse
Affiliation(s)
- Mohan R Badhe
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Priyanka Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Sonalina Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Anirban Paul
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Pramoda Kumar Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | | | | | | | - Kanta Das Mahapatra
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Naresh S Nagpure
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Mukunda Goswami
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Jyotirmaya Mohanty
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India.
| |
Collapse
|
4
|
Zinta R, Tiwari JK, Buckseth T, Goutam U, Singh RK, Thakur AK, Singh S, Kumar V, Kumar M. Phenotypic and transcriptomics characterization uncovers genes underlying tuber yield traits and gene expression marker development in potato under aeroponics. PLANTA 2024; 260:74. [PMID: 39153022 DOI: 10.1007/s00425-024-04507-x] [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: 05/05/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
MAIN CONCLUSION Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log2 fold change) and down-regulated (< -2 Log2 fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time-quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics.
Collapse
Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- Indian Council of Agricultural Research- Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Shwetank Singh
- Indian Council of Agricultural Research- Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Vinod Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Manoj Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| |
Collapse
|
5
|
Rahmat NL, Zifruddin AN, Yusoff NS, Sulaiman S, Zainal Abidin CMR, Othman NW, Nor Muhammad NA, Hassan M. Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana. Comput Biol Chem 2024; 112:108176. [PMID: 39181100 DOI: 10.1016/j.compbiolchem.2024.108176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
Metisa plana is a widespread insect pest infesting oil palm plantations in Malaysia. Farnesyl acetate (FA), a juvenile hormone analogue, has been reported to exert in vitro and in vivo insecticidal activity against other insect pests. However, the insecticidal mechanism of FA on M. plana remains unclear. Therefore, this study aims to elucidate responsive genes in M. plana in response to FA treatment. The RNA-sequencing reads of FA-treated M. plana were de novo-assembled with existing raw reads from non-treated third instar larvae, and 55,807 transcripts were functionally annotated to multiple protein databases. Several insecticide detoxification-related genes were differentially regulated among the 321 differentially expressed transcripts. Cytochrome P450 monooxygenase, carboxylesterase, and ATP-binding cassette protein were upregulated, while peptidoglycan recognition protein was downregulated. Innate immune response genes, such as glutathione S-transferases, acetylcholinesterase, and heat shock protein, were also identified in the transcriptome. The findings signify that changes occurred in the insect's receptor and signaling, metabolic detoxification of insecticides, and immune responses upon FA treatment on M. plana. This valuable information on FA toxicity may be used to formulate more effective biorational insecticides for better M. plana pest management strategies in oil palm plantations.
Collapse
Affiliation(s)
- Nur Lina Rahmat
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Anis Nadyra Zifruddin
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Nur Syamimi Yusoff
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Suhaila Sulaiman
- Bioinformatics Unit, FGV R&D Sdn. Bhd., FGV Innovation Centre, PT23417 Lengkuk Teknologi,Bandar Enstek, Nilai, Negeri Sembilan 71760, Malaysia
| | | | - Nurul Wahida Othman
- Centre for Insect Systematics, Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia; Bioinformatics and Molecular Simulations Group, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor 43600 UKM, Malaysia; Systems and Synthetic Biology Group, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
| |
Collapse
|
6
|
Guzmán LF, Tirado B, Cruz-Cárdenas CI, Rojas-Anaya E, Aragón-Magadán MA. De Novo Transcriptome Assembly of Cedar ( Cedrela odorata L.) and Differential Gene Expression Involved in Herbivore Resistance. Curr Issues Mol Biol 2024; 46:8794-8806. [PMID: 39194737 DOI: 10.3390/cimb46080520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/01/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Timber trees are targets of herbivorous attacks. The identification of genes associated with pest resistance can be accomplished through differential expression analysis using transcriptomes. We reported the de novo assembly of cedar (Cedrela odorata L.) transcriptome and the differential expression of genes involved in herbivore resistance. The assembly and annotation of the transcriptome were obtained using RNAseq from healthy cedar plants and those infested with Chrysobothris yucatanensis. A total of 325.6 million reads were obtained, and 127,031 (97.47%) sequences were successfully assembled. A total of 220 herbivory-related genes were detected, of which 170 genes were annotated using GO terms, and 161 genes with 245 functions were identified-165, 75, and 5 were molecular functions, biological processes, and cellular components, respectively. To protect against herbivorous infestation, trees produce toxins and volatile compounds which are modulated by signaling pathways and gene expression related to molecular functions and biological processes. The limited number of genes identified as cellular components suggests that there are minimal alterations in cellular structure in response to borer attack. The chitin recognition protein, jasmonate ZIM-domain (JAZ) motifs, and response regulator receiver domain were found to be overexpressed, whereas the terpene synthase, cytochrome P450, and protein kinase domain gene families were underexpressed. This is the first report of a cedar transcriptome focusing on genes that are overexpressed in healthy plants and underexpressed in infested plants. This method may be a viable option for identifying genes associated with herbivore resistance.
Collapse
Affiliation(s)
- Luis Felipe Guzmán
- National Genetic Resources Center, National Agricultural, Forestry and Livestock Researches Institute, Tepatitlán 47600, Jalisco, Mexico
| | - Bibiana Tirado
- Centro Universitario de los Altos, University of Guadalajara, Tepatitlán 47600, Jalisco, Mexico
| | - Carlos Iván Cruz-Cárdenas
- National Genetic Resources Center, National Agricultural, Forestry and Livestock Researches Institute, Tepatitlán 47600, Jalisco, Mexico
| | - Edith Rojas-Anaya
- National Genetic Resources Center, National Agricultural, Forestry and Livestock Researches Institute, Tepatitlán 47600, Jalisco, Mexico
| | - Marco Aurelio Aragón-Magadán
- National Genetic Resources Center, National Agricultural, Forestry and Livestock Researches Institute, Tepatitlán 47600, Jalisco, Mexico
| |
Collapse
|
7
|
Hu W, Peng Z, Lv J, Zhang Q, Wang X, Xia Q. Developmental and nuclear proteomic signatures characterize the temporal regulation of fibroin synthesis during the last molting-feeding transition of silkworm. Int J Biol Macromol 2024; 274:133028. [PMID: 38857725 DOI: 10.1016/j.ijbiomac.2024.133028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
Silkworm fibroins are natural proteinaceous macromolecules and provide core mechanical properties to silk fibers. The synthesis process of fibroins is posterior silk gland (PSG)-exclusive and appears active at the feeding stage and inactive at the molting stage. However, the molecular mechanisms controlling it remain elusive. Here, the silk gland's physiological and nuclear proteomic features were used to characterize changes in its structure and development from molting to feeding stages. The temporal expression profile and immunofluorescence analyses revealed a synchronous transcriptional on-off mode of fibroin genes. Next, the comparative nuclear proteome of the PSG during the last molting-feeding transition identified 798 differentially abundant proteins (DAPs), including 42 transcription factors and 15 epigenetic factors. Protein-protein interaction network analysis showed a "CTCF-FOX-HOX-SOX" association with activated expressions at the molting stage, suggesting a relatively complex and multifactorial regulation of the PSG at the molting stage. In addition, FAIRE-seq verification indicated "closed" and "open" conformations of fibroin gene promoters at the molting and feeding stages, respectively. Such proteome combined with chromatin accessibility analysis revealed the detailed signature of protein factors involved in the temporal regulation of fibroin synthesis and provided insights into silk gland development as well as silk production in silkworms.
Collapse
Affiliation(s)
- Wenbo Hu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Zhangchuan Peng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Institute of Advanced Pathology, Jinfeng Laboratory, Chongqing 401329, China
| | - Jinfeng Lv
- Institute for Silk and Related Biomaterials Research, Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Quan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Xiaogang Wang
- School of Basic Medical Science, Chongqing College of Traditional Chinese Medicine, Chongqing 400065, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| |
Collapse
|
8
|
Klimov PB, Hubert J, Erban T, Alejandra Perotti M, Braig HR, Flynt A, He Q, Cui Y. Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q). Int J Parasitol 2024:S0020-7519(24)00138-3. [PMID: 38992783 DOI: 10.1016/j.ijpara.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.
Collapse
Affiliation(s)
- Pavel B Klimov
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA; Tyumen State University, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen, Russia.
| | - Jan Hubert
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia; Czech University of Life Science, Faculty of Microbiology Nutrient and Dietics, Prague, Czechia
| | - Tomas Erban
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia
| | - M Alejandra Perotti
- University of Reading, Ecology and Evolutionary Biology Section, School of Biological Sciences, Reading RG6 6AS, United Kingdom
| | - Henk R Braig
- Institute and Museum of Natural Sciences, Faculty of Natural and Exact Sciences, National University of San Juan, San Juan, J5400 DNQ, Argentina
| | - Alex Flynt
- University of Southern Mississippi, School of Biological, Environmental, and Earth Sciences, Hattiesburg, MS, USA
| | - Qixin He
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA.
| | - Yubao Cui
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University.Wuxi, PR Chin.
| |
Collapse
|
9
|
Mutemi KN, Simakov O, Pan L, Santangeli L, Null RW, Handberg-Thorsager M, Vellutini BC, Larsson T, Savage EL, Lopez MO, Hercog R, Provaznik J, Ordoñez-Rueda D, Azevedo N, Gazave E, Vervoort M, Tomancak P, Tan W, Winkler S, Benes V, Hui J, Helm C, Özpolat BD, Arendt D. A genome resource for the marine annelid Platynereis dumerilii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600153. [PMID: 38948846 PMCID: PMC11213123 DOI: 10.1101/2024.06.21.600153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii and of the closely related P. massiliensis and P. megalops, to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ~1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 580 miRNA loci. We further explore the high genetic variation (~3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.
Collapse
Affiliation(s)
- Kevin Nzumbi Mutemi
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Austria
| | - Leslie Pan
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Luca Santangeli
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Ryan W. Null
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Mette Handberg-Thorsager
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | | | - Tomas Larsson
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. Current: Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Emily L. Savage
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Current: Centre for Organismal Studies, University of Heidelberg, Heidelberg
| | - Mireia Osuna Lopez
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rajna Hercog
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany - not at EMBL anymore, do not know current address
| | - Jan Provaznik
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nayara Azevedo
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany. - not at EMBL anymore, do not know current address
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France. - deceased
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Vladimir Benes
- EMBL, Genomics Core Facility, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Conrad Helm
- Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - B. Duygu Özpolat
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Centre for Organismal Studies (COS) University of Heidelberg, 69120 Heidelberg, Germany
| |
Collapse
|
10
|
Li X, Lin Y, Li W, Cheng Y, Zhang J, Qiu J, Fu Y. Comparative Analysis of mRNA, microRNA of Transcriptome, and Proteomics on CIK Cells Responses to GCRV and Aeromonas hydrophila. Int J Mol Sci 2024; 25:6438. [PMID: 38928143 PMCID: PMC11204273 DOI: 10.3390/ijms25126438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Grass Carp Reovirus (GCRV) and Aeromonas hydrophila (Ah) are the causative agents of haemorrhagic disease in grass carp. This study aimed to investigate the molecular mechanisms and immune responses at the miRNA, mRNA, and protein levels in grass carp kidney cells (CIK) infected by Grass Carp Reovirus (GCRV, NV) and Aeromonas hydrophilus (Bacteria, NB) to gain insight into their pathogenesis. Within 48 h of infection with Grass Carp Reovirus (GCRV), 99 differentially expressed microRNA (DEMs), 2132 differentially expressed genes (DEGs), and 627 differentially expressed proteins (DEPs) were identified by sequencing; a total of 92 DEMs, 3162 DEGs, and 712 DEPs were identified within 48 h of infection with Aeromonas hydrophila. It is worth noting that most of the DEGs in the NV group were primarily involved in cellular processes, while most of the DEGs in the NB group were associated with metabolic pathways based on KEGG enrichment analysis. This study revealed that the mechanism of a grass carp haemorrhage caused by GCRV infection differs from that caused by the Aeromonas hydrophila infection. An important miRNA-mRNA-protein regulatory network was established based on comprehensive transcriptome and proteome analysis. Furthermore, 14 DEGs and 6 DEMs were randomly selected for the verification of RNA/small RNA-seq data by RT-qPCR. Our study not only contributes to the understanding of the pathogenesis of grass carp CIK cells infected with GCRV and Aeromonas hydrophila, but also serves as a significant reference value for other aquatic animal haemorrhagic diseases.
Collapse
Affiliation(s)
- Xike Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yue Lin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Wenjuan Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuejuan Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junling Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junqiang Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| |
Collapse
|
11
|
Sun W, Li M, Wang J. Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus. BMC PLANT BIOLOGY 2024; 24:518. [PMID: 38851683 PMCID: PMC11162574 DOI: 10.1186/s12870-024-05245-8] [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: 03/04/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
Plant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution and enhanced adaptability. However, few studies have been conducted on the relationship between gene expression and epigenetic modification in different plant tissues after allopolyploidization. In this study, we studied gene expression and DNA methylation modification patterns in four tissues (stems, leaves, flowers and siliques) of Brassica napusand its diploid progenitors. On this basis, the alternative splicing patterns and cis-trans regulation patterns of four tissues in B. napus and its diploid progenitors were also analyzed. It can be seen that the number of alternative splicing occurs in the B. napus is higher than that in the diploid progenitors, and the IR type increases the most during allopolyploidy. In addition, we studied the fate changes of duplicated genes after allopolyploidization in B. napus. We found that the fate of most duplicated genes is conserved, but the number of neofunctionalization and specialization is also large. The genetic fate of B. napus was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study also analyzed generational transmission analysis of expression and DNA methylation patterns. Our study provides a reference for the fate differentiation of duplicated genes during allopolyploidization.
Collapse
Affiliation(s)
- Weiqi Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
12
|
Petijová L, Henzelyová J, Kuncová J, Matoušková M, Čellárová E. In silico prediction of polyketide biosynthetic gene clusters in the genomes of Hypericum-borne endophytic fungi. BMC Genomics 2024; 25:555. [PMID: 38831295 PMCID: PMC11149221 DOI: 10.1186/s12864-024-10475-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND The search for new bioactive natural compounds with anticancer activity is still of great importance. Even though their potential for diagnostics and treatment of cancer has already been proved, the availability is still limited. Hypericin, a naphthodianthrone isolated essentially from plant source Hypericum perforatum L. along with other related anthraquinones and bisanthraquinones belongs to this group of compounds. Although it has been proven that hypericin is synthesized by the polyketide pathway in plants, none of the candidate genes coding for key enzymes has been experimentally validated yet. Despite the rare occurrence of anthraquinones in plants, their presence in microorganisms, including endophytic fungi, is quite common. Unlike plants, several biosynthetic genes grouped into clusters (BGCs) in fungal endophytes have already been characterized. RESULTS The aim of this work was to predict, identify and characterize the anthraquinone BGCs in de novo assembled and functionally annotated genomes of selected endophytic fungal isolates (Fusarium oxysporum, Plectosphaerella cucumerina, Scedosporium apiospermum, Diaporthe eres, Canariomyces subthermophilus) obtained from different tissues of Hypericum spp. The number of predicted type I polyketide synthase (PKS) BGCs in the studied genomes varied. The non-reducing type I PKS lacking thioesterase domain and adjacent discrete gene encoding protein with product release function were identified only in the genomes of C. subthermophilus and D. eres. A candidate bisanthraquinone BGC was predicted in C. subthermophilus genome and comprised genes coding the enzymes that catalyze formation of the basic anthraquinone skeleton (PKS, metallo-beta-lactamase, decarboxylase, anthrone oxygenase), putative dimerization enzyme (cytochrome P450 monooxygenase), other tailoring enzymes (oxidoreductase, dehydrogenase/reductase), and non-catalytic proteins (fungal transcription factor, transporter protein). CONCLUSIONS The results provide an insight into genetic background of anthraquinone biosynthesis in Hypericum-borne endophytes. The predicted bisanthraquinone gene cluster represents a basis for functional validation of the candidate biosynthetic genes in a simple eukaryotic system as a prospective biotechnological alternative for production of hypericin and related bioactive anthraquinones.
Collapse
Affiliation(s)
- Linda Petijová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia.
| | - Jana Henzelyová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
| | - Júlia Kuncová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
| | - Martina Matoušková
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
| | - Eva Čellárová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
| |
Collapse
|
13
|
Yang S, Tang X, Yan F, Yang H, Xu L, Jian Z, Deng H, He Q, Zhu G, Wang Q. A time-course transcriptome analysis revealing the potential molecular mechanism of early gonadal differentiation in the Chinese giant salamander. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101200. [PMID: 38320446 DOI: 10.1016/j.cbd.2024.101200] [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: 11/15/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
The Chinese giant salamander (CGS) Andrias davidianus is the largest extant amphibian and has recently become an important species for aquaculture with high economic value. Meanwhile, its wild populations and diversity are in urgent need of protection. Exploring the mechanism of its early gonadal differentiation will contribute to the development of CGS aquaculture and the recovery of its wild population. In this study, transcriptomic and phenotypic research was conducted on the critical time points of early gonadal differentiation of CGS. The results indicate that around 210 days post-hatching (dph) is the critical window for female CGS's gonadal differentiation, while 270 dph is that of male CGS. Besides, the TRPM1 gene may be the crucial gene among many candidates determining the sex of CGS. More importantly, in our study, key genes involved in CGS's gonadal differentiation and development are identified and their potential pathways and regulatory models at early stage are outlined. This is an initial exploration of the molecular mechanisms of CGS's early gonadal differentiation at multiple time points, providing essential theoretical foundations for its captive breeding and offering unique insights into the conservation of genetic diversity in wild populations from the perspective of sex development.
Collapse
Affiliation(s)
- Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xiong Tang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Fan Yan
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Han Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Lishan Xu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhijie Jian
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Huidan Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Qu He
- School of Foreign Languages, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| |
Collapse
|
14
|
Thakkar N, Gajera G, Mehta D, Kothari V. Silversol ® (a Colloidal Nanosilver Formulation) Inhibits Growth of Antibiotic-Resistant Staphylococcus aureus by Disrupting Its Physiology in Multiple Ways. Pharmaceutics 2024; 16:726. [PMID: 38931848 PMCID: PMC11206351 DOI: 10.3390/pharmaceutics16060726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Antibiotic-resistant strains of Staphylococcus aureus are being viewed as a serious threat by various public health agencies. Identifying novel targets in this important pathogen is crucial to the development of new effective antibacterial formulations. We investigated the antibacterial effect of a colloidal nanosilver formulation, Silversol®, against an antibiotic-resistant strain of S. aureus using appropriate in vitro assays. Moreover, we deciphered the molecular mechanisms underlying this formulation's anti-S. aureus activity using whole transcriptome analysis. Lower concentrations of the test formulation exerted a bacteriostatic effect against this pathogen, and higher concentrations exerted a bactericidal effect. Silversol® at sub-lethal concentration was found to disturb multiple physiological traits of S. aureus such as growth, antibiotic susceptibility, membrane permeability, efflux, protein synthesis and export, biofilm and exopolysaccharide production, etc. Transcriptome data revealed that the genes coding for transcriptional regulators, efflux machinery, transferases, β-lactam resistance, oxidoreductases, metal homeostasis, virulence factors, and arginine biosynthesis are expressed differently under the influence of the test formulation. Genes (argG and argH) involved in arginine biosynthesis emerged among the major targets of Silversol®'s antibacterial activity against S. aureus.
Collapse
Affiliation(s)
- Nidhi Thakkar
- Institute of Science, Nirma University, Ahmedabad 382481, India; (N.T.); (G.G.)
| | - Gemini Gajera
- Institute of Science, Nirma University, Ahmedabad 382481, India; (N.T.); (G.G.)
| | - Dilip Mehta
- Viridis BioPharma Pvt. Ltd., Mumbai 400043, India;
| | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad 382481, India; (N.T.); (G.G.)
| |
Collapse
|
15
|
Guo Y, Jiao L, Wang J, Ma L, Lu Y, Zhang Y, Guo J, Yin Y. Analyses of high spatial resolution datasets identify genes associated with multi-layered secondary cell wall thickening in Pinus bungeana. ANNALS OF BOTANY 2024; 133:953-968. [PMID: 38366549 PMCID: PMC11089263 DOI: 10.1093/aob/mcae023] [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: 12/12/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND AND AIMS Secondary cell wall (SCW) thickening is a major cellular developmental stage determining wood structure and properties. Although the molecular regulation of cell wall deposition during tracheary element differentiation has been well established in primary growth systems, less is known about the gene regulatory processes involved in the multi-layered SCW thickening of mature trees. METHODS Using third-generation [long-read single-molecule real-time (SMRT)] and second-generation [short-read sequencing by synthesis (SBS)] sequencing methods, we established a Pinus bungeana transcriptome resource with comprehensive functional and structural annotation for the first time. Using these approaches, we generated high spatial resolution datasets for the vascular cambium, xylem expansion regions, early SCW thickening, late SCW thickening and mature xylem tissues of 71-year-old Pinus bungeana trees. KEY RESULTS A total of 79 390 non-redundant transcripts, 31 808 long non-coding RNAs and 5147 transcription factors were annotated and quantified in different xylem tissues at all growth and differentiation stages. Furthermore, using this high spatial resolution dataset, we established a comprehensive transcriptomic profile and found that members of the NAC, WRKY, SUS, CESA and LAC gene families are major players in early SCW formation in tracheids, whereas members of the MYB and LBD transcription factor families are highly expressed during late SCW thickening. CONCLUSIONS Our results provide new molecular insights into the regulation of multi-layered SCW thickening in conifers. The high spatial resolution datasets provided can serve as important gene resources for improving softwoods.
Collapse
Affiliation(s)
- Yu Guo
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| | - Lichao Jiao
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| | - Jie Wang
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| | - Lingyu Ma
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| | - Yang Lu
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| | - Yonggang Zhang
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| | - Juan Guo
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| | - Yafang Yin
- Wood Anatomy and Utilization Department, Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
- Wood Specimen Resource Center (WOODPEDIA) of National Forestry and Grassland Administration, Beijing 100091, China
| |
Collapse
|
16
|
Li Z, Chen X, Zhao F, Miao M. Genomic insights into the cellular specialization of predation in raptorial protists. BMC Biol 2024; 22:107. [PMID: 38715037 PMCID: PMC11077807 DOI: 10.1186/s12915-024-01904-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Predation is a fundamental mechanism for organisms to acquire energy, and various species have evolved diverse tools to enhance their hunting abilities. Among protozoan predators, raptorial Haptorian ciliates are particularly fascinating as they possess offensive extrusomes known as toxicysts, which are rapidly discharged upon prey contact. However, our understanding of the genetic processes and specific toxins involved in toxicyst formation and discharge is still limited. RESULTS In this study, we investigated the predation strategies and subcellular structures of seven Haptoria ciliate species and obtained their genome sequences using single-cell sequencing technology. Comparative genomic analysis revealed distinct gene duplications related to membrane transport proteins and hydrolytic enzymes in Haptoria, which play a crucial role in the production and discharge of toxicysts. Transcriptomic analysis further confirmed the abundant expression of genes related to membrane transporters and cellular toxins in Haptoria compared to Trichostomatia. Notably, polyketide synthases (PKS) and L-amino acid oxidases (LAAO) were identified as potentially toxin genes that underwent extensive duplication events in Haptoria. CONCLUSIONS Our results shed light on the evolutionary and genomic adaptations of Haptorian ciliates for their predation strategies in evolution and provide insights into their toxic mechanisms.
Collapse
Affiliation(s)
- Zaihan Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Miao Miao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
17
|
Suppiyar V, Bonthala VS, Shrestha A, Krey S, Stich B. Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.). BMC Genomics 2024; 25:442. [PMID: 38702658 PMCID: PMC11069243 DOI: 10.1186/s12864-024-10367-2] [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: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.
Collapse
Affiliation(s)
- Vithusan Suppiyar
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Venkata Suresh Bonthala
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany.
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany.
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Stephanie Krey
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| |
Collapse
|
18
|
Jarva TM, Phillips NM, Von Eiff C, Poulakis GR, Naylor G, Feldheim KA, Flynt AS. Gene expression, evolution, and the genetics of electrosensing in the smalltooth sawfish, Pristis pectinata. Ecol Evol 2024; 14:e11260. [PMID: 38694751 PMCID: PMC11057056 DOI: 10.1002/ece3.11260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 03/14/2024] [Accepted: 03/28/2024] [Indexed: 05/04/2024] Open
Abstract
Sawfishes (Pristidae) are large, highly threatened rays named for their tooth-studded rostrum, which is used for prey sensing and capture. Of all five species, the smalltooth sawfish, Pristis pectinata, has experienced the greatest decline in range, currently found in only ~20% of its historic range. To better understand the genetic underpinnings of these taxonomically and morphologically unique animals, we collected transcriptomic data from several tissue types, mapped them to the recently completed reference genome, and contrasted the patterns observed with comparable data from other elasmobranchs. Evidence of positive selection was detected in 79 genes in P. pectinata, several of which are involved in growth factor/receptor tyrosine kinase signaling and body symmetry and may be related to the unique morphology of sawfishes. Changes in these genes may impact cellular responses to environmental conditions such as temperature, dissolved oxygen, and salinity. Data acquired also allow for examination of the molecular components of P. pectinata electrosensory systems, which are highly developed in sawfishes and have likely been influential in their evolutionary success.
Collapse
Affiliation(s)
- Taiya M. Jarva
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | - Nicole M. Phillips
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | - Cory Von Eiff
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| | - Gregg R. Poulakis
- Charlotte Harbor Field LaboratoryFish and Wildlife Research Institute, Florida Fish and Wildlife Conservation CommissionPort CharlotteFloridaUSA
| | - Gavin Naylor
- Florida Program for Shark ResearchUniversity of FloridaGainesvilleFloridaUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, the Field MuseumChicagoIllinoisUSA
| | - Alex S. Flynt
- School of Biological, Environmental, and Earth SciencesThe University of Southern MississippiHattiesburgMississippiUSA
| |
Collapse
|
19
|
Li C, Cai R, Shi W, Zhang H, Liu Z, Xie F, Chen Y, Hong Q. Comparative transcriptome analysis of ovaries and testes reveals sex-biased genes and pathways in zebrafish. Gene 2024; 901:148176. [PMID: 38242380 DOI: 10.1016/j.gene.2024.148176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Zebrafish (Danio rerio) is a widely recognized and extensively studied model organism in scientific research. The regulatory mechanism of gonadal development and differentiation of this species has aroused considerable attention. Nonetheless, the major sex-biased genes and pathways associated with gonadal development remain elusive. Therefore, to comprehend this intricate process, gonadal transcriptome sequencing was carried out to identify differentially expressed genes (DEGs) between the testes and ovaries of adult zebrafish. The preliminary assessment yielded a total of 23,529,272 and 23,521,368 clean reads from the cDNA libraries of ovaries and testes. Afterward, a comparative analysis of the transcriptome revealed 3,604 upregulated and 11,371 downregulated DEGs in the ovaries compared to the testes. Of these genes, 428 were exclusively expressed in females, while 3,516 were exclusively expressed in males. Additionally, further assessments were conducted to explore the functions associated with these DEGs in various biological processes. The data revealed their involvement in sex-biased pathways, such as progesterone-mediated oocyte maturation, oocyte meiosis, cytokine-cytokine receptor interaction, and cardiac muscle contraction. Finally, the expression levels of 14 sex-biased DEGs (cdc20, ccnb1, ypel3, chn1, bmp15, rspo1, tnfsf10, egfra, acta2, cox8a, gsdf, dmrt1, star, and cyp17a1) associated with the enriched pathways were subjected to further validation through qRT-PCR. The data acquired from these investigations offer valuable resources to support further exploration of the mechanisms governing sexual dimorphism and gonadal development in zebrafish.
Collapse
Affiliation(s)
- Cong Li
- Department of Hematology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Rui Cai
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Wenhui Shi
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Hao Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Zhuang Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Fenfen Xie
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| | - Yuanhua Chen
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| | - Qiang Hong
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| |
Collapse
|
20
|
Sahu S, Rao AR, Sahu TK, Pandey J, Varshney S, Kumar A, Gaikwad K. Predictive Role of Cluster Bean ( Cyamopsis tetragonoloba) Derived miRNAs in Human and Cattle Health. Genes (Basel) 2024; 15:448. [PMID: 38674383 PMCID: PMC11049822 DOI: 10.3390/genes15040448] [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: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 04/28/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding conserved molecules with lengths varying between 18-25nt. Plants miRNAs are very stable, and probably they might have been transferred across kingdoms via food intake. Such miRNAs are also called exogenous miRNAs, which regulate the gene expression in host organisms. The miRNAs present in the cluster bean, a drought tolerant legume crop having high commercial value, might have also played a regulatory role for the genes involved in nutrients synthesis or disease pathways in animals including humans due to dietary intake of plant parts of cluster beans. However, the predictive role of miRNAs of cluster beans for gene-disease association across kingdoms such as cattle and humans are not yet fully explored. Thus, the aim of the present study is to (i) find out the cluster bean miRNAs (cb-miRs) functionally similar to miRNAs of cattle and humans and predict their target genes' involvement in the occurrence of complex diseases, and (ii) identify the role of cb-miRs that are functionally non-similar to the miRNAs of cattle and humans and predict their targeted genes' association with complex diseases in host systems. Here, we predicted a total of 33 and 15 functionally similar cb-miRs (fs-cb-miRs) to human and cattle miRNAs, respectively. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the participation of targeted genes of fs-cb-miRs in 24 and 12 different pathways in humans and cattle, respectively. Few targeted genes in humans like LCP2, GABRA6, and MYH14 were predicted to be associated with disease pathways of Yesinia infection (hsa05135), neuroactive ligand-receptor interaction (hsa04080), and pathogenic Escherichia coli infection (hsa05130), respectively. However, targeted genes of fs-cb-miRs in humans like KLHL20, TNS1, and PAPD4 are associated with Alzheimer's, malignant tumor of the breast, and hepatitis C virus infection disease, respectively. Similarly, in cattle, targeted genes like ATG2B and DHRS11 of fs-cb-miRs participate in the pathways of Huntington disease and steroid biosynthesis, respectively. Additionally, the targeted genes like SURF4 and EDME2 of fs-cb-miRs are associated with mastitis and bovine osteoporosis, respectively. We also found a few cb-miRs that do not have functional similarity with human and cattle miRNAs but are found to target the genes in the host organisms and as well being associated with human and cattle diseases. Interestingly, a few genes such as NRM, PTPRE and SUZ12 were observed to be associated with Rheumatoid Arthritis, Asthma and Endometrial Stromal Sarcoma diseases, respectively, in humans and genes like SCNN1B associated with renal disease in cattle.
Collapse
Affiliation(s)
- Sarika Sahu
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Atmakuri Ramakrishna Rao
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Indian Council of Agricultural Research, New Delhi 110001, India
| | - Tanmaya Kumar Sahu
- Indian Grassland and Fodder Research Institute, ICAR, Jhansi 284003, India;
| | - Jaya Pandey
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Shivangi Varshney
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Archna Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Kishor Gaikwad
- National Institute for Plant Biotechnology, ICAR, New Delhi 110012, India;
| |
Collapse
|
21
|
Manzoor MA, Xu Y, Lv Z, Xu J, Wang Y, Sun W, Liu X, Wang L, Abdullah M, Liu R, Jiu S, Zhang C. Comparative genomics of N-acetyl-5-methoxytryptamine members in four Prunus species with insights into bud dormancy and abiotic stress responses in Prunus avium. PLANT CELL REPORTS 2024; 43:89. [PMID: 38462577 DOI: 10.1007/s00299-024-03184-0] [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: 01/11/2024] [Accepted: 02/23/2024] [Indexed: 03/12/2024]
Abstract
KEY MESSAGE This study provides novel insights into the evolution, diversification, and functions of melatonin biosynthesis genes in Prunus species, highlighting their potential role in regulating bud dormancy and abiotic stresses. The biosynthesis of melatonin (MEL) in plants is primarily governed by enzymatic reactions involving key enzymes such as serotonin N-acetyltransferase (SNAT), tryptamine 5-hydroxylase (T5H), N-acetylserotonin methyltransferase (ASMT) and tryptophan decarboxylase (TDC). In this study, we analyzed Melatonin genes in four Prunus species such as Prunus avium (Pavi), Prunus pusilliflora (Ppus), Prunus serulata (Pser), and Prunus persica (Pper) based on comparative genomics approach. Among the four Prunus species, a total of 29 TDCs, 998 T5Hs, 16 SNATs, and 115 ASMTs within the genome of four Prunus genomes. A thorough investigation of melatonin-related genes was carried out using systematic biological methods and comparative genomics. Through phylogenetic analysis, orthologous clusters, Go enrichment, syntenic relationship, and gene duplication analysis, we discovered both similarities and variations in Melatonin genes among these Prunus species. Additionally, our study revealed the existence of unique subgroup members in the Melatonin genes of these species, which were distinct from those found in Arabidopsis genes. Furthermore, the transcriptomic expression analysis revealed the potential significance of melatonin genes in bud dormancy regulation and abiotic stresses. Our extensive results offer valuable perspectives on the evolutionary patterns, intricate expansion, and functions of PavMEL genes. Given their promising attributes, PavTDCs, PavT5H, PavNAT, and three PavASMT genes warrant in-depth exploration as prime candidates for manipulating dormancy in sweet cherry. This was done to lay the foundation for future explorations into the structural and functional aspects of these factors in Prunus species. This study offers significant insights into the functions of ASMT, SNAT, T5H, and TDC genes and sheds light on their roles in Prunus avium. Moreover, it established a robust foundation for further exploration functional characterization of melatonin genes in fruit species.
Collapse
Affiliation(s)
- Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Jieming Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Yuxuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Li Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Muhammad Abdullah
- Queensland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China.
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang District Jianchuan Road No.601, Shanghai, 200240, People's Republic of China.
| |
Collapse
|
22
|
Bouza C, Losada AP, Fernández C, Álvarez-Dios JA, de Azevedo AM, Barreiro A, Costas D, Quiroga MI, Martínez P, Vázquez S. A comprehensive coding and microRNA transcriptome of vertebral bone in postlarvae and juveniles of Senegalese sole (Solea senegalensis). Genomics 2024; 116:110802. [PMID: 38290593 DOI: 10.1016/j.ygeno.2024.110802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Understanding vertebral bone development is essential to prevent skeletal malformations in farmed fish related to genetic and environmental factors. This is an important issue in Solea senegalensis, with special impact of spinal anomalies in postlarval and juvenile stages. Vertebral bone transcriptomics in farmed fish mainly comes from coding genes, and barely on miRNA expression. Here, we used RNA-seq of spinal samples to obtain the first comprehensive coding and miRNA transcriptomic repertoire for postlarval and juvenile vertebral bone, covering different vertebral phenotypes and egg-incubation temperatures related to skeleton health in S. senegalensis. Coding genes, miRNA and pathways regulating bone development and growth were identified. Differential transcriptomic profiles and suggestive mRNA-miRNA interactions were found between postlarvae and juveniles. Bone-related genes and functions were associated with the extracellular matrix, development and regulatory processes, calcium binding, retinol and lipid metabolism or response to stimulus, including those revealed by the miRNA targets related to signaling, cellular and metabolic processes, growth, cell proliferation and biological adhesion. Pathway enrichment associated with fish skeleton were identified when comparing postlarvae and juveniles: growth and bone development functions in postlarvae, while actin cytoskeleton, focal adhesion and proteasome related to bone remodeling in juveniles. The transcriptome data disclosed candidate coding and miRNA gene markers related to bone cell processes, references for functional studies of the anosteocytic bone of S. senegalensis. This study establishes a broad transcriptomic foundation to study healthy and anomalous spines under early thermal conditions across life-stages in S. senegalensis, and for comparative analysis of skeleton homeostasis and pathology in fish and vertebrates.
Collapse
Affiliation(s)
- Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
| | - Ana P Losada
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - José A Álvarez-Dios
- Department of Applied Mathematics, Faculty of Mathematics, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Ana Manuela de Azevedo
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Andrés Barreiro
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Damián Costas
- Centro de Investigación Mariña, Universidade de Vigo, ECIMAT, Vigo 36331, Spain
| | - María Isabel Quiroga
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Sonia Vázquez
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| |
Collapse
|
23
|
Xing C, Lei C, Yang Y, Zhou D, Liu S, Xu J, Liu Z, Wu T, Zhou X, Huang S, Liu W. Drought responses and population differentiation of Calohypnum plumiforme inferred from comparative transcriptome analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108456. [PMID: 38417308 DOI: 10.1016/j.plaphy.2024.108456] [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: 07/03/2023] [Revised: 01/16/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Bryophytes, known as poikilohydric plants, possess vegetative desiccation-tolerant (DT) ability to withstand water deficit stress. Consequently, they offer valuable genetic resources for enhancing resistance to water scarcity stress. In this research, we examined the physiological, phytohormonal, and transcriptomic changes in DT mosses Calohypnum plumiforme from two populations, with and without desiccation treatment. Comparative analysis revealed population differentiation at physiological, gene sequence, and expression levels. Under desiccation stress, the activities of superoxide dismutase (SOD) and peroxidase (POD) showed significant increases, along with elevation of soluble sugars and proteins, consistent with the transcriptome changes. Notable activation of the bypass pathway of JA biosynthesis suggested their roles in compensating for JA accumulation. Furthermore, our analysis revealed significant correlations among phytohormones and DEGs in their respective signaling pathway, indicating potential complex interplays of hormones in C plumiforme. Protein phosphatase 2C (PP2C) in the abscisic acid signaling pathway emerged as the pivotal hub in the phytohormone crosstalk regulation network. Overall, this study was one of the first comprehensive transcriptome analyses of moss C. plumiforme under slow desiccation rates, expanding our knowledge of bryophyte transcriptomes and shedding light on the gene regulatory network involved in response to desiccation, as well as the evolutionary processes of local adaptation across moss populations.
Collapse
Affiliation(s)
- Chengguang Xing
- Guangdong Key Laboratory of Plant Resources, School of Ecology, Sun Yat-sen University, Shenzhen, 518100, China.
| | - Chunyi Lei
- Department of Scientific Research and Education, Heishiding Nature Reserve, Zhaoqing, 526536, China.
| | - Yuchen Yang
- Guangdong Key Laboratory of Plant Resources, School of Ecology, Sun Yat-sen University, Shenzhen, 518100, China.
| | - Dandan Zhou
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China.
| | - Shanshan Liu
- Guangdong Key Laboratory of Plant Resources, School of Ecology, Sun Yat-sen University, Shenzhen, 518100, China.
| | - Jianqu Xu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Zhiwei Liu
- Guangdong Key Laboratory of Plant Resources, School of Ecology, Sun Yat-sen University, Shenzhen, 518100, China.
| | - Tao Wu
- Guangdong Key Laboratory of Plant Resources, School of Ecology, Sun Yat-sen University, Shenzhen, 518100, China.
| | - Xiaohang Zhou
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shuzhen Huang
- Guangdong Key Laboratory of Plant Resources, School of Ecology, Sun Yat-sen University, Shenzhen, 518100, China.
| | - Weiqiu Liu
- Guangdong Key Laboratory of Plant Resources, School of Ecology, Sun Yat-sen University, Shenzhen, 518100, China.
| |
Collapse
|
24
|
Bhardwaj RG, Khalaf ME, Karched M. Secretome analysis and virulence assessment in Abiotrophia defectiva. J Oral Microbiol 2024; 16:2307067. [PMID: 38352067 PMCID: PMC10863525 DOI: 10.1080/20002297.2024.2307067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Background Abiotrophia defectiva, although infrequently occurring, is a notable cause of culture-negative infective endocarditis with limited research on its virulence. Associated with oral infections such as dental caries, exploring its secretome may provide insights into virulence mechanisms. Our study aimed to analyze and characterize the secretome of A. defectiva strain CCUG 27639. Methods Secretome of A. defectiva was prepared from broth cultures and subjected to mass spectrometry and proteomics for protein identification. Inflammatory potential of the secretome was assessed by ELISA. Results Eighty-four proteins were identified, with diverse subcellular localizations predicted by PSORTb. Notably, 20 were cytoplasmic, 12 cytoplasmic membrane, 5 extracellular, and 9 cell wall-anchored proteins. Bioinformatics tools revealed 54 proteins secreted via the 'Sec' pathway and 8 via a non-classical pathway. Moonlighting functions were found in 23 proteins, with over 20 exhibiting potential virulence properties, including peroxiredoxin and oligopeptide ABC transporter substrate-binding protein. Gene Ontology and KEGG analyses categorized protein sequences in various pathways. STRING analysis revealed functional protein association networks. Cytokine profiling demonstrated significant proinflammatory cytokine release (IL-8, IL-1β, and CCL5) from human PBMCs. Conclusions Our study provides a comprehensive understanding of A. defectiva's secretome, laying the foundation for insights into its pathogenicity.
Collapse
Affiliation(s)
- Radhika G Bhardwaj
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences College of Dentistry, Kuwait University, Safat, Kuwait
| | - Mai E Khalaf
- Department of General Dental Practice, College of Dentistry, Kuwait University, Safat, Kuwait
| | - Maribasappa Karched
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences College of Dentistry, Kuwait University, Safat, Kuwait
| |
Collapse
|
25
|
Miranda J, Veneza I, Ferreira C, Santana P, Lutz I, Furtado C, Pereira P, Rabelo L, Guerreiro-Diniz C, Melo M, Sampaio I, Vallinoto M, Evangelista-Gomes G. First neurotranscriptome of adults Tambaquis (Colossoma macropomum) with characterization and differential expression between males and females. Sci Rep 2024; 14:3130. [PMID: 38326509 PMCID: PMC10850070 DOI: 10.1038/s41598-024-53734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/04/2024] [Indexed: 02/09/2024] Open
Abstract
The Tambaqui is one of the most representative Amazon fish species, being highly exploited in fisheries, aquaculture and as a research model. Nonetheless, data about functional genome are still required to evaluate reproductive and nutrition parameters as well as resistance to pathogens. The of next-generation sequencing has allows assessing the transcriptional processes in non-model species by providing comprehensive gene collections to be used as a database in further genomic applications and increased performance of captive populations. In this study, we relied on RNAseq approach to generate the first transcriptome of the telencephalon from adult males and females of Colossoma macropomum, resulting in a reference dataset for future functional studies. We retrieved 896,238 transcripts, including the identification of 267,785 contigs and 203,790 genes. From this total, 91 transcripts were differentially expressed, being 63 and 28 of them positively regulated for females and males, respectively. The functional annotation resulted in a library of 40 candidate genes for females and 20 for males. The functional enrichment classes comprised reproductive processes (GO:0,048,609; GO:0,003,006; GO:0,044,703; GO:0,032,504; GO:0,019,953) being related to sex differentiation (e.g., SAFB) and immune response (e.g., SLC2A6, AHNAK, NLRC3, NLRP3 and IgC MHC I alpha3), thus indicating that the genes in the neurotranscriptome of Tambaqui participate in sex differentiation and homeostasis of captive specimens. These data are useful to design the selection of genes related to sex determination and animal welfare in raising systems of Tambaqui.
Collapse
Affiliation(s)
- Josy Miranda
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Ivana Veneza
- Universidade Federal do Oeste do Pará, Campus Monte Alegre, Av. Major Francisco Mariano - Bairro Cidade Alta, Monte Alegre, Pará, ZIP Code 68220-000, Brazil
| | - Charles Ferreira
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Paula Santana
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Italo Lutz
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Carolina Furtado
- Divisão de Genética, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA), Pr. da Cruz Vermelha, 23 - Bairro Centro, Rio de Janeiro, ZIP Code: 20230-130, Brazil
| | - Patrick Pereira
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência E Tecnologia Do Pará, - Campus Bragança, Rua da Escola Agrícola S/N - Bairro Vila Sinhá - Caixa Postal 72, Bragança, PA, ZIP Code: 68600-000, Brazil
| | - Luan Rabelo
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Cristovam Guerreiro-Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência E Tecnologia Do Pará, - Campus Bragança, Rua da Escola Agrícola S/N - Bairro Vila Sinhá - Caixa Postal 72, Bragança, PA, ZIP Code: 68600-000, Brazil
| | - Mauro Melo
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência E Tecnologia Do Pará, - Campus Bragança, Rua da Escola Agrícola S/N - Bairro Vila Sinhá - Caixa Postal 72, Bragança, PA, ZIP Code: 68600-000, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Grazielle Evangelista-Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil.
| |
Collapse
|
26
|
Anuradha C, Chandrasekar A, Backiyarani S, Thangavelu R, Uma S, Selvarajan R. Dataset from transcriptome profiling of Musa resistant and susceptible cultivars in response to Fusarium oxysporum f.sp. cubense race1 and TR4 challenges using Illumina NovaSeq. Data Brief 2024; 52:109803. [PMID: 38370021 PMCID: PMC10873869 DOI: 10.1016/j.dib.2023.109803] [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: 09/15/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 02/20/2024] Open
Abstract
In this investigation, the study focused on the RNAseq data generated in response to Fusarium oxysporum f.sp. cubense (Foc) race1 (Cavendish infecting strain VCG 0124), targeting both resistant (cv. Rose, AA) and susceptible cultivars (Namarai, AA), and Tropical Race 4 (TR4, strain VCG 01213/16), involving resistant (cv. Rose, AA) and susceptible cultivars (Matti, AA). The respective contrasting cultivars were independently challenged with Foc race1 and TR4, and the root and corm samples were collected in two replications at varying time intervals [0th (control), 2nd, 4th, 6th, and 8th days] in duplicates. The RNA samples underwent stringent quality checks, with all 80 samples meeting the primary parameters, including a satisfactory RNA integrity number (>7). Subsequent library preparation and secondary quality control steps were executed successfully for all samples, paving the way for the sequencing phase. Sequencing generated an extensive amount of data, yielding a range of 10 to 31 million paired-end raw reads per sample, resulting in a cumulative raw data size of 11-50 GB. These raw reads were aligned against the reference genome of Musa acuminata ssp. malaccensis version 2 (DH Pahang), as well as the pathogen genomes of Foc race 1 and Foc TR4, using the HISAT2 alignment tool. The focal point of this study was the investigation of differential gene expression patterns of Musa spp. upon Foc infection. In Foc race1 resistant and susceptible root samples across the designated day intervals, a significant number of genes displayed up-regulation (ranging from 1 to 228) and down-regulation (ranging from 1 to 274). In corm samples, the up-regulated genes ranged from 1 to 149, while down-regulated genes spanned from 3 to 845. For Foc TR4 resistant and susceptible root samples, the expression profiles exhibited a notable up-regulation of genes (ranging from 31 to 964), along with a down-regulation range of 316-1315. In corm samples, up-regulated genes ranged from 57 to 929, while down-regulated genes were observed in the range of 40-936. In addition to the primary analysis, a comprehensive secondary analysis was conducted, including Gene Ontology (GO), euKaryotic Orthologous Groups (KOG) classification, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and investigations into Simple Sequence Repeats (SSRs), Single Nucleotide Polymorphisms (SNPs), and microRNA (miRNA). The complete dataset was carefully curated and housed at ICAR-NRCB, Trichy, ensuring its accuracy and accessibility for the duration of the study. Further, the raw transcriptome read datasets have been successfully submitted to the National Center for Biotechnology Information - Sequence Read Archive (NCBI-SRA) database, ensuring the accessibility and reproducibility of this valuable dataset for further research endeavors.
Collapse
Affiliation(s)
- C. Anuradha
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - A. Chandrasekar
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - S. Backiyarani
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - R. Thangavelu
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - S. Uma
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - R. Selvarajan
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| |
Collapse
|
27
|
Jia K, Yang M, Liu X, Zhang Q, Cao G, Ge F, Zhao J. Deciphering the structure, function, and mechanism of lysine acetyltransferase cGNAT2 in cyanobacteria. PLANT PHYSIOLOGY 2024; 194:634-661. [PMID: 37770070 DOI: 10.1093/plphys/kiad509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023]
Abstract
Lysine acetylation is a conserved regulatory posttranslational protein modification that is performed by lysine acetyltransferases (KATs). By catalyzing the transfer of acetyl groups to substrate proteins, KATs play critical regulatory roles in all domains of life; however, no KATs have yet been identified in cyanobacteria. Here, we tested all predicted KATs in the cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) and demonstrated that A1596, which we named cyanobacterial Gcn5-related N-acetyltransferase (cGNAT2), can catalyze lysine acetylation in vivo and in vitro. Eight amino acid residues were identified as the key residues in the putative active site of cGNAT2, as indicated by structural simulation and site-directed mutagenesis. The loss of cGNAT2 altered both growth and photosynthetic electron transport in Syn7002. In addition, quantitative analysis of the lysine acetylome identified 548 endogenous substrates of cGNAT2 in Syn7002. We further demonstrated that cGNAT2 can acetylate NAD(P)H dehydrogenase J (NdhJ) in vivo and in vitro, with the inability to acetylate K89 residues, thus decreasing NdhJ activity and affecting both growth and electron transport in Syn7002. In summary, this study identified a KAT in cyanobacteria and revealed that cGNAT2 regulates growth and photosynthesis in Syn7002 through an acetylation-mediated mechanism.
Collapse
Affiliation(s)
- Kun Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430070, China
| | - Qi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaoxiang Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
28
|
Solano LE, D’Sa NM, Nikolaidis N. PRRGO: A Tool for Visualizing and Mapping Globally Expressed Genes in Public Gene Expression Omnibus RNA-Sequencing Studies to PageRank-scored Gene Ontology Terms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576540. [PMID: 38328158 PMCID: PMC10849496 DOI: 10.1101/2024.01.21.576540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
We herein report PageRankeR Gene Ontology (PRRGO), a downloadable web application that can integrate differentially expressed gene (DEG) data from the gene expression omnibus (GEO) GEO2R web tool with the gene ontology (GO) database [1]. Unlike existing tools, PRRGO computes the PageRank for the entire GO network and can generate both interactive GO networks on the web interface and comma-separated values (CSV) files containing the DEG statistics categorized by GO term. These hierarchical and tabular GO-DEG data are especially conducive to hypothesis generation and overlap studies with the use of PageRank data, which can provide a metric of GO term centrality. We verified the tool for accuracy and reliability across nine independent heat shock (HS) studies for which the RNA-seq data was publicly available on GEO and found that the tool produced increasing concordance between study DEGs, GO terms, and select HS-specific GO terms.
Collapse
Affiliation(s)
- Luis E. Solano
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA
| | - Nicholas M. D’Sa
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850
- University of California, Irvine, Irvine, CA
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850
| |
Collapse
|
29
|
Kim M, Kim J, Lee S, Khanh N, Li Z, Polle JEW, Jin E. Deciphering the β-carotene hyperaccumulation in Dunaliella by the comprehensive analysis of Dunaliella salina and Dunaliella tertiolecta under high light conditions. PLANT, CELL & ENVIRONMENT 2024; 47:213-229. [PMID: 37727131 DOI: 10.1111/pce.14724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023]
Abstract
The green microalga Dunaliella salina hyperaccumulates β-carotene in the chloroplast, which turns its cells orange. This does not occur in the sister species Dunaliella tertiolecta. However, the molecular mechanisms of β-carotene hyperaccumulation were still unclear. Here, we discovered the reasons for β-carotene hyperaccumulation by comparing the morphology, physiology, genome, and transcriptome between the carotenogenic D. salina and the noncarotenogenic D. tertiolecta after transfer to high light. The differences in photosynthetic capacity, cell growth, and the concentration of stored carbon suggest that these species regulate the supply and utilization of carbon differently. The number of β-carotene-containing plastid lipid globules increased in both species, but much faster and to a greater extent in D. salina than in D. tertiolecta. Consistent with the accumulation of plastid lipid globules, the expression of the methyl-erythritol-phosphate and carotenoid biosynthetic pathways increased only in D. salina, which explains the de novo synthesis of β-carotene. In D. salina, the concomitantly upregulated expression of the carotene globule proteins suggests that hyperaccumulation of β-carotene also requires a simultaneous increase in its sink capacity. Based on genomic analysis, we propose that D. salina has genetic advantages for routing carbon from growth to carotenoid metabolism.
Collapse
Affiliation(s)
- Minjae Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Jongrae Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Sangmuk Lee
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Nguyen Khanh
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Zhun Li
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Juergen E W Polle
- Department of Biology, Brooklyn College of the City University of New York, New York, Brooklyn, USA
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
| |
Collapse
|
30
|
Chen Y, Chen Y, Yu XQ, Feng Q, Wang X, Liu L. Expression profiles of lncRNAs, miRNAs, and mRNAs and interaction analysis indicate their potential involvement during testicular fusion in Spodoptera litura. Genomics 2024; 116:110758. [PMID: 38065236 DOI: 10.1016/j.ygeno.2023.110758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024]
Abstract
Testicular fusion of Spodoptera litura occures during metamorphosis, which benefits sperms development. Previous research identified involvement of ECM-integrin interaction pathways, MMPs in testicular fusion, but the regulatory mechanism remains unclear. RNA-seq was performed to analyze long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in testes, aiming to uncover potential regulatory mechanisms of testicular fusion. 2150 lncRNAs, 2742 targeted mRNAs, and 347 miRNAs were identified in testes at three different developmental stages. Up-regulated DElncRNAs and DEmRNAs, as well as down-regulated DEmiRNAs, were observed during testicular fusion, while the opposite expression pattern was observed after fusion. Enrichment analysis of DEmRNAs revealed that cAMP signal pathway, ECM remodeling enzymes, ECM-integrin interaction pathways, and cell adhesion molecules were potentially associated with testicular fusion. The identified DElncRNA-DEmiRNA-DEmRNA regulatory network related to cAMP signal pathway, ECM remodeling enzymes suggests their roles during testicular fusion. Our research will provide new targets for studying the mechanism of testicular fusion.
Collapse
Affiliation(s)
- Yaqing Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yu Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao-Qiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiaoyun Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| |
Collapse
|
31
|
Li H, Zhao J, Li Y, Dong Z, Lin S, Guo B, Qi P. Transcriptome analysis reveals tissue-specific responses of Mytilus unguiculatus to Vibrio alginolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109301. [PMID: 38110106 DOI: 10.1016/j.fsi.2023.109301] [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: 09/12/2023] [Revised: 11/27/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Mytilus unguiculatus is an important economic bivalve species with wide consumption and aquaculture value. Disease is one of the primary limiting factors in mussel aquaculture, thus understanding the response of different tissues of M. unguiculatus to pathogens is crucial for disease prevention and control. In this study, we investigated the physiological and transcriptomic responses of the gills, adductor muscle, and mantle of M. unguiculatus infected with Vibrio alginolyticus. The results showed that V. alginolyticus infection caused inflammation and tissue structure changes in the gill, adductor muscle and mantle of M. unguiculatus. Meanwhile, the activities of superoxide dismutase and catalase in the three tissues increased, while the total antioxidant capacity decreased, suggesting that M. unguiculatus have an activated defense mechanism against infection-induced oxidative stress, despite a compromised total antioxidant capacity. Transcriptomic studies reveal that infected M. unguiculatus exhibits upregulation of endocytosis, lysosome activity, cellular apoptosis, and immune-related signaling pathways, indicating that M. unguiculatus responds to pathogen invasion by upregulating efferocytosis. Compared with the gill and adductor muscle, the mantle had a higher level of mytimycin, mytilin and myticin, and the three tissues also increased the expression of mytimycin to cope with the invasion of pathogens. In addition, the analysis of genes related to taste transduction pathways and muscle contraction and relaxation found that after infection with V. alginolyticus, M. unguiculatus may reduce appetite by inhibiting taste transduction in the gill, while improving muscle contraction of the adductor muscle and keeping the shell closed, to resist further invasion of pathogens and reduce the risk of pathogen transmission in the population.
Collapse
Affiliation(s)
- Hongfei Li
- Donghai Laboratory, Zhoushan, Zhejiang, 316021, China; National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China.
| | - Jiemei Zhao
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Yaru Li
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Zhenyu Dong
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Shuangrui Lin
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Baoying Guo
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Pengzhi Qi
- Donghai Laboratory, Zhoushan, Zhejiang, 316021, China; National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China.
| |
Collapse
|
32
|
Parmar S, Gajera G, Thakkar N, Palep HS, Kothari V. Deciphering the molecular mechanisms underlying anti-pathogenic potential of a polyherbal formulation Enteropan® against multidrug-resistant Pseudomonas aeruginosa. Drug Target Insights 2024; 18:54-69. [PMID: 39224464 PMCID: PMC11367655 DOI: 10.33393/dti.2024.3082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Objective Anti-pathogenic potential of a polyherbal formulation Enteropan® was investigated against a multidrug-resistant strain of the bacterium Pseudomonas aeruginosa. Methods Growth, pigment production, antibiotic susceptibility, etc., were assessed through appropriate in vitro assays. Virulence of the test pathogen was assessed employing the nematode worm Caenorhabditis elegans as a model host. Molecular mechanisms underlining the anti-pathogenic activity of the test formulation were elucidated through whole transcriptome analysis of the extract-exposed bacterial culture. Results Enteropan-pre-exposed P. aeruginosa displayed reduced (~70%↓) virulence towards the model host C. elegans. Enteropan affected various traits like biofilm formation, protein synthesis and secretion, quorum-modulated pigment production, antibiotic susceptibility, nitrogen metabolism, etc., in this pathogen. P. aeruginosa could not develop complete resistance to the virulence-attenuating activity of Enteropan even after repeated exposure to this polyherbal formulation. Whole transcriptome analysis showed 17% of P. aeruginosa genome to get differentially expressed under influence of Enteropan. Major mechanisms through which Enteropan exerted its anti-virulence activity were found to be generation of nitrosative stress, oxidative stress, envelop stress, quorum modulation, disturbance of protein homeostasis and metal homeostasis. Network analysis of the differently expressed genes resulted in identification of 10 proteins with high network centrality as potential targets from among the downregulated genes. Differential expression of genes coding for five (rpoA, tig, rpsB, rpsL, and rpsJ) of these targets was validated through real-time polymerase chain reaction too, and they can further be pursued as potential targets by various drug discovery programmes.
Collapse
Affiliation(s)
- Sweety Parmar
- Institute of Science, Nirma University, Ahmedabad - India
| | - Gemini Gajera
- Institute of Science, Nirma University, Ahmedabad - India
| | - Nidhi Thakkar
- Institute of Science, Nirma University, Ahmedabad - India
| | | | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad - India
| |
Collapse
|
33
|
Song YY, Zhang XZ, Wang BN, Cheng YK, Guo X, Zhang X, Long SR, Liu RD, Wang ZQ, Cui J. A novel Trichinella spiralis serine proteinase disrupted gut epithelial barrier and mediated larval invasion through binding to RACK1 and activating MAPK/ERK1/2 pathway. PLoS Negl Trop Dis 2024; 18:e0011872. [PMID: 38190388 PMCID: PMC10798628 DOI: 10.1371/journal.pntd.0011872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/19/2024] [Accepted: 12/19/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Gut epithelium is the first natural barrier against Trichinella spiralis larval invasion, but the mechanism by which larval penetration of gut epithelium is not completely elucidated. Previous studies showed that proteases secreted by T. spiralis intestinal infective larvae (IIL) degraded tight junctions (TJs) proteins of gut epithelium and mediated larval invasion. A new T. spiralis serine proteinase (TsSPc) was identified in the IIL surface proteins and ES proteins, rTsSPc bound to the intestinal epithelial cell (IECs) and promoted larval invasion of IECs. The aim of this study was to characterize the interacted proteins of TsSPc and IECs, and to investigate the molecular mechanisms of TsSPc mediating larval invasion of gut mucosa. METHODOLOGY/PRINCIPAL FINDING IIFT results showed natural TsSPc was detected in infected murine intestine at 6, 12 hours post infection (hpi) and 3 dpi. The results of GST pull-down, mass spectrometry (MS) and Co-IP indicated that rTsSPc bound and interacted specifically with receptor for activated protein C kinase 1 (RACK1) in Caco-2 cells. rTsSPc did not directly hydrolyze the TJs proteins. qPCR and Western blot showed that rTsSPc up-regulated RACK1 expression, activated MAPK/ERK1/2 pathway, reduced the expression levels of gut TJs (occludin and claudin-1) and adherent protein E-cad, increased the paracellular permeability and damaged the integrity of intestinal epithelial barrier. Moreover, the RACK1 inhibitor HO and ERK1/2 pathway inhibitor PD98059 abolished the rTsSPc activating ERK1/2 pathway, they also inhibited and abrogated the rTsSPc down-regulating expression of occludin, claudin-1 and E-cad in Caco-2 monolayer and infected murine intestine, impeded larval invasion and improved intestinal epithelial integrity and barrier function, reduced intestinal worm burdens and alleviated intestinal inflammation. CONCLUSIONS rTsSPc bound to RACK1 receptor in gut epithelium, activated MAPK/ERK1/2 pathway, decreased the expression of gut epithelial TJs proteins and disrupted the epithelial integrity, consequently mediated T. spiralis larval invasion of gut epithelium. The results are valuable to understand T. spiralis invasion mechanism, and TsSPc might be regarded as a vaccine target against T. spiralis invasion and infection.
Collapse
Affiliation(s)
- Yan Yan Song
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Xin Zhuo Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Bo Ning Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Yong Kang Cheng
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Xin Guo
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Xi Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Shao Rong Long
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Ruo Dan Liu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Zhong Quan Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cui
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
34
|
Parrish SB, Paudel D, Deng Z. Transcriptome analysis of Lantana camara flower petals reveals candidate anthocyanin biosynthesis genes mediating red flower color development. G3 (BETHESDA, MD.) 2023; 14:jkad259. [PMID: 37974306 PMCID: PMC10755171 DOI: 10.1093/g3journal/jkad259] [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: 07/05/2023] [Revised: 07/05/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Flower color plays a crucial role in the appeal and selection of ornamental plants, directly influencing breeding strategies and the broader horticulture industry. Lantana camara, a widely favored flowering shrub, presents a rich palette of flower colors. Yet, the intricate molecular mechanisms governing this color variation in the species have remained largely unidentified. With the aim of filling this gap, this study embarked on a comprehensive de novo transcriptome assembly and differential gene expression analysis across 3 distinct lantana accessions, each showcasing a unique flower color. By harnessing the capabilities of both PacBio and Illumina sequencing platforms, a robust transcriptome assembly, encompassing 123,492 gene clusters and boasting 94.2% BUSCO completeness, was developed. The differential expression analysis unveiled 72,862 unique gene clusters that exhibited varied expression across different flower stages. A pronounced upregulation of 8 candidate core anthocyanin biosynthesis genes in the red-flowered accession was uncovered. This was further complemented by an upregulation of candidate MYB75 (PAP1) and bHLH42 (TT8) transcription factors. A candidate carotenoid cleavage dioxygenase (CCD4a) gene cluster also manifested a marked upregulation in white flowers. The study unveils the molecular groundwork of lantana's flower color variation, offering insights for future research and potential applications in breeding ornamental plants with desired color traits.
Collapse
Affiliation(s)
- Stephen Brooks Parrish
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
| | - Dev Paudel
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
| |
Collapse
|
35
|
Chot E, Medicherla KM, Reddy MS. Comparative transcriptome analysis of ectomycorrhizal fungus Pisolithus albus in response to individual and combined stress of copper and cadmium. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:118616-118633. [PMID: 37917254 DOI: 10.1007/s11356-023-30592-8] [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: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
An ectomycorrhizal fungus Pisolithus albus establishes the natural symbiosis with plant roots on extreme heavy metal (HM)-rich soil and enables their survival in toxic metal concentrations. Understanding P. albus key genes and pathways behind strong metal tolerance is crucial for its successful application in the rehabilitation of metal-contaminated barren lands. Therefore, this study aimed to analyze the whole transcriptome profile of P. albus under individual and combined metal stress of copper (Cu) and cadmium (Cd). At 480 µM Cu and 16 µM Cd toxic concentrations, P. albus has shown growth and survival and accumulated high metal (1.46 µg Cu and 1.13 µg Cd per mg of dry mycelia). The study found a stronger response of P. albus to single-metal stress in high concentration as compared to multi-metal stress in relatively lower concentration. Hence, the intensity of fungal response to HM stress is mainly determined by the metal concentration involved in stress. We have found a total of 11 pathways significantly associated with HM stress, among which amino acid, lipid, and carbohydrate metabolisms were highly affected. The functional enrichment of differentially expressed genes has shown the induced biosynthesis of arginine, melanin, metal chelating agents, membrane phospholipids, fatty acids, folate, pantothenate, ergothioneine, and other antioxidant agents; upregulation of zinc ion uptake, potassium transporters, and lysine degradation; and reduction of phosphatidylcholine degradation, incorrect protein folding, iron uptake, and potassium efflux as the top efficient tolerance mechanisms of P. albus against HM stress. The current study would contribute to understanding fungal HM tolerance and its further utilization in the bioremediation of metal-contaminated abandoned lands. The validation of RNA-sequencing analysis with RT-qPCR of selected genes showed the high credibility of the presented data.
Collapse
Affiliation(s)
- Eetika Chot
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab, 147004, India
| | | | - Mondem Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab, 147004, India.
| |
Collapse
|
36
|
Suhaimi AH, Kobayashi MJ, Satake A, Ng CC, Lee SL, Muhammad N, Numata S, Otani T, Kondo T, Tani N, Yeoh SH. An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii. PeerJ 2023; 11:e16368. [PMID: 38047035 PMCID: PMC10693236 DOI: 10.7717/peerj.16368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/08/2023] [Indexed: 12/05/2023] Open
Abstract
Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation.
Collapse
Affiliation(s)
- Ahmad Husaini Suhaimi
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Masaki J. Kobayashi
- Forestry Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Ching Ching Ng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Soon Leong Lee
- Forestry Biotechnology Division, Forest Research Institute Malaysia, Selangor, Malaysia
| | - Norwati Muhammad
- Forestry Biotechnology Division, Forest Research Institute Malaysia, Selangor, Malaysia
| | - Shinya Numata
- Department of Tourism Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Tatsuya Otani
- Shikoku Research Center, Forestry Research and Management Organization, Kochi, Japan
| | - Toshiaki Kondo
- Bio-Resources and Utilization Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Naoki Tani
- Forestry Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Suat Hui Yeoh
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
37
|
Gajera G, Thakkar N, Godse C, DeSouza A, Mehta D, Kothari V. Sub-lethal concentration of a colloidal nanosilver formulation (Silversol®) triggers dysregulation of iron homeostasis and nitrogen metabolism in multidrug resistant Pseudomonas aeruginosa. BMC Microbiol 2023; 23:303. [PMID: 37872532 PMCID: PMC10591374 DOI: 10.1186/s12866-023-03062-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a notorious pathogen. Its multidrug resistant strains are listed among priority pathogens against whom discovery of novel antibacterial agents and, elucidation of new anti-pathogenicity mechanisms are urgently warranted. This study describes multiple antibacterial effects of a colloidal nano-silver formulation- Silversol® against a multi-drug resistant strain of P. aeruginosa. RESULTS Minimum inhibitory concentration (MIC) of Silversol® against P. aeruginosa was found to be 1.5 ppm; and at sub-MIC of 1 ppm, it was able to alter quorum-sensing regulated pigmentation (pyocanin 82%↓; pyoverdine 48%↑), exopolysaccharide synthesis (76%↑) and biofilm formation, susceptibility to antibiotics (streptomycin and augmentin), protein synthesis and export (65%↑), nitrogen metabolism (37%↑ nitrite accumulation), and siderophore production in this pathogen. Network analysis of the differentially expressed genes in the transcriptome of the silversol-treated bacterium identified ten genes as the potential molecular targets: norB, norD, nirS, nirF, nirM, nirQ, nosZ, nosY, narK1, and norE (all associated with nitrogen metabolism or denitrification). Three of them (norB, narK1, and norE) were also validated through RT-PCR. CONCLUSIONS Generation of nitrosative stress and disturbance of iron homeostasis were found to be the major mechanisms associated with anti-Pseudomonas activity of Silversol®.
Collapse
Affiliation(s)
- Gemini Gajera
- Institute of Science, Nirma University, Ahmedabad, 382481, India
| | - Nidhi Thakkar
- Institute of Science, Nirma University, Ahmedabad, 382481, India
| | | | | | | | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad, 382481, India.
| |
Collapse
|
38
|
Ning HJ, Gui FF, Tian EW, Yang LY. The novel developed microsatellite markers revealed potential hybridization among Cymbidium species and the interspecies sub-division of C. goeringii and C. ensifolium. BMC PLANT BIOLOGY 2023; 23:492. [PMID: 37833649 PMCID: PMC10571305 DOI: 10.1186/s12870-023-04499-y] [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: 03/25/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Orchids (Cymbidium spp.) exhibit significant variations in floral morphology, pollinator relations, and ecological habitats. Due to their exceptional economic and ornamental value, Cymbidium spp. have been commercially cultivated for centuries. SSR markers are extensively used genetic tools for biology identification and population genetics analysis. RESULT In this study, nine polymorphic EST-SSR loci were isolated from Cymbidium goeringii using RNA-Seq technology. All nine SSR loci showed transferability in seven other congeneric species, including 51 cultivars. The novel SSR markers detected inter-species gene flow among the Cymbidium species and intra-species sub-division of C. goeringii and C. ensifolium, as revealed by neighborhood-joining and Structure clustering analyses. CONCLUSION In this study, we developed nine microsatellites using RNA-Seq technology. These SSR markers aided in detecting potential gene flow among Cymbidium species and identified the intra-species sub-division of C. goeringii and C. ensifolium.
Collapse
Affiliation(s)
- Hui-Juan Ning
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Fang-Fang Gui
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - En-Wei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
| | - Li-Yuan Yang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou, 311300, Zhejiang, China.
| |
Collapse
|
39
|
Hechler RM, Yates MC, Chain FJJ, Cristescu ME. Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms? Mol Ecol 2023. [PMID: 37792902 DOI: 10.1111/mec.17152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species-specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test whether broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20°C) and heat stress (28°C) conditions for 7 days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA-based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across eight taxa. Our study demonstrates that environmental transcriptomics based on extra-organismal eRNA can noninvasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of health across the trophic chain.
Collapse
Affiliation(s)
- Robert M Hechler
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Matthew C Yates
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | | |
Collapse
|
40
|
Liu Q, Wen J, Wang S, Chen J, Sun Y, Liu Q, Li X, Dong S. Genome-wide identification, expression analysis, and potential roles under low-temperature stress of bHLH gene family in Prunus sibirica. FRONTIERS IN PLANT SCIENCE 2023; 14:1267107. [PMID: 37799546 PMCID: PMC10548393 DOI: 10.3389/fpls.2023.1267107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
The basic helix-loop-helix (bHLH) family is one of the most well-known transcription factor families in plants, and it regulates growth, development, and abiotic stress responses. However, systematic analyses of the bHLH gene family in Prunus sibirica have not been reported to date. In this study, 104 PsbHLHs were identified and classified into 23 subfamilies that were unevenly distributed on eight chromosomes. Nineteen pairs of segmental replication genes and ten pairs of tandem replication genes were identified, and all duplicated gene pairs were under purifying selection. PsbHLHs of the same subfamily usually share similar motif compositions and exon-intron structures. PsbHLHs contain multiple stress-responsive elements. PsbHLHs exhibit functional diversity by interacting and coordinating with other members. Twenty PsbHLHs showed varying degrees of expression. Eleven genes up-regulated and nine genes down-regulated in -4°C. The majority of PsbHLHs were highly expressed in the roots and pistils. Transient transfection experiments demonstrated that transgenic plants with overexpressed PsbHLH42 have better cold tolerance. In conclusion, the results of this study have significant implications for future research on the involvement of bHLH genes in the development and stress responses of Prunus sibirica.
Collapse
Affiliation(s)
- Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jiaxing Wen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shipeng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Qingbai Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Xi Li
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
41
|
Xiao R, Sun Y, Yang S, Yang Y, Wang D, Wang Z, Zhou W. Systematic Identification and Functional Analysis of the Hypericum perforatum L. bZIP Gene Family Indicating That Overexpressed HpbZIP69 Enhances Drought Resistance. Int J Mol Sci 2023; 24:14238. [PMID: 37762543 PMCID: PMC10531856 DOI: 10.3390/ijms241814238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Basic leucine zipper (bZIP) transcription factors play significant roles in plants' growth and development processes, as well as in response to biological and abiotic stresses. Hypericum perforatum is one of the world's top three best-selling herbal medicines, mainly used to treat depression. However, there has been no systematic identification or functional analysis of the bZIP gene family in H. perforatum. In this study, 79 HpbZIP genes were identified. Based on phylogenetic analysis, the HpbZIP gene family was divided into ten groups, designated A-I and S. The physicochemical properties, gene structures, protein conserved motifs, and Gene Ontology enrichments of all HpbZIPs were systematically analyzed. The expression patterns of all genes in different tissues of H. perforatum (i.e., root, stem, leaf, and flower) were analyzed by qRT-PCR, revealing the different expression patterns of HpbZIP under abiotic stresses. The HpbZIP69 protein is localized in the nucleus. According to the results of the yeast one-hybrid (Y1H) assays, HpbZIP69 can bind to the HpASMT2 (N-acetylserotonin O-methyltransferase) gene promoter (G-box cis-element) to activate its activity. Overexpressing HpbZIP69 in Arabidopsis wild-type lines enhanced their tolerance to drought. The MDA and H2O2 contents were significantly decreased, and the activity of superoxide dismutase (SOD) was considerably increased under the drought stress. These results may aid in additional functional studies of HpbZIP transcription factors, and in cultivating drought-resistant medicinal plants.
Collapse
Affiliation(s)
| | | | | | | | | | - Zhezhi Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (R.X.); (Y.S.); (S.Y.); (Y.Y.); (D.W.)
| | - Wen Zhou
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an 710119, China; (R.X.); (Y.S.); (S.Y.); (Y.Y.); (D.W.)
| |
Collapse
|
42
|
Jayaprakash A, Roy A, Thanmalagan RR, Arunachalam A, P T V L. Understanding the mechanism of pathogenicity through interactome studies between Arachis hypogaea L. and Aspergillus flavus. J Proteomics 2023; 287:104975. [PMID: 37482270 DOI: 10.1016/j.jprot.2023.104975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/28/2023] [Accepted: 07/15/2023] [Indexed: 07/25/2023]
Abstract
Aspergillus flavus (A. flavus) infects the peanut seeds during pre-and post-harvest stages, causing seed quality destruction for humans and livestock consumption. Even though many resistant varieties were developed, the molecular mechanism of defense interactions of peanut against A. flavus still needs further investigation. Hence, an interologous host-pathogen protein interaction (HPPI) network was constructed to understand the subcellular level interaction mechanism between peanut and A. flavus. Out of the top 10 hub proteins of both organisms, protein phosphatase 2C and cyclic nucleotide-binding/kinase domain-containing protein and different ribosomal proteins were identified as candidate proteins involved in defense. Functional annotation and subcellular localization based characterization of HPPI identified protein SGT1 homolog, calmodulin and Rac-like GTP-binding proteins to be involved in defense response against fungus. The relevance of HPPI in infectious conditions was assessed using two transcriptome data which identified the interplay of host kinase class R proteins, bHLH TFs and cell wall related proteins to impart resistance against pathogen infection. Further, the pathogenicity analysis identified glycogen phosphorylase and molecular chaperone and allergen Mod-E/Hsp90/Hsp1 as potential pathogen targets to enhance the host defense mechanism. Hence, the computationally predicted host-pathogen PPI network could provide valuable support for molecular biology experiments to understand the host-pathogen interaction. SIGNIFICANCE: Protein-protein interactions execute significant cellular interactions in an organism and are influenced majorly by stress conditions. Here we reported the host-pathogen protein-protein interaction between peanut and A. flavus, and a detailed network analysis based on function, subcellular localization, gene co-expression, and pathogenicity was performed. The network analysis identified key proteins such as host kinase class R proteins, calmodulin, SGT1 homolog, Rac-like GTP-binding proteins bHLH TFs and cell wall related to impart resistance against pathogen infection. We observed the interplay of defense related proteins and cell wall related proteins predominantly, which could be subjected to further studies. The network analysis described in this study could be applied to understand other host-pathogen systems generally.
Collapse
Affiliation(s)
- Aiswarya Jayaprakash
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Abhijeet Roy
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Raja Rajeswary Thanmalagan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Annamalai Arunachalam
- Department of Food Science & Technology, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Lakshmi P T V
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India.
| |
Collapse
|
43
|
Lee MB, Han H, Lee S. The role of WRKY transcription factors, FaWRKY29 and FaWRKY64, for regulating Botrytis fruit rot resistance in strawberry (Fragaria × ananassa Duch.). BMC PLANT BIOLOGY 2023; 23:420. [PMID: 37691125 PMCID: PMC10494375 DOI: 10.1186/s12870-023-04426-1] [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: 04/19/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND The cultivated strawberry (Fragaria × ananassa Duch.) is one of the most economically important horticultural crops worldwide. Botrytis fruit rot (BFR) caused by the necrotrophic fungal pathogen Botrytis cinerea is the most devasting disease of cultivated strawberries. Most commercially grown strawberry varieties are susceptible to BFR, and controlling BFR relies on repeated applications of various fungicides. Despite extensive efforts, breeding for BFR resistance has been unsuccessful, primarily due to lack of information regarding the mechanisms of disease resistance and genetic resources available in strawberry. RESULTS Using a reverse genetics approach, we identified candidate genes associated with BFR resistance and screened Arabidopsis mutants using strawberry isolates of B. cinerea. Among the five Arabidopsis T-DNA knockout lines tested, the mutant line with AtWRKY53 showed the greatest reduction in disease symptoms of BFR against the pathogen. Two genes, FaWRKY29 and FaWRKY64, were identified as orthologs in the latest octoploid strawberry genome, 'Florida Brilliance'. We performed RNAi-mediated transient assay and found that the disease frequencies were significantly decreased in both FaWRKY29- and FaWRKY64-RNAi fruits of the strawberry cultivar, 'Florida Brilliance'. Furthermore, our transcriptomic data analysis revealed significant regulation of genes associated with ABA and JA signaling, plant cell wall composition, and ROS in FaWRKY29 or FaWRKY64 knockdown strawberry fruits in response to the pathogen. CONCLUSION Our study uncovered the foundational role of WRKY transcription factor genes, FaWRKY29 and FaWRKY64, in conferring resistance against B. cinerea. The discovery of susceptibility genes involved in BFR presents significant potential for developing resistance breeding strategies in cultivated strawberries, potentially leveraging CRISPR-based gene editing techniques.
Collapse
Affiliation(s)
- Man Bo Lee
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Korea
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL, 33598, USA
| | - Hyeondae Han
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL, 33598, USA
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL, 33598, USA.
| |
Collapse
|
44
|
He Q, Gong G, Wan T, Hu H, Yu P. An integrated transcriptomic and metabolic phenotype analysis to uncover the metabolic characteristics of a genetically engineered Candida utilis strain expressing δ-zein gene. Front Microbiol 2023; 14:1241462. [PMID: 37744922 PMCID: PMC10513430 DOI: 10.3389/fmicb.2023.1241462] [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: 06/23/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Candida utilis (C. utilis) has been extensively utilized as human food or animal feed additives. With its ability to support heterologous gene expression, C. utilis proves to be a valuable platform for the synthesis of proteins and metabolites that possess both high nutritional and economic value. However, there remains a dearth of research focused on the characteristics of C. utilis through genomic, transcriptomic and metabolic approaches. Methods With the aim of unraveling the molecular mechanism and genetic basis governing the biological process of C. utilis, we embarked on a de novo sequencing endeavor to acquire comprehensive sequence data. In addition, an integrated transcriptomic and metabolic phenotype analysis was performed to compare the wild-type C. utilis (WT) with a genetically engineered strain of C. utilis that harbors the heterologous δ-zein gene (RCT). Results δ-zein is a protein rich in methionine found in the endosperm of maize. The integrated analysis of transcriptomic and metabolic phenotypes uncovered significant metabolic diversity between the WT and RCT C. utilis. A total of 252 differentially expressed genes were identified, primarily associated with ribosome function, peroxisome activity, arginine and proline metabolism, carbon metabolism, and fatty acid degradation. In the experimental setup using PM1, PM2, and PM4 plates, a total of 284 growth conditions were tested. A comparison between the WT and RCT C. utilis demonstrated significant increases in the utilization of certain carbon source substrates by RCT. Gelatin and glycogen were found to be significantly utilized to a greater extent by RCT compared to WT. Additionally, in terms of sulfur source substrates, RCT exhibited significantly increased utilization of O-Phospho-L-Tyrosine and L-Methionine Sulfone when compared to WT. Discussion The introduction of δ-zein gene into C. utilis may lead to significant changes in the metabolic substrates and metabolic pathways, but does not weaken the activity of the strain. Our study provides new insights into the transcriptomic and metabolic characteristics of the genetically engineered C. utilis strain harboring δ-zein gene, which has the potential to advance the utilization of C. utilis as an efficient protein feed in agricultural applications.
Collapse
Affiliation(s)
- Qiburi He
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Science, Hohhot, China
| | - Gaowa Gong
- Inner Mongolia Academy of Agricultural and Animal Husbandry Science, Hohhot, China
| | - Tingting Wan
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - He Hu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Science, Hohhot, China
| | - Peng Yu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| |
Collapse
|
45
|
Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
Collapse
Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| |
Collapse
|
46
|
Arredondo-Espinoza R, Ibarra AM, Roberts SB, Sicard-González MT, Escobedo-Fregoso C. Transcriptome profile in heat resilient Pacific oyster Crassostrea gigas families under thermal challenge. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101089. [PMID: 37269757 DOI: 10.1016/j.cbd.2023.101089] [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: 01/26/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/05/2023]
Abstract
Since the introduction of the Pacific oyster Crassostrea gigas in Baja California Sur, Mexico, its culture has faced environmental challenges, specifically increasing temperatures that result in high mortalities. The inter-tidal zone seawater temperature during a year at the Baja California Peninsula broadly ranges from 7 °C to 39 °C. Therefore, to understand how oysters respond to heat stress during daily temperature oscillations, heat-resistant (RR, father, and mother resistant) and heat-susceptible (SS, both parents susceptible) phenotypes families from a C. gigas breeding program were exposed to a thermal challenge. Based on a laboratory-simulated daily oscillatory thermal challenge (26 to 34 °C) for 30 days, RR phenotype presented differences compared to SS phenotype since the beginning (day 0) of the thermal challenge. Gene expression analyses revealed 1822 differentially expressed up-regulated transcripts in RR, related to functions of metabolic processes, biological regulation, and response to stimulus and signaling. At the end of the experiment (day 30), 2660 differentially expressed up-regulated transcripts were identified in RR. Functional analysis of the genes expressed indicates responses of regulation of biological processes and response to a stimulus. Additionally, 340 genes were differentially expressed among RR vs. SS from the beginning to the end of the thermal challenge, where 170 genes were up-regulated, and 170 were down-regulated. These transcriptomic profiles represent the first report to identify gene expression markers associated with RR phenotypes for the Pacific oyster to the future broodstock selection.
Collapse
Affiliation(s)
- Roberto Arredondo-Espinoza
- Centro de Investigaciones Biológicas del Noroeste S.C. (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste S.C. (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA. https://twitter.com/sr320
| | - Maria Teresa Sicard-González
- Centro de Investigaciones Biológicas del Noroeste S.C. (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico
| | - Cristina Escobedo-Fregoso
- Consejo Nacional de Ciencia y Tecnología-Centro de Investigaciones Biológicas del Noroeste S.C. (CONACYT-CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, Baja California Sur, Mexico.
| |
Collapse
|
47
|
Otero-Ruiz A, Rodriguez-Anaya LZ, Lares-Villa F, Lozano Aguirre Beltrán LF, Lares-Jiménez LF, Gonzalez-Galaviz JR, Cruz-Mendívil A. Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes. Sci Rep 2023; 13:14318. [PMID: 37653073 PMCID: PMC10471605 DOI: 10.1038/s41598-023-41657-6] [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: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Balamuthia mandrillaris is a pathogenic protozoan that causes a rare but almost always fatal infection of the central nervous system and, in some cases, cutaneous lesions. Currently, the genomic data for this free-living amoeba include the description of several complete mitochondrial genomes. In contrast, two complete genomes with draft quality are available in GenBank, but none of these have a functional annotation. In the present study, the complete genome of B. mandrillaris isolated from a freshwater artificial lagoon was sequenced and assembled, obtaining an assembled genome with better assembly quality parameter values than the currently available genomes. Afterward, the genome mentioned earlier, along with strains V039 and 2046, were subjected to functional annotation. Finally, comparative genomics analysis was performed, and it was found that homologous genes in the core genome potentially involved in the virulence of Acanthamoeba spp. and Trypanosoma cruzi. Moreover, eleven of fifteen genes were identified in the three strains described as potential target genes to develop new treatment approaches for B. mandrillaris infections. These results describe proteins in this protozoan's complete genome and help prioritize which target genes could be used to develop new treatments.
Collapse
Affiliation(s)
- Alejandro Otero-Ruiz
- Programa de Doctorado en Ciencias Especialidad en Biotecnología, Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | - Luis Fernando Lozano Aguirre Beltrán
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas de la Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Abraham Cruz-Mendívil
- CONAHCYT-Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, 81101, Guasave, Sinaloa, Mexico
| |
Collapse
|
48
|
Liu C, Jiang Y, Yun Z, Zhang K, Zhao M, Wang Y, Zhang M, Tian Z, Wang K. Small RNA-Seq to Unveil the miRNA Expression Patterns and Identify the Target Genes in Panax ginseng. PLANTS (BASEL, SWITZERLAND) 2023; 12:3070. [PMID: 37687317 PMCID: PMC10490192 DOI: 10.3390/plants12173070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Panax ginseng, renowned for its medicinal properties, relies on adventitious roots and hairy roots as crucial sources for the production of ginsenosides. Despite the widespread utilization of ginseng, investigations into its miRNAs have remained scarce. To address this gap, two samples of ginseng adventitious roots and ginseng hairy roots were collected, and subsequent construction and sequencing of small RNA libraries of ginseng adventitious roots and hairy roots were performed using the Illumina HiSeq X Ten platform. The analysis of the sequencing data unveiled total miRNAs 2432. The miR166 and miR396 were the most highly expressed miRNA families in ginseng. The miRNA expression analysis results were used to validate the qRT-PCR. Target genes of miRNA were predicted and GO function annotation and KEGG pathway analysis were performed on target genes. It was found that miRNAs are mainly involved in synthetic pathways and biological processes in plants, which include metabolic and bioregulatory processes. The plant miRNAs enriched KEGG pathways are associated with some metabolism, especially amino acid metabolism and carbohydrate metabolism. These results provide valuable insights miRNAs and their roles in metabolic processes in ginseng.
Collapse
Affiliation(s)
- Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| | - Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| | - Ziyi Yun
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| | - Kexin Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| | - Zhuo Tian
- College of Information Technology, Jilin Agricultural University, Changchun 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (C.L.); (Y.J.); (Z.Y.); (K.Z.); (M.Z.); (Y.W.); (M.Z.)
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
| |
Collapse
|
49
|
Wang BH, Du LF, Zhang MZ, Xia LY, Li C, Lin ZT, Wang N, Gao WY, Ye RZ, Liu JY, Han XY, Shi WQ, Shi XY, Jiang JF, Jia N, Cui XM, Zhao L, Cao WC. Genomic Characterization of Theileria luwenshuni Strain Cheeloo. Microbiol Spectr 2023; 11:e0030123. [PMID: 37260375 PMCID: PMC10434005 DOI: 10.1128/spectrum.00301-23] [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: 01/19/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
Theileria, a tick-borne intracellular protozoan, can cause infections of various livestock and wildlife around the world, posing a threat to veterinary health. Although more and more Theileria species have been identified, genomes have been available only from four Theileria species to date. Here, we assembled a whole genome of Theileria luwenshuni, an emerging Theileria, through next-generation sequencing of purified erythrocytes from the blood of a naturally infected goat. We designated it T. luwenshuni str. Cheeloo because its genome was assembled by the researchers at Cheeloo College of Medicine, Shandong University, China. The genome of T. lunwenshuni str. Cheeloo was the smallest in comparison with the other four Theileria species. T. luwenshuni str. Cheeloo possessed the fewest gene gains and gene family expansion. The protein count of each category was always comparable between T. luwenshuni str. Cheeloo and T. orientalis str. Shintoku in the Eukaryote Orthologs annotation, though there were remarkable differences in genome size. T. luwenshuni str. Cheeloo had lower counts than the other four Theileria species in most categories at level 3 of Gene Ontology annotation. Kyoto Encyclopedia of Genes and Genomes annotation revealed a loss of the c-Myb in T. luwenshuni str. Cheeloo. The infection rate of T. luwenshuni str. Cheeloo was up to 81.5% in a total of 54 goats from three flocks. The phylogenetic analyses based on both 18S rRNA and cox1 genes indicated that T. luwenshuni had relatively low diversity. The first characterization of the T. luwenshuni genome will promote better understanding of the emerging Theileria. IMPORTANCE Theileria has led to substantial economic losses in animal husbandry. Whole-genome sequencing data of the genus Theileria are currently limited, which has prohibited us from further understanding their molecular features. This work depicted whole-genome sequences of T. luwenshuni str. Cheeloo, an emerging Theileria species, and reported a high prevalence of T. luwenshuni str. Cheeloo infection in goats. The first assembly and characterization of T. luwenshuni genome will benefit exploring the infective and pathogenic mechanisms of the emerging Theileria to provide scientific basis for future control strategies of theileriosis.
Collapse
Affiliation(s)
- Bai-Hui Wang
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Li-Feng Du
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Cheng Li
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Zhe-Tao Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Ning Wang
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Wan-Ying Gao
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Jin-Yue Liu
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Xiao-Yu Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Wen-Qiang Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiao-Yu Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| |
Collapse
|
50
|
Das P, Grover M, Mishra DC, Guha Majumdar S, Shree B, Kumar S, Mir ZA, Chaturvedi KK, Bhardwaj SC, Singh AK, Rai A. Genome-wide identification and characterization of Puccinia striiformis-responsive lncRNAs in Triticum aestivum. FRONTIERS IN PLANT SCIENCE 2023; 14:1120898. [PMID: 37650000 PMCID: PMC10465180 DOI: 10.3389/fpls.2023.1120898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/10/2023] [Indexed: 09/01/2023]
Abstract
Wheat stripe rust (yellow rust) caused by Puccinia striiformis f. sp. tritici (Pst) is a serious biotic stress factor limiting wheat production worldwide. Emerging evidence demonstrates that long non-coding RNAs (lncRNAs) participate in various developmental processes in plants via post-transcription regulation. In this study, RNA sequencing (RNA-seq) was performed on a pair of near-isogenic lines-rust resistance line FLW29 and rust susceptible line PBW343-which differed only in the rust susceptibility trait. A total of 6,807 lncRNA transcripts were identified using bioinformatics analyses, among which 10 lncRNAs were found to be differentially expressed between resistance and susceptible lines. In order to find the target genes of the identified lncRNAs, their interactions with wheat microRNA (miRNAs) were predicted. A total of 199 lncRNAs showed interactions with 65 miRNAs, which further target 757 distinct mRNA transcripts. Moreover, detailed functional annotations of the target genes were used to identify the candidate genes, pathways, domains, families, and transcription factors that may be related to stripe rust resistance response in wheat plants. The NAC domain protein, disease resistance proteins RPP13 and RPM1, At1g58400, monodehydroascorbate reductase, NBS-LRR-like protein, rust resistance kinase Lr10-like, LRR receptor, serine/threonine-protein kinase, and cysteine proteinase are among the identified targets that are crucial for wheat stripe rust resistance. Semiquantitative PCR analysis of some of the differentially expressed lncRNAs revealed variations in expression profiles of two lncRNAs between the Pst-resistant and Pst-susceptible genotypes at least under one condition. Additionally, simple sequence repeats (SSRs) were also identified from wheat lncRNA sequences, which may be very useful for conducting targeted gene mapping studies of stripe rust resistance in wheat. These findings improved our understanding of the molecular mechanism responsible for the stripe rust disease that can be further utilized to develop wheat varieties with durable resistance to this disease.
Collapse
Affiliation(s)
- Parinita Das
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Monendra Grover
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | | | - Bharti Shree
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| |
Collapse
|