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Transcriptomic and Genomic Insights into Invertebrates

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 February 2023) | Viewed by 14540

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Prof. Dr. Antonio Figueras

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Instituto Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
Interests: immunology; innate immunity; disease; transcriptomic; genomics
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Special Issue Information

Dear Colleagues,

After infection with a pathogen, vertebrates produce antibodies to protect themselves against future encounters with the same pathogen, but invertebrates rely only on their innate immune system to respond to potential infections. Recently, an increasing number of studies have revealed that the innate immune response of invertebrates exhibits diversity and specificity based on their diverse immune molecules. Besides well known model organisms, a number of invertebrate species differing in life cycles and adaptive strategies support the current understanding of the innate immunity, especially those living in fluctuating marine systems. Immunocompetent mollusc cells, at least the circulating hemocytes, and a variety of molecular effectors provide a rapid and robust line of defence against potential pathogens. Once activated by the interaction between pathogen associated molecular patterns (PAMPs) and pathogen recognition receptors (PRR), such cells display chemotactic and chemokinetic reactions, participate in encapsulation and melanization, carry out phagocytic or lytic killing. These events are made possible by the concerted action of transmembrane and soluble lectins, Toll-like and virus sensing receptors, hydrolytic enzymes and proteolytic reaction cascades, short-lived cytotoxic by-products and antimicrobial peptides (AMP) .

The Mediterranean mussel (Mytilus galloprovincialis) is a cultured bivalve species with an important commercial and ecological value worldwide. M. galloprovincialis displays an extraordinary resistance to a variety of pathogens. Although molluscs lack a specific immune response, their innate response, which involves circulating hemocytes and a large variety of molecular effectors, constitutes an efficient defense mechanism. While a wide range of molecules involved in the bivalve immune system have been described, particularly for mussels and oysters, the information is very limited compared, for example, to vertebrates. Unfortunately, most bivalve genomic resources are not annotated or well described. In order to shed light on the diversity and specificity of the innate immune response in invertebrates, this Special Issue is dedicated to current progress of Innate Immunity in Invertebrates.

Prof. Dr. Antonio Figueras
Guest Editor

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Published Papers (6 papers)

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Research

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19 pages, 4970 KiB

Open AccessArticle

In Silico Characterisation of the Aedes aegypti Gustatory Receptors

by Maria Bibi, Adil Hussain, Farman Ali, Asad Ali, Fazal Said, Kaleem Tariq and Byung-Wook Yun

Int. J. Mol. Sci. 2023, 24(15), 12263; https://doi.org/10.3390/ijms241512263 - 31 Jul 2023

Viewed by 1857

Abstract

Aedes aegypti, also known as the dengue mosquito or the yellow fewer mosquito, is the vector of dengue, chikungunya, Zika, Mayaro and yellow fever viruses. The A. aegypti genome contains an array of gustatory receptor (GR) proteins that are related to the recognition of taste. In this study, we performed in silico molecular characterization of all 72 A. aegypti GRs reported in the latest version of A. aegypti genome AaegL5. Phylogenetic analysis classified the receptors into three major clads. Multiple GRs were found to encode multiple transcripts. Physicochemical attributes such as the aliphatic index, hydropathicity index and isoelectric point indicated that A. aegypti gustatory receptors are highly stable and are tailored to perform under a variety of cellular environments. Analysis for subcellular localization indicated that all the GRs are located either in the extracellular matrix or the plasma membrane. Results also indicated that the GRs are distributed mainly on chromosomes 2 and 3, which house 22 and 49 GRs, respectively, whereas chromosome 1 houses only one GR. NCBI-CDD analysis showed the presence of a highly conserved 7tm_7 chemosensory receptor protein superfamily that includes gustatory and odorant receptors from insect species Anopheles gambiae and Drosophila melanogaster. Further, three significantly enriched ungapped motifs in the protein sequence of all 72 A. aegypti gustatory receptors were found. High-quality 3D models for the tertiary structures were predicted with significantly higher confidence, along with ligand-binding residues. Prediction of S-nitrosylation sites indicated the presence of target cysteines in all the GRs with close proximity to the ligand-bindings sites within the 3D structure of the receptors. In addition, two highly conserved motifs inside the GR proteins were discovered that house a tyrosine (Y) and a cysteine (C) residue which may serve as targets for NO-mediated tyrosine nitration and S-nitrosylation, respectively. This study will help devise strategies for functional genomic studies of these important receptor molecules in A. aegypti and other mosquito species through in vitro and in vivo studies. Full article

(This article belongs to the Special Issue Transcriptomic and Genomic Insights into Invertebrates)

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20 pages, 5736 KiB

Open AccessArticle

Adult and Larval Tracheal Systems Exhibit Different Molecular Architectures in Drosophila

by Judith Bossen, Ruben Prange, Jan-Philip Kühle, Sven Künzel, Xiao Niu, Jörg U. Hammel, Laura Krieger, Mirjam Knop, Birte Ehrhardt, Karin Uliczka, Susanne Krauss-Etschmann and Thomas Roeder

Int. J. Mol. Sci. 2023, 24(6), 5628; https://doi.org/10.3390/ijms24065628 - 15 Mar 2023

Cited by 3 | Viewed by 3041

Abstract

Knowing the molecular makeup of an organ system is required for its in-depth understanding. We analyzed the molecular repertoire of the adult tracheal system of the fruit fly Drosophila melanogaster using transcriptome studies to advance our knowledge of the adult insect tracheal system. Comparing this to the larval tracheal system revealed several major differences that likely influence organ function. During the transition from larval to adult tracheal system, a shift in the expression of genes responsible for the formation of cuticular structure occurs. This change in transcript composition manifests in the physical properties of cuticular structures of the adult trachea. Enhanced tonic activation of the immune system is observed in the adult trachea, which encompasses the increased expression of antimicrobial peptides. In addition, modulatory processes are conspicuous, in this case mainly by the increased expression of G protein-coupled receptors in the adult trachea. Finally, all components of a peripheral circadian clock are present in the adult tracheal system, which is not the case in the larval tracheal system. Comparative analysis of driver lines targeting the adult tracheal system revealed that even the canonical tracheal driver line breathless (btl)-Gal4 is not able to target all parts of the adult tracheal system. Here, we have uncovered a specific transcriptome pattern of the adult tracheal system and provide this dataset as a basis for further analyses of the adult insect tracheal system. Full article

(This article belongs to the Special Issue Transcriptomic and Genomic Insights into Invertebrates)

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18 pages, 3225 KiB

Open AccessArticle

Transcriptomic and Bioinformatic Analyses Identifying a Central Mif-Cop9-Nf-kB Signaling Network in Innate Immunity Response of Ciona robusta

by Laura La Paglia, Mirella Vazzana, Manuela Mauro, Francesca Dumas, Antonino Fiannaca, Alfonso Urso, Vincenzo Arizza and Aiti Vizzini

Int. J. Mol. Sci. 2023, 24(4), 4112; https://doi.org/10.3390/ijms24044112 - 18 Feb 2023

Cited by 1 | Viewed by 1851

Abstract

The Ascidian C. robusta is a powerful model for studying innate immunity. LPS induction activates inflammatory-like reactions in the pharynx and the expression of several innate immune genes in granulocyte hemocytes such as cytokines, for instance, macrophage migration inhibitory factors (CrMifs). This leads to intracellular signaling involving the Nf-kB signaling cascade that triggers downstream pro-inflammatory gene expression. In mammals, the COP9 (Constitutive photomorphogenesis 9) signalosome (CSN) complex also results in the activation of the NF-kB pathway. It is a highly conserved complex in vertebrates, mainly engaged in proteasome degradation which is essential for maintaining processes such as cell cycle, DNA repair, and differentiation. In the present study, we used bioinformatics and in-silico analyses combined with an in-vivo LPS exposure strategy, next-generation sequencing (NGS), and qRT-PCR to elucidate molecules and the temporal dynamics of Mif cytokines, Csn signaling components, and the Nf-κB signaling pathway in C. robusta. A qRT-PCR analysis of immune genes selected from transcriptome data revealed a biphasic activation of the inflammatory response. A phylogenetic and STRING analysis indicated an evolutionarily conserved functional link between the Mif-Csn-Nf-kB axis in ascidian C. robusta during LPS-mediated inflammation response, finely regulated by non-coding molecules such as microRNAs (miRNAs). Full article

(This article belongs to the Special Issue Transcriptomic and Genomic Insights into Invertebrates)

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17 pages, 2913 KiB

Open AccessArticle

Peritrophin-like Genes Are Associated with Delousing Drug Response and Sensitivity in the Sea Louse Caligus rogercresseyi

by Antonio Casuso, Gustavo Núñez-Acuña, Valentina Valenzuela-Muñoz, Constanza Sáez-Vera and Cristian Gallardo-Escárate

Int. J. Mol. Sci. 2022, 23(21), 13341; https://doi.org/10.3390/ijms232113341 - 1 Nov 2022

Viewed by 1731

Abstract

Caligus rogercresseyi is the main ectoparasite that affects the salmon industry in Chile. The mechanisms used by the parasite to support its life strategy are of great interest for developing control strategies. Due to the critical role of insect peritrophins in host–parasite interactions and response to pest control drugs, this study aimed to identify and characterize the peritrophin-like genes present in C. rogercresseyi. Moreover, the expression of peritrophin-like genes was evaluated on parasites exposed to delousing drugs such as pyrethroids and azamethiphos. Peritrophin genes were identified by homology analysis among the sea louse transcriptome database and arthropods peritrophin-protein database obtained from GenBank and UniProt. Moreover, the gene loci in the parasite genome were located. Furthermore, peritrophin gene expression levels were evaluated by RNA-Seq analysis in sea louse developmental stages and sea lice exposed to delousing drugs deltamethrin, cypermethrin, and azamethiphos. Seven putative peritrophin-like genes were identified in C. rogercresseyi with high homology with other crustacean peritrophins. Differences in the presence of signal peptides, the number of chitin-binding domains, and the position of conserved cysteines were found. In addition, seven peritrophin-like gene sequences were identified in the C. rogercresseyi genome. Gene expression analysis revealed a stage-dependent expression profile. Notably, differential regulation of peritrophin genes in resistant and susceptible populations to delousing drugs was found. These data are the first report and characterization of peritrophin genes in the sea louse C. rogercresseyi, representing valuable knowledge to understand sea louse biology. Moreover, this study provides evidence for a deeper understanding of the molecular basis of C. rogercresseyi response to delousing drugs. Full article

(This article belongs to the Special Issue Transcriptomic and Genomic Insights into Invertebrates)

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21 pages, 3785 KiB

Open AccessArticle

C/N-Dependent Element Bioconversion Efficiency and Antimicrobial Protein Expression in Food Waste Treatment by Black Soldier Fly Larvae

by Ning Jin, Yanxia Liu, Shouyu Zhang, Shibo Sun, Minghuo Wu, Xiaoying Dong, Huiyan Tong, Jianqiang Xu, Hao Zhou, Shui Guan and Weiping Xu

Int. J. Mol. Sci. 2022, 23(9), 5036; https://doi.org/10.3390/ijms23095036 - 1 May 2022

Cited by 7 | Viewed by 2627

Abstract

The black soldier fly (BSF), Hermetia illucens, has emerged as a promising species for waste bioconversion and source of antimicrobial proteins (AMPs). However, there is a scarcity of research on the element transformation efficiency and molecular characterization of AMPs derived from waste management. Here, food waste treatment was performed using BSF larvae (BSFL) in a C/N ratio of 21:1–10:1, with a focus on the C/N-dependent element bioconversion, AMP antimicrobial activity, and transcriptome profiling. The C-larvae transformation rates were found to be similar among C/Ns (27.0–35.5%, p = 0.109), while the N-larvae rates were different (p = 0.001), with C/N 21:1–16:1 (63.5–75.0%) being higher than C/N 14:1–10:1 (35.0–45.7%). The C/N ratio did not alter the antimicrobial spectrum of AMPs, but did affect the activities, with C/N 21:1 being significantly lower than C/N 18:1–10:1. The lysozyme genes were found to be significantly more highly expressed than the cecropin, defensin, and attacin genes in the AMP gene family. Out of 51 lysozyme genes, C/N 18:1 and C/N 16:1 up-regulated (p < 0.05) 14 and 12 genes compared with C/N 21:1, respectively, corresponding to the higher activity of AMPs. Overall, the element bioconversion efficiency and AMP expression can be enhanced through C/N ratio manipulation, and the C/N-dependent transcriptome regulation is the driving force of the AMP difference. Full article

(This article belongs to the Special Issue Transcriptomic and Genomic Insights into Invertebrates)

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Review

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10 pages, 619 KiB

Open AccessReview

Current Knowledge on Bee Innate Immunity Based on Genomics and Transcriptomics

by Xiaomeng Zhao and Yanjie Liu

Int. J. Mol. Sci. 2022, 23(22), 14278; https://doi.org/10.3390/ijms232214278 - 18 Nov 2022

Cited by 6 | Viewed by 2614

Abstract

As important pollinators, bees play a critical role in maintaining the balance of the ecosystem and improving the yield and quality of crops. However, in recent years, the bee population has significantly declined due to various pathogens and environmental stressors including viruses, bacteria, parasites, and increased pesticide application. The above threats trigger or suppress the innate immunity of bees, their only immune defense system, which is essential to maintaining individual health and that of the colony. In addition, bees can be divided into solitary and eusocial bees based on their life traits, and eusocial bees possess special social immunities, such as grooming behavior, which cooperate with innate immunity to maintain the health of the colony. The omics approach gives us an opportunity to recognize the distinctive innate immunity of bees. In this regard, we summarize innate bee immunity from a genomic and transcriptomic perspective. The genetic characteristics of innate immunity were revealed by the multiple genomes of bees with different kinds of sociality, including honeybees, bumblebees, wasps, leaf-cutter bees, and so on. Further substantial transcriptomic data of different tissues from diverse bees directly present the activation or suppression of immune genes under the infestation of pathogens or toxicity of pesticides. Full article

(This article belongs to the Special Issue Transcriptomic and Genomic Insights into Invertebrates)

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