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Mueller HM, Franzisky BL, Messerer M, Du B, Lux T, White PJ, Carpentier SC, Winkler JB, Schnitzler JP, El-Serehy HA, Al-Rasheid KAS, Al-Harbi N, Alfarraj S, Kudla J, Kangasjärvi J, Reichelt M, Mithöfer A, Mayer KFX, Rennenberg H, Ache P, Hedrich R, Geilfus CM. Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water. THE PLANT GENOME 2024; 17:e20372. [PMID: 37518859 DOI: 10.1002/tpg2.20372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 08/01/2023]
Abstract
Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well-known salt-tolerance strategies are combined to fine-tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt-tolerance mechanisms are integrated to fine-tune this remarkable resilience. To address this shortcoming, we exposed date palm to a salt stress dose equivalent to seawater for up to 4 weeks and applied integrative multi-omics analyses followed by targeted metabolomics, hormone, and ion analyses. Integration of proteomic into transcriptomic data allowed a view beyond simple correlation, revealing a remarkably high degree of convergence between gene expression and protein abundance. This sheds a clear light on the acclimatization mechanisms employed, which depend on reprogramming of protein biosynthesis. For growth in highly saline habitats, date palm effectively combines various salt-tolerance mechanisms found in both halophytes and glycophytes: "avoidance" by efficient sodium and chloride exclusion at the roots, and "acclimation" by osmotic adjustment, reactive oxygen species scavenging in leaves, and remodeling of the ribosome-associated proteome in salt-exposed root cells. Combined efficiently as in P. dactylifera L., these sets of mechanisms seem to explain the palm's excellent salt stress tolerance.
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Affiliation(s)
- Heike M Mueller
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Bastian L Franzisky
- Department of Soil Science and Plant Nutrition, Hochschule Geisenheim University, Geisenheim, Germany
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Baoguo Du
- College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, China
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
| | | | - Sebastien Christian Carpentier
- Facility for SYstems BIOlogy based MAss Spectrometry, SYBIOMA, Proteomics Core Facility, KU Leuven, Leuven, Belgium
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
| | - Jana Barbro Winkler
- Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Center Munich, Neuherberg, Germany
| | - Joerg-Peter Schnitzler
- Research Unit Environmental Simulation (EUS), Institute of Biochemical Plant Pathology, Helmholtz Center Munich, Neuherberg, Germany
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Naif Al-Harbi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Alfarraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jaakko Kangasjärvi
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Peter Ache
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Würzburg, Germany
| | - Christoph-Martin Geilfus
- Department of Soil Science and Plant Nutrition, Hochschule Geisenheim University, Geisenheim, Germany
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Rahim MS, Sharma V, Pragati Yadav, Parveen A, Kumar A, Roy J, Kumar V. Rethinking underutilized cereal crops: pan-omics integration and green system biology. PLANTA 2023; 258:91. [PMID: 37777666 DOI: 10.1007/s00425-023-04242-9] [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: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
MAIN CONCLUSION Due to harsh lifestyle changes, in the present era, nutritional security is needed along with food security so it is necessary to include underutilized cereal crops (UCCs) in our daily diet to counteract the rising danger of human metabolic illness. We can attain both the goal of zero hunger and nutritional security by developing improved UCCs using advanced pan-omics (genomics, transcriptomics, proteomics, metabolomics, nutrigenomics, phenomics and ionomics) practices. Plant sciences research progressed profoundly since the last few decades with the introduction of advanced technologies and approaches, addressing issues of food demand of the growing population, nutritional security challenges and climate change. However, throughout the expansion and popularization of commonly consumed major cereal crops such as wheat and rice, other cereal crops such as millet, rye, sorghum, and others were impeded, despite their potential medicinal and nutraceutical qualities. Undoubtedly neglected underutilized cereal crops (UCCs) also have the capability to withstand diverse climate change. To relieve the burden of major crops, it is necessary to introduce the new crops in our diet in the way of UCCs. Introgression of agronomically and nutritionally important traits by pan-omics approaches in UCCs could be a defining moment for the population's well-being on the globe. This review discusses the importance of underutilized cereal crops, as well as the application of contemporary omics techniques and advanced bioinformatics tools that could open up new avenues for future study and be valuable assets in the development and usage of UCCs in the perspective of green system biology. The increased and improved use of UCCs is dependent on number of factors that necessitate a concerted research effort in agricultural sciences. The emergence of functional genomics with molecular genetics might gear toward the reawakening of interest in underutilized cereals crops. The need of this era is to focus on potential UCCs in advanced agriculture and breeding programmes. Hence, targeting the UCCs, might provide a bright future for better health and scientific rationale for its use.
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Affiliation(s)
- Mohammed Saba Rahim
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Pragati Yadav
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Afsana Parveen
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India
| | - Adarsh Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab, 140 306, India.
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Punjab, 151401, India.
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Rajpal VR, Sharma S, Sehgal D, Sharma P, Wadhwa N, Dhakate P, Chandra A, Thakur RK, Deb S, Rama Rao S, Mir BA, Raina SN. Comprehending the dynamism of B chromosomes in their journey towards becoming unselfish. Front Cell Dev Biol 2023; 10:1072716. [PMID: 36684438 PMCID: PMC9846793 DOI: 10.3389/fcell.2022.1072716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Investigated for more than a century now, B chromosomes (Bs) research has come a long way from Bs being considered parasitic or neutral to becoming unselfish and bringing benefits to their hosts. B chromosomes exist as accessory chromosomes along with the standard A chromosomes (As) across eukaryotic taxa. Represented singly or in multiple copies, B chromosomes are largely heterochromatic but also contain euchromatic and organellar segments. Although B chromosomes are derived entities, they follow their species-specific evolutionary pattern. B chromosomes fail to pair with the standard chromosomes during meiosis and vary in their number, size, composition and structure across taxa and ensure their successful transmission through non-mendelian mechanisms like mitotic, pre-meiotic, meiotic or post-meiotic drives, unique non-disjunction, self-pairing or even imparting benefits to the host when they lack drive. B chromosomes have been associated with cellular processes like sex determination, pathogenicity, resistance to pathogens, phenotypic effects, and differential gene expression. With the advancements in B-omics research, novel insights have been gleaned on their functions, some of which have been associated with the regulation of gene expression of A chromosomes through increased expression of miRNAs or differential expression of transposable elements located on them. The next-generation sequencing and emerging technologies will further likely unravel the cellular, molecular and functional behaviour of these enigmatic entities. Amidst the extensive fluidity shown by B chromosomes in their structural and functional attributes, we perceive that the existence and survival of B chromosomes in the populations most likely seem to be a trade-off between the drive efficiency and adaptive significance versus their adverse effects on reproduction.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
| | - Suman Sharma
- Department of Botany, Ramjas College, University of Delhi, Delhi, India
| | - Deepmala Sehgal
- Syngenta, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Prashansa Sharma
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Sohini Deb
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Bilal Ahmad Mir
- Department of Botany, University of Kashmir, Srinagar, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
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Oliveira JIN, Cardoso AL, Wolf IR, de Oliveira RA, Martins C. First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome. BMC Biol 2022; 20:204. [PMID: 36127679 PMCID: PMC9490952 DOI: 10.1186/s12915-022-01403-2] [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: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND B chromosomes are extra elements found in several eukaryote species. Usually, they do not express a phenotype in the host. However, advances in bioinformatics over the last decades have allowed us to describe several genes and molecular functions related to B chromosomes. These advances enable investigations of the relationship between the B chromosome and the host to understand how this element has been preserved in genomes. However, considering that transposable elements (TEs) are highly abundant in this supernumerary chromosome, there is a lack of knowledge concerning the dynamics of TE control in B-carrying cells. Thus, the present study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of TEs in gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. RESULTS Through small RNA-seq and genome assembly, we predicted and annotated piRNA clusters in the A. latifasciata genome for the first time. We observed that these clusters had biased expression related to sex and the presence of the B chromosome. Furthermore, three piRNA clusters, named curupira, were identified in the B chromosome. Two of them were expressed exclusively in gonads of samples with the B chromosome. The composition of these curupira sequences was derived from LTR, LINE, and DNA elements, representing old and recent transposition events in the A. latifasciata genome and the B chromosome. The presence of the B chromosome also affected the expression of piRNA pathway genes. The mitochondrial cardiolipin hydrolase-like (pld6) gene is present in the B chromosome, as previously reported, and an increase in its expression was detected in gonads with the B chromosome. CONCLUSIONS Due to the high abundance of TEs in the B chromosome, it was possible to investigate the origin of piRNA from these jumping genes. We hypothesize that the B chromosome has evolved its own genomic guardians to prevent uncontrolled TE mobilization. Furthermore, we also detected an expression bias in the presence of the B chromosome over A. latifasciata piRNA clusters and pathway genes.
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Affiliation(s)
- Jordana Inácio Nascimento Oliveira
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Ivan Rodrigo Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Rogério Antônio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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Boudichevskaia A, Fiebig A, Kumke K, Himmelbach A, Houben A. Rye B chromosomes differently influence the expression of A chromosome-encoded genes depending on the host species. Chromosome Res 2022; 30:335-349. [PMID: 35781770 PMCID: PMC9771852 DOI: 10.1007/s10577-022-09704-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 01/25/2023]
Abstract
The B chromosome (B) is a dispensable component of the genome in many species. To evaluate the impact of Bs on the transcriptome of the standard A chromosomes (A), comparative RNA-seq analyses of rye and wheat anthers with and without additional rye Bs were conducted. In both species, 5-6% of the A-derived transcripts across the entire genomes were differentially expressed in the presence of 2Bs. The GO term enrichment analysis revealed that Bs influence A chromosome encoded processes like "gene silencing"; "DNA methylation or demethylation"; "chromatin silencing"; "negative regulation of gene expression, epigenetic"; "post-embryonic development"; and "chromosome organization." 244 B chromosome responsive A-located genes in + 2B rye and + B wheat shared the same biological function. Positively correlated with the number of Bs, 939 and 1391 B-specific transcripts were identified in + 2B and + 4B wheat samples, respectively. 85% of B-transcripts in + 2B were also found in + 4B transcriptomes. 297 B-specific transcripts were identified in + 2B rye, and 27% were common to the B-derived transcripts identified in + B wheat. Bs encode mobile elements and housekeeping genes, but most B-transcripts were without detectable similarity to known genes. Some of these genes are involved in cell division-related functions like Nuf2 and might indicate their importance in maintaining Bs. The transcriptome analysis provides new insights into the complex interrelationship between standard A chromosomes and supernumerary B chromosomes.
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Affiliation(s)
- Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
- KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany.
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
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