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Insect herbivory can seriously hinder plant performance and reduce crop yield. Thrips are minute cell‐content‐feeding insects that are important vectors of viral plant pathogens, and are serious crop pests. We investigated the role of a sweet pepper (Capsicum annuum) lipoxygenase gene, CaLOX2, in the defense of pepper plants against Western flower thrips (Frankliniella occidentalis). This was done through a combination of in‐silico, transcriptional, behavioral and chemical analyses. Our data show that CaLOX2 is involved in jasmonic acid (JA) biosynthesis and mediates plant resistance. Expression of the JA‐related marker genes, CaLOX2 and CaPIN II, was induced by thrips feeding. Silencing of CaLOX2 in pepper plants through virus‐induced gene silencing (VIGS) resulted in low levels of CaLOX2 transcripts, as well as significant reduction in the accumulation of JA, and its derivatives, upon thrips feeding compared to control plants. CaLOX2‐silenced pepper plants exhibited enhanced susceptibility to thrips. This indicates that CaLOX2 mediates JA‐dependent signaling, resulting in defense against thrips. Furthermore, exogenous application of JA to pepper plants increased plant resistance to thrips, constrained thrips population development and made plants less attractive to thrips. Thus, a multidisciplinary approach shows that an intact lipoxygenase pathway mediates various components of sweet pepper defense against F. occidentalis. [ABSTRACT FROM AUTHOR]

A large number of spliceosomal proteins are required for proper RNA splicing. While spliceosomal proteins from several model organisms have been analysed, only limited studies are available for fungal species. Hence, we have performed a comparative genomic analysis using eight fungal species belonging to three taxa (Ascomycetes, Basidiomycetes and Glomeromycota). We identified variable number of spliceosomal proteins in fungal species. From the small nuclear ribonucleoproteins (snRNPs), all the snRNPs were identified. In non-snRNPs, only some sub-groups were found extensively conserved in all fungal species, including PRP19 complex proteins, catalytic step II and late-acting proteins. In heterogeneous nuclear ribonucleoproteins (hnRNPs), variable number of proteins was identified. The number of spliceosomal proteins identified in filamentous fungi was higher than that in yeast. The collection of these spliceosomal proteins provides further insight into pre-mRNA splicing in fungi. [ABSTRACT FROM AUTHOR]

Highlights: [•] Two novel introns are inserted in AGT from selected ray-finned fishes. [•] AGT is conserved on same syntenic fragment from 500 MY. [•] AGT became non-inhibitory from inhibitory serpin via RCL mutations. [•] AGT has 690 variants in 1092 human genomes from 14 populations. [•] 121 missense variants identified in human AGT protein with 32 deleterious mutants. [ABSTRACT FROM AUTHOR]

The recombination-activating genes (RAGs) encode for V(D)J recombinases responsible for rearrangements of antigen-receptor genes during T and B cell development, and RAG expression is known to correlate strictly with the process of rearrangement. There have been several studies of RAG1 illustrating biochemical, physiological and immunological properties. Hitherto, there are limited studies on RAG1 focusing molecular phylogenetic analyses, evolutionary traits, and genetic variants in human populations. Hence, there is a need of a comprehensive study on this topic. In the current report, we have shed light into insights of evolutionary traits and genetic variants of human RAG1 gene using 1092 genomes from human populations. Syntenic analyses revealed that two RAG genes are physically linked and conserved on the same locus in head-to-head orientation from sea urchin to human for about 550 MY. Spliceosomal introns have been in invaded in fishes and sea urchin, whereas gene structures of RAG1 gene from tetrapods remained single exon architecture. We compiled 751 genetic variants in human RAG1 gene using 1092 human genomes; where major stockholders of variant classes are 79% single nucleotide polymorphisms (SNPs), 12.2% somatic single nucleotide variants (somatic SNVs) and 6.8% deletion. Out of 267 missense variants, 140 are deleterious mutations. We identified 284 non-coding variants with 94% regulatory in nature. [ABSTRACT FROM AUTHOR]

Heparin cofactor II (HCII) belongs to serpin superfamily and it acts as a thrombin inhibitor in the coagulation cascade, in a glycosaminoglycan-dependent pathway using the release of a sequestered hirudin-like N-terminal tail for interaction with thrombin. This serpin belongs to multiple member group V2 of vertebrate serpin classification. However, there is no comprehensive study illustrating the exact phylogenetic history of HCII, to date. Herein, we explored phylogenetic traits of HCII genes. Structures of HCII gene from selected ray-finned fishes and lamprey varied in exon I and II with insertions of novel introns of which one in core domain for ray-finned fishes in exon II at the position 241c. We found HCII remain nested in the largest intron of phosphatidylinositol (PI) 4-kinase (PIK4CA) gene (genetic variants of this gene cause schizophrenia) at the origin of vertebrates, dated about 500 MY old. We found that sequence features such as two acidic repeats (AR1-II), GAG-binding helix-D, three serpin motifs and inhibitory reactive center loop (RCL) of HCII protein are highly conserved in 55 vertebrates analyzed. We identified 985 HCII variants by analysis of 1092 human genomes with top three variation classes belongs to SNPs (84.3%), insertion (7.1%) and deletion (5.0%). We identified 37 deleterious mutations in the human HCII protein and we have described these mutations in relation to HCII sequence-structure-function relationships. These understandings may have clinical and medical importance as well. [ABSTRACT FROM AUTHOR]

C1 inhibitor (C1IN) is a multi-facet serine protease inhibitor in the plasma cascades, inhibiting several proteases, notably, regulates both complement and contact system activation. Despite huge advancements in the understanding of C1IN based on biochemical properties and its roles in the plasma cascades, the phylogenetic history of C1IN remains uncharacterized. To date, there is no comprehensive study illustrating the phylogenetic history of C1IN. Herein, we explored phylogenetic history of C1IN gene in vertebrates. Fishes have C1IN with two immunoglobulin like domains attached in the N-terminal region. The RCL regions of CIIN from fishes and tetrapod genomes have variations at the positions P2 and P1'. Gene structures of C1IN gene from selected ray-finned fishes varied in the Ig domain region with creation of novel intron splitting exon Im2 into Im2a and Im2b. This intron is limited to ray-finned fishes with genome size reduced below 1 Gb. Hence, we suggest that genome compaction and associated double-strand break repairs are behind this intron gain. This study reveals the evolutionary history of C1IN and confirmed that this gene remains the same locus for ~450 MY in 52 vertebrates analysed, but it is not found in frogs and lampreys. [ABSTRACT FROM AUTHOR]

Highlights: [•] ATIII possesses additional intron 262c is maintained in ray-finned fishes, but lost in other vertebrates. [•] ATIII is maintained in same genomic loci with few changes in fishes. [•] ATIII has 1997 variants in 1092 human genomes from 14 populations. [•] Three top variation classes are 76.2% SNPs, 11.8% deletions and 8.1% insertions. [•] There are 63 missense variants of human ATIII causes change in amino acids. [ABSTRACT FROM AUTHOR]