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Manee MM, Alqahtani FH, Al-Shomrani BM, El-Shafie HAF, Dias GB. Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest. Insects 2023; 14:255. [PMID: 36975940 PMCID: PMC10054242 DOI: 10.3390/insects14030255] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.
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Affiliation(s)
- Manee M. Manee
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Institute of Advanced Agricultural and Food Technologies, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Fahad H. Alqahtani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Institute of Advanced Agricultural and Food Technologies, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Badr M. Al-Shomrani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Institute of Advanced Agricultural and Food Technologies, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
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Ibrahim MA, Al-Shomrani BM, Alharbi SN, Elliott TA, Alsuabeyl MS, Alqahtani FH, Manee MM. Genome-wide comparative analysis of transposable elements in Palmae genomes. Front Biosci (Landmark Ed) 2021; 26:1119-1131. [PMID: 34856758 DOI: 10.52586/5014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022]
Abstract
Background: Transposable elements (TEs) are the largest component of the genetic material of most eukaryotes and can play roles in shaping genome architecture and regulating phenotypic variation; thus, understanding genome evolution is only possible if we comprehend the contributions of TEs. However, the quantitative and qualitative contributions of TEs can vary, even between closely related lineages. For palm species, in particular, the dynamics of the process through which TEs have differently shaped their genomes remains poorly understood because of a lack of comparative studies. Materials and methods: We conducted a genome-wide comparative analysis of palm TEs, focusing on identifying and classifying TEs using the draft assemblies of four palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, and Elaeis oleifera. Our TE library was generated using both de novo structure-based and homology-based methodologies. Results: The generated libraries revealed the TE component of each assembly, which varied from 41-81%. Class I retrotransposons covered 36-75% of these species' draft genome sequences and primarily consisted of LTR retroelements, while non-LTR elements covered about 0.56-2.31% of each assembly, mainly as LINEs. The least represented were Class DNA transposons, comprising 1.87-3.37%. Conclusion: The current study contributes to a detailed identification and characterization of transposable elements in Palmae draft genome assemblies.
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Affiliation(s)
- Mohanad A Ibrahim
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Badr M Al-Shomrani
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Sultan N Alharbi
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Mohammed S Alsuabeyl
- National Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Fahad H Alqahtani
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
| | - Manee M Manee
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia.,National Center for Agricultural Technology, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
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Ibrahim MA, Al-Shomrani BM, Simenc M, Alharbi SN, Alqahtani FH, Al-Fageeh MB, Manee MM. Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus. BMC Genomics 2021; 22:842. [PMID: 34800971 PMCID: PMC8605555 DOI: 10.1186/s12864-021-08117-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available. RESULTS We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies ( https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline ). Annotation results indicated a similar proportion of each genomes comprising TEs (35-36%). Class I LTR retrotransposons comprised 16-20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1-2% of each genome. CONCLUSIONS The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.
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Affiliation(s)
- Mohanad A Ibrahim
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Badr M Al-Shomrani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mathew Simenc
- Department of Biological Sciences, California State University, Fullerton, USA
| | - Sultan N Alharbi
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fahad H Alqahtani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohamed B Al-Fageeh
- Life Sciences and Environment Research Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Manee M Manee
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
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Alshehri MA, Manee MM, Alqahtani FH, Al-Shomrani BM, Uversky VN. On the Prevalence and Potential Functionality of an Intrinsic Disorder in the MERS-CoV Proteome. Viruses 2021; 13:v13020339. [PMID: 33671602 PMCID: PMC7926987 DOI: 10.3390/v13020339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/14/2022] Open
Abstract
Middle East respiratory syndrome is a severe respiratory illness caused by an infectious coronavirus. This virus is associated with a high mortality rate, but there is as of yet no effective vaccine or antibody available for human immunity/treatment. Drug design relies on understanding the 3D structures of viral proteins; however, arriving at such understanding is difficult for intrinsically disordered proteins, whose disorder-dependent functions are key to the virus’s biology. Disorder is suggested to provide viral proteins with highly flexible structures and diverse functions that are utilized when invading host organisms and adjusting to new habitats. To date, the functional roles of intrinsically disordered proteins in the mechanisms of MERS-CoV pathogenesis, transmission, and treatment remain unclear. In this study, we performed structural analysis to evaluate the abundance of intrinsic disorder in the MERS-CoV proteome and in individual proteins derived from the MERS-CoV genome. Moreover, we detected disordered protein binding regions, namely, molecular recognition features and short linear motifs. Studying disordered proteins/regions in MERS-CoV could contribute to unlocking the complex riddles of viral infection, exploitation strategies, and drug development approaches in the near future by making it possible to target these important (yet challenging) unstructured regions.
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Affiliation(s)
- Manal A. Alshehri
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Manee M. Manee
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Fahad H. Alqahtani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
| | - Badr M. Al-Shomrani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia; (M.A.A.); (M.M.M.); (F.H.A.)
- Correspondence: (B.M.A.-S.); (V.N.U.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612, USA
- Correspondence: (B.M.A.-S.); (V.N.U.)
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Manee MM, Al-Shomrani BM, Al-Fageeh MB. Genome-wide characterization of simple sequence repeats in Palmae genomes. Genes Genomics 2020; 42:597-608. [PMID: 32246355 PMCID: PMC7181556 DOI: 10.1007/s13258-020-00924-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/10/2020] [Indexed: 11/17/2022]
Abstract
Background Microsatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm trees are tropical and subtropical plants with agricultural and economic importance due to the nutritional value of their fruit cultivars. Objective This is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species. Methods We identified and compared perfect SSRs with 1–6 bp nucleotide motifs to characterize microsatellites in Palmae species using PERF v0.2.5. We analyzed their relative abundance, relative density, and GC content in five palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, Elaeis oleifera, and Elaeis guineensis. Results A total of 118241, 328189, 450753, 176608, and 70694 SSRs were identified, respectively. The six repeat types were not evenly distributed across the five genomes. Mono- and dinucleotide SSRs were the most abundant, and GC content was highest in tri- and hexanucleotide SSRs. Conclusion We envisage that this analysis would further substantiate more in-depth computational, biochemical, and molecular studies on the roles SSRs may play in the genome organization of the palm species. The current study contributes a detailed characterization of simple sequence repeats in palm genomes. Electronic supplementary material The online version of this article (10.1007/s13258-020-00924-w) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manee M Manee
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Center of Excellence for Genomics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Badr M Al-Shomrani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohamed B Al-Fageeh
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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Manee MM, Alshehri MA, Binghadir SA, Aldhafer SH, Alswailem RM, Algarni AT, Al-Shomrani BM, Al-Fageeh MB. Comparative analysis of camelid mitochondrial genomes. J Genet 2019; 98:88. [PMID: 31544791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Camelus dromedarius has played a pivotal role in both culture and way of life in the Arabian peninsula, particularly in arid regions where other domestic animals cannot be easily domesticated. Although, the mitochondrial genomes have recently been sequenced for several camelid species, wider phylogenetic studies are yet to be performed. The features of conserved gene elements, rapid evolutionary rate, and rare recombination make the mitochondrial genome a useful molecular marker for phylogenetic studies of closely related species. Here we carried out a comparative analysis of previously sequenced mitochondrial genomes of camelids with an emphasis on C. dromedarius, revealing a number of noticeable findings. First, the arrangement of mitochondrial genes in C. dromedarius is similar to those of the other camelids. Second, multiple sequence alignment of intergenic regions shows up to 90% similarity across different kinds of camels, with dromedary camels to reach 99%. Third, we successfully identified the three domains (termination-associated sequence, conserved domain and conserved sequence block) of the control region structure. The phylogenetic tree analysis showed that C. dromedarius mitogenomes were significantly clustered in the same clade with Lama pacos mitogenome. These findings will enhance our understanding of the nucleotide composition and molecular evolution of the mitogenomes of the genus Camelus, and provide more data for comparative mitogenomics in the family Camelidae.
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Affiliation(s)
- Manee M Manee
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia.
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Wu H, Guang X, Al-Fageeh MB, Cao J, Pan S, Zhou H, Zhang L, Abutarboush MH, Xing Y, Xie Z, Alshanqeeti AS, Zhang Y, Yao Q, Al-Shomrani BM, Zhang D, Li J, Manee MM, Yang Z, Yang L, Liu Y, Zhang J, Altammami MA, Wang S, Yu L, Zhang W, Liu S, Ba L, Liu C, Yang X, Meng F, Wang S, Li L, Li E, Li X, Wu K, Zhang S, Wang J, Yin Y, Yang H, Al-Swailem AM, Wang J. Erratum: Camelid genomes reveal evolution and adaptation to desert environments. Nat Commun 2015; 6:6107. [PMID: 25629688 DOI: 10.1038/ncomms7107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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