Where the Minor Things Are: A Pan-Eukaryotic Survey Suggests Neutral Processes May Dominate Minor Spliceosomal Intron Evolution

Larue, Graham E.; Roy, Scott William

doi:10.1101/2022.09.24.509304

Cited by 2 publications

(1 citation statement)

References 98 publications

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“…The vast majority of splice sites in Phaeophyceae are of the canonical GT-AG type (Figure S18C) and no signatures of minor U12 introns were identified in intronic sequences, in accordance with a previous study 120 . Consistent with this observation, an analysis of spliceosome proteins using a recent reference dataset 121 found that, with the exception of ZCRB1, none of the 12 minor spliceosome genes were present in brown algal genomes (Table S26), indicating that the minor intron spliceosomal associated machinery was lost in the Phaeophyceae.…”

Section: Brown Algal Introns and The Spliceosomesupporting

confidence: 91%

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Denoeud,

Godfroy,

Cruaud

et al. 2024

Preprint

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SUMMARYBrown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. Here we analyse 60 new genomes that include species from all the major brown algal orders. Comparative analysis of these genomes indicated the occurrence of several major events coinciding approximately with the emergence of the brown algal lineage. These included marked gain of new orthologous gene families, enhanced protein domain rearrangement, horizontal gene transfer events and the acquisition of novel signalling molecules and metabolic pathways. The latter include enzymes implicated in processes emblematic of the brown algae such as biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. These early genomic innovations enabled the adaptation of brown algae to their intertidal habitats. The subsequent diversification of the brown algal orders tended to involve loss of gene families, and genomic features were identified that correlated with the emergence of differences in life cycle strategy, flagellar structure and halogen metabolism. We show that integration of large viral genomes has had a significant impact on brown algal genome content and propose that this process has persisted throughout the evolutionary history of the lineage. Finally, analysis of microevolutionary patterns within the genusEctocarpusindicated that deep gene flow between species may be an important factor in genome evolution on more recent timescales.

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Section: Brown Algal Introns and The Spliceosomesupporting

confidence: 91%

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Denoeud,

Godfroy,

Cruaud

et al. 2024

Preprint

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Genome wide identification and characterization of Bax inhibitor-1 gene family in cucumber (Cucumis sativus) under biotic and abiotic stress

Anwar,

Siddique,

Ahmad

et al. 2024

BMC Genomics

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In plants, the BAX inhibitor-1 ( BI-1 ) gene plays a crucial part in controlling cell death under stress conditions. This mechanism of Programmed Cell Death (PCD) is genetically regulated and is crucial for the elimination of unwanted or damaged cells in a controlled manner, which is essential for normal development and tissue maintenance. A study on cucumber identified and characterized five BI-1 genes: CsBI1 , CsBI2 , CsBI3 , CsBI4 , and CsBI5 . These genes share conserved domains, indicating common evolutionary history and function. Physicochemical analysis revealed their molecular weights and isoelectric points, while subcellular localization showed their presence in different cellular compartments. The phylogenetic analysis highlighted evolutionary relationships with related crops. Chromosomal distribution and synteny analysis suggested segmental or tandem duplications within the gene family. Protein-protein interaction analysis revealed extensive interactions with other cucumber proteins. Cis-regulatory elements in the promoter regions provided insights into potential functions and transcriptional regulation. miRNAs showed diverse regulatory mechanisms, including mRNA cleavage and translational inhibition. The CsBI3 , CsBI4 and CsBI5 genes exhibit elevated expression levels during cold stress, suggesting their vital involvement in cucumber plant defense mechanisms. The application of chitosan oligosaccharides externally confirms their distinct expression patterns. The qRT-PCR confirms the upregulation of CsBI genes in ToLCNDV-infected plants, indicating their potential to mitigate biotic and abiotic stresses. The comprehensive genome-wide exploration provides opportunities for the development of cold-tolerant and virus-resistant cucumber variants by traditional breeding or gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-10704-5.

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Where the Minor Things Are: A Pan-Eukaryotic Survey Suggests Neutral Processes May Dominate Minor Spliceosomal Intron Evolution

Cited by 2 publications

References 98 publications

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Genome wide identification and characterization of Bax inhibitor-1 gene family in cucumber (Cucumis sativus) under biotic and abiotic stress

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