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Collier TC, Lee Y, Mathias DK, Del Amo VL. CRISPR-Cas9 and Cas12a target site richness reflects genomic diversity in natural populations of Anopheles gambiae and Aedes aegypti mosquitoes. BMC Genomics 2024; 25:700. [PMID: 39020310 PMCID: PMC11253549 DOI: 10.1186/s12864-024-10597-4] [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: 05/28/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024] Open
Abstract
Due to limitations in conventional disease vector control strategies including the rise of insecticide resistance in natural populations of mosquitoes, genetic control strategies using CRISPR gene drive systems have been under serious consideration. The identification of CRISPR target sites in mosquito populations is a key aspect for developing efficient genetic vector control strategies. While genome-wide Cas9 target sites have been explored in mosquitoes, a precise evaluation of target sites focused on coding sequence (CDS) is lacking. Additionally, target site polymorphisms have not been characterized for other nucleases such as Cas12a, which require a different DNA recognition site (PAM) and would expand the accessibility of mosquito genomes for genetic engineering. We undertook a comprehensive analysis of potential target sites for both Cas9 and Cas12a nucleases within the genomes of natural populations of Anopheles gambiae and Aedes aegypti from multiple continents. We demonstrate that using two nucleases increases the number of targets per gene. Also, we identified differences in nucleotide diversity between North American and African Aedes populations, impacting the abundance of good target sites with a minimal degree of polymorphisms that can affect the binding of gRNA. Lastly, we screened for gRNAs targeting sex-determination genes that could be widely applicable for developing field genetic control strategies. Overall, this work highlights the utility of employing both Cas9 and Cas12a nucleases and underscores the importance of designing universal genetic strategies adaptable to diverse mosquito populations.
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Affiliation(s)
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32962, USA
| | - Derrick K Mathias
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32962, USA
| | - Víctor López Del Amo
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, 77030, USA.
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Yang B, Cheng Z, Luo L, Cheng K, Gan S, Shi Y, Liu C, Wang D. Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins. Front Microbiol 2023; 14:1320060. [PMID: 38156001 PMCID: PMC10752978 DOI: 10.3389/fmicb.2023.1320060] [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: 10/12/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Background Plasmodium falciparum is a protozoan parasite that causes the most severe form of malaria in humans worldwide, which is predominantly found in sub-Saharan Africa, where it is responsible for the majority of malaria-related deaths. Plasmodium helical interspersed subtelomeric (PHIST) proteins are a family of proteins, with a conserved PHIST domain, which are typically located at the subtelomeric regions of the Plasmodium falciparum chromosomes and play crucial roles in the interaction between the parasite and its human host, such as cytoadherence, immune evasion, and host cell remodeling. However, the specific utilization of synonymous codons by PHIST proteins in Plasmodium falciparum is still unknown. Methods Codon usage bias (CUB) refers to the unequal usage of synonymous codons during translation, resulting in over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact various cellular processes, including protein expression levels and genetic variation. To investigate this, the CUB of 88 PHIST protein coding sequences (CDSs) from 5 subgroups were analyzed in this study. Results The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis identified a higher occurrence of AT-ended codons (AGA and UUA) in PHIST proteins of Plasmodium falciparum. The average effective number of codons (ENC) for these PHIST proteins was 36.69, indicating a weak codon preference among them, as it was greater than 35. Additionally, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) revealed the influence of base composition and codon usage indices on codon usage bias, with GC1 having a significant impact in this study. Furthermore, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis provided additional evidence that natural selection plays a crucial role in determining codon bias in PHIST proteins. Conclusion In conclusion, this study has enhanced our understanding of the characteristics of codon usage and genetic evolution in PHIST proteins, thereby providing data foundation for further research on antimalarial drugs or vaccines.
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Affiliation(s)
- Baoling Yang
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Ziwen Cheng
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Like Luo
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Kuo Cheng
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Shengqi Gan
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Yuyi Shi
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Che Liu
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Dawei Wang
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
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Wang D, Yang B. Analysis of codon usage bias of thioredoxin in apicomplexan protozoa. Parasit Vectors 2023; 16:431. [PMID: 37990340 PMCID: PMC10664530 DOI: 10.1186/s13071-023-06002-w] [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: 06/26/2023] [Accepted: 10/06/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as malaria, toxoplasmosis, and cryptosporidiosis. Apicomplexan protozoa possess unique thioredoxins (Trxs) that have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, and host immune evasion. However, it is still unknown how synonymous codons are used by apicomplexan protozoa Trxs. METHODS Codon usage bias (CUB) is the unequal usage of synonymous codons during translation which leads to the over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact a variety of cellular processes including protein expression levels and genetic variation. This study analyzed the CUB of 32 Trx coding sequences (CDS) from 11 apicomplexan protozoa. RESULTS The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in Cryptosporidium spp. and Plasmodium spp., while the Eimeria spp., Babesia spp., Hammondia hammondi, Neospora caninum, and Toxoplasma gondii tended to end in G/C. The average effective number of codon (ENC) value of these apicomplexan protozoa is 46.59, which is > 35, indicating a weak codon preference among apicomplexan protozoa Trxs. Furthermore, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) indicated the influence of base composition and codon usage indices on CUB. Additionally, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis further demonstrated that natural selection plays an important role in apicomplexan protozoa Trxs codon bias. CONCLUSIONS In conclusion, this study increased the understanding of codon usage characteristics and genetic evolution of apicomplexan protozoa Trxs, which expanded new ideas for vaccine and drug research.
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Affiliation(s)
- Dawei Wang
- Jinzhou Medical University, Jinzhou, 121000, Liaoning Province, China
| | - Baoling Yang
- Jinzhou Medical University, Jinzhou, 121000, Liaoning Province, China.
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Rajput A, Chauhan SM, Mohite OS, Hyun JC, Ardalani O, Jahn LJ, Sommer MO, Palsson BO. Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family. Food Microbiol 2023; 115:104334. [PMID: 37567624 DOI: 10.1016/j.fm.2023.104334] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023]
Abstract
Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Omkar S Mohite
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Omid Ardalani
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
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Bours A, Pruisscher P, Bascón-Cardozo K, Odenthal-Hesse L, Liedvogel M. The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons. Sci Rep 2023; 13:16471. [PMID: 37777595 PMCID: PMC10542752 DOI: 10.1038/s41598-023-43090-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can move around the genome, and as such are a source of genomic variability. Based on their characteristics we can annotate TEs within the host genome and classify them into specific TE types and families. The increasing number of available high-quality genome references in recent years provides an excellent resource that will enhance the understanding of the role of recently active TEs on genetic variation and phenotypic evolution. Here we showcase the use of a high-quality TE annotation to understand the distinct effect of recent and ancient TE insertions on the evolution of genomic variation, within our study species the Eurasian blackcap (Sylvia atricapilla). We investigate how these distinct TE categories are distributed along the genome and evaluate how their coverage across the genome is correlated with four genomic features: recombination rate, gene coverage, CpG island coverage and GC content. We found within the recent TE insertions an accumulation of LTRs previously not seen in birds. While the coverage of recent TE insertions was negatively correlated with both GC content and recombination rate, the correlation with recombination rate disappeared and turned positive for GC content when considering ancient TE insertions.
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Affiliation(s)
- Andrea Bours
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
| | - Peter Pruisscher
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Karen Bascón-Cardozo
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Miriam Liedvogel
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
- Institute of Avian Research "Vogelwarte Helgoland", 26386, Wilhelmshaven, Germany.
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Matoulek D, Ježek B, Vohnoutová M, Symonová R. Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution. Genes (Basel) 2023; 14:genes14020244. [PMID: 36833171 PMCID: PMC9956151 DOI: 10.3390/genes14020244] [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: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Cytogenetic and compositional studies considered fish genomes rather poor in guanine-cytosine content (GC%) because of a putative "sharp increase in genic GC% during the evolution of higher vertebrates". However, the available genomic data have not been exploited to confirm this viewpoint. In contrast, further misunderstandings in GC%, mostly of fish genomes, originated from a misapprehension of the current flood of data. Utilizing public databases, we calculated the GC% in animal genomes of three different, technically well-established fractions: DNA (entire genome), cDNA (complementary DNA), and cds (exons). Our results across chordates help set borders of GC% values that are still incorrect in literature and show: (i) fish in their immense diversity possess comparably GC-rich (or even GC-richer) genomes as higher vertebrates, and fish exons are GC-enriched among vertebrates; (ii) animal genomes generally show a GC-enrichment from the DNA, over cDNA, to the cds level (i.e., not only the higher vertebrates); (iii) fish and invertebrates show a broad(er) inter-quartile range in GC%, while avian and mammalian genomes are more constrained in their GC%. These results indicate no sharp increase in the GC% of genes during the transition to higher vertebrates, as stated and numerously repeated before. We present our results in 2D and 3D space to explore the compositional genome landscape and prepared an online platform to explore the AT/GC compositional genome evolution.
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Affiliation(s)
- Dominik Matoulek
- Department of Physics, Faculty of Science, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic
| | - Bruno Ježek
- Faculty of Informatics and Management, University of Hradec Králové, Rokitanského 62, 500 02 Hradec Králové, Czech Republic
| | - Marta Vohnoutová
- Department of Computer Science, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Radka Symonová
- Department of Computer Science, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- Correspondence:
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