scholarly journals Birth-and-death evolution of the fatty acyl-CoA reductase (FAR) gene family and diversification of cuticular hydrocarbon synthesis in Drosophila

2019 ◽  
Author(s):  
Cédric Finet ◽  
Kailey Slavik ◽  
Jian Pu ◽  
Sean B. Carroll ◽  
Henry Chung
Keyword(s):  
Fatty Acid ◽  
Gene Family ◽  
Cuticular Hydrocarbon ◽  
Evolutionary Model ◽  
Gene Families ◽  
Single Copy ◽  
Fatty Acyl ◽  
Comparative Approach ◽  
Hydrocarbon Synthesis ◽  
Functional Studies

AbstractThe birth-and-death evolutionary model proposes that some members of a multigene family are phylogenetically stable and persist as a single copy over time whereas other members are phylogenetically unstable and undergo frequent duplication and loss. Functional studies suggest that stable genes are likely to encode essential functions, while rapidly evolving genes reflect phenotypic differences in traits that diverge rapidly among species. One such class of rapidly diverging traits are insect cuticular hydrocarbons (CHCs), which play dual roles in chemical communications as short-range recognition pheromones as well as protecting the insect from desiccation. Insect CHCs diverge rapidly between related species leading to ecological adaptation and/or reproductive isolation. Because the CHC and essential fatty acid biosynthetic pathways share common genes, we hypothesized that genes involved in the synthesis of CHCs would be evolutionary unstable, while those involved in fatty acid-associated essential functions would be evolutionary stable. To test this hypothesis, we investigated the evolutionary history of the fatty acyl-CoA reductases (FARs) gene family that encodes enzymes in CHC synthesis. We compiled a unique dataset of 200 FAR proteins across 12 Drosophila species. We uncovered a broad diversity in FAR content which is generated by gene duplications, subsequent gene losses, and alternative splicing. We also show that FARs expressed in oenocytes and presumably involved in CHC synthesis are more unstable than FARs from other tissues. We suggest that a comparative approach investigating the birth-and-death evolution of gene families can identify candidate genes involved in rapidly diverging traits between species.

scholarly journals Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tao Fan ◽  
Yu-Zhen Zhao ◽  
Jing-Fang Yang ◽  
Qin-Lai Liu ◽  
Yuan Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Splice Site ◽  
Messenger Rna ◽  
Expression Patterns ◽  
Protein Structures ◽  
Single Copy ◽  
Central Component ◽  
Animal Kingdom ◽  
Functional Studies ◽  
U1 Snrnp

AbstractEukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

scholarly journals Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera

2018 ◽  
Author(s):  
Michal Tupec ◽  
Aleš Buček ◽  
Heiko Vogel ◽  
Václav Janoušek ◽  
Darina Prchalová ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Gene Family ◽  
Fat Body ◽  
Functional Characterization ◽  
Acid Methyl Ester ◽  
Fatty Acyl ◽  
Sequencing Analysis ◽  
Pheromone Communication ◽  
Marking Pheromone ◽  
Fatty Acyl Reductase

AbstractThe conserved fatty acyl reductase (FAR) family is involved in biosynthesis of fatty alcohols that serve a range of biological roles. In moths, butterflies (Lepidoptera), and bees (Hymenoptera), FARs biosynthesize fatty alcohol pheromones participating in mate-finding strategies. Using a combination of next-generation sequencing, analysis of transposable elements (TE) in the genomic environment of FAR genes, and functional characterization of FARs from Bombus lucorum, B. lapidarius, and B. terrestris, we uncovered a massive expansion of the FAR gene family in Hymenoptera, presumably facilitated by TEs. Expansion occurred in the common ancestor of bumblebees (Bombini) and stingless bees (Meliponini) after their divergence from the honeybee lineage. We found that FARs from the expanded FAR-A orthology group contributed to the species-specific male marking pheromone composition. Our results indicate that TE-mediated expansion and functional diversification of the FAR gene family played a key role in the evolution of pheromone communication in the crown group of Hymenoptera.AbbreviationsMMP: male marking pheromone, FA: fatty acid, FAME: fatty acid methyl ester, FAR: fatty acyl reductase, LG: labial gland, FB: fat body, TE: transposable element.

scholarly journals Integrated Analysis of Fatty Acid Metabolism and Transcriptome Involved in Olive Fruit Development to Improve Oil Composition

Forests ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1773
Author(s):  
Xiaoxia Liu ◽  
Liqin Guo ◽  
Jianguo Zhang ◽  
Li Xue ◽  
Ying Luo ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Molecular Mechanism ◽  
Fruit Development ◽  
Gene Families ◽  
Fatty Acyl ◽  
Gas Chromatography Mass Spectrometry ◽  
Integrated Analysis ◽  
Oil Composition ◽  
Olive Fruit ◽  
Triacylglycerol Synthesis

Olea europaea L. is an important oil crop with excellent nutritional properties. In this study, a full-length transcriptome combined with fatty acid composition was used to investigate the molecular mechanism of fatty acid (FA) metabolism of olive fruits at various stages of development (S1–S5). A total of 34 fatty acids (FAs) were measured using gas chromatography-mass spectrometry (GC-MS). All transcripts of FA metabolism during olive fruit development were studied, including glycolysis, fatty acid synthesis, triacylglycerol synthesis, and FA degradation. A total of 100 transcripts of 11 gene families, 68 transcripts of 12 gene families, 55 transcripts of 7 gene families, and 28 transcripts of 7 gene families were identified as encoding for enzymes involved in FA metabolism. Furthermore, one of the critical reactions in TAG metabolism is the activation of fatty acyl chains to fatty acyl CoA, which is catalyzed by long-chain acyl CoA synthetases (LACS). Phylogenetic analysis showed that 13 putative LACS-encoding genes clustered into five groups, of which two putative transcripts encoding LACS6/7 may participate in FA degradation. The aim of this study was to evaluate the fatty acid from synthesis to degradation pathways during olive fruit development to provide a better understanding of the molecular mechanism of FA metabolism during olive fruit maturation and provide information to improve the synthesis of oil components that are beneficial to human health.

scholarly journals A likelihood framework to analyse phyletic patterns

2008 ◽  
Vol 363 (1512) ◽  
pp. 3903-3911 ◽  
Author(s):  
Ofir Cohen ◽  
Nimrod D Rubinstein ◽  
Adi Stern ◽  
Uri Gophna ◽  
Tal Pupko
Keyword(s):  
Gene Family ◽  
Sequence Data ◽  
Evolutionary Model ◽  
Gene Families ◽  
Simulation Studies ◽  
Genome Wide ◽  
Gain And Loss ◽  
Presence And Absence ◽  
Gains And Losses ◽  
Evolutionary Role

Probabilistic evolutionary models revolutionized our capability to extract biological insights from sequence data. While these models accurately describe the stochastic processes of site-specific substitutions, single-base substitutions represent only a fraction of all the events that shape genomes. Specifically, in microbes, events in which entire genes are gained (e.g. via horizontal gene transfer) and lost play a pivotal evolutionary role. In this research, we present a novel likelihood-based evolutionary model for gene gains and losses, and use it to analyse genome-wide patterns of the presence and absence of gene families. The model assumes a Markovian stochastic process, where gains and losses are represented by the transition between presence and absence, respectively, given an underlying phylogenetic tree. To account for differences in the rates of gain and loss of different gene families, we assume among-gene family rate variability, thus allowing for more accurate description of the data. Using the Bayesian approach, we estimated an evolutionary rate for each gene family. Simulation studies demonstrated that our methodology accurately infers these rates. Our methodology was applied to analyse a large corpus of data, consisting of 4873 gene families spanning 63 species and revealed novel insights regarding the evolutionary nature of genome-wide gain and loss dynamics.

scholarly journals Candidate genes involved in cuticular hydrocarbon differentiation between cryptic, parabiotic ant species

2021 ◽  
Author(s):  
Philipp P Sprenger ◽  
Juliane Hartke ◽  
Thomas Schmitt ◽  
Florian Menzel ◽  
Barbara Feldmeyer
Keyword(s):  
Gene Expression ◽  
Cryptic Species ◽  
Candidate Genes ◽  
Fat Body ◽  
Cuticular Hydrocarbon ◽  
Common Garden ◽  
Gene Families ◽  
Fatty Acyl ◽  
Specific Complex ◽  
Species Specific

Abstract Insect cuticular hydrocarbons (CHCs) are highly diverse and have multiple functions, including communication and waterproofing. CHC profiles form species-specific, complex blends of up to 150 compounds. Especially in ants, even closely related species can have largely different profiles, raising the question how CHC differences are mirrored in the regulation of biosynthetic pathways. The neotropical ants Crematogaster levior and Camponotus femoratus both consist of two cryptic species each that are morphologically similar, but express strongly different CHC profiles. This is ideal to study the molecular basis of CHC differences. We thus investigated gene expression differences in fat-body transcriptomes of these ants. Despite common garden conditions, we found several thousand differentially expressed transcripts within each cryptic species pair. Many of these were related to metabolic processes, probably accounting for physiological differences. Moreover, we identified candidate genes from five gene families involved in CHC biosynthesis. By assigning candidate transcripts to orthologs in Drosophila, we inferred which CHCs might be influenced by differential gene expression. Expression of these candidate genes was often mirrored in the CHC profiles. For example, Cr. levior A, which has longer CHCs than its cryptic sister species, had a higher expression of elongases and a lower expression of fatty acyl- CoA reductases. This study is one of the first to identify CHC candidate genes in ants and will provide a basis for further research on the genetic basis of CHC biosynthesis.

scholarly journals Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats

2020 ◽  
Vol 12 (4) ◽  
pp. 259-272
Author(s):  
Balaji Chattopadhyay ◽  
Kritika M Garg ◽  
Rajasri Ray ◽  
Ian H Mendenhall ◽  
Frank E Rheindt
Keyword(s):  
Gene Family ◽  
De Novo ◽  
Gene Families ◽  
Radical Change ◽  
Comparative Approach ◽  
Family Composition ◽  
Fruit Bats ◽  
Fruit Bat ◽  
Abrupt Shifts ◽  
Cynopterus Brachyotis

Abstract Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as compared with other bats (e.g., loss of echolocation, large size, and frugivory), fruit bats have undergone surprisingly limited change in their genic composition, perhaps apart from a potentially novel gene family expansion relating to telomere protection and longevity. In sharp contrast, within fruit bats, the new Cynopterus genome bears the signal of unusual gene loss and gene family contraction, despite its similar morphology and lifestyle to two other major fruit bat lineages. Most missing genes are regulatory, immune-related, and olfactory in nature, illustrating the diversity of genomic strategies employed by bats to contend with responses to viral infection and olfactory requirements. Our results underscore that significant fluctuations in gene family composition are not always associated with obvious examples of novel physiological and phenotypic adaptations but may often relate to less-obvious shifts in immune strategies.

scholarly journals Conserved Molecular Function and Regulatory Subfunctionalization of the LORELEI Gene Family in Brassicaceae

2020 ◽  
Author(s):  
Jennifer A. Noble ◽  
Ming-Che James Liu ◽  
Thomas A. DeFalco ◽  
Martin Stegmann ◽  
Kara McNamara ◽  
...  
Keyword(s):  
Gene Family ◽  
Functional Divergence ◽  
Gene Families ◽  
Single Copy ◽  
Gene Family Evolution ◽  
Duplicated Genes ◽  
Evolutionary Mechanisms ◽  
Functional Conservation ◽  
Signaling Complex ◽  
And Function

AbstractA signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, development, reproduction, and immunity in Arabidopsis thaliana. Duplications in each component, which potentially could generate thousands of combinations of this signaling complex, are also evident in other angiosperms. Widespread duplication in angiosperms raises the question what evolutionary mechanisms underlie the expansion and retention of these gene families, as duplicated genes are typically rendered non-functional. As genetic and genomic resources make it a tractable model system, here we investigated this question using LLG gene family evolution and function in Brassicaceae. We first established that the LLG homologs in the Brassicaceae resulted from duplication events that pre-date the divergence of species in this family. Complementation of vegetative phenotypes in llg1 by LRE, LLG2, and LLG3 showed that the molecular functions of LLG homologs in A. thaliana are conserved. We next tested the possibility that differences in gene expression (regulatory subfunctionalization), rather than functional divergence, played a role in retention of these duplicated genes. For this, we examined the function and expression of LRE and LLG1 in A. thaliana and their single copy ortholog in Cleome violacea (Clevi LRE/LLG1), a representative species outside the Brassicaceae, but from the same order (Brassicales). We showed that expression of LLG1 and LRE did not overlap in A. thaliana and that Clevi-LRE/LLG1 expression in C. violacea encompassed all the expression domains of A. thaliana LRE + LLG1. Still, complementation experiments showed that LLG1 rescued reproductive phenotypes in lre and that Clevi LRE/LLG1 rescued both vegetative and reproductive phenotypes in llg1 and lre. Additionally, we found that expression of LLG2 and LLG3 in A. thaliana have also diverged from the expression of their corresponding single copy ortholog (Clevi LLG2/LLG3) in C. violacea. Our findings demonstrated how regulatory subfunctionalization, rather than functional divergence, underlies the retention of the LLG gene family in Brassicaceae. Our findings on the regulatory divergence and functional conservation provide an experimental framework to characterize the combinatorial assembly and function of this critical plant cell signaling complex.

scholarly journals Phylogenetic analyses for orthogroup-based classification of GDSL-type esterase/lipase (GELP) family in angiosperms

2021 ◽  
Author(s):  
Alberto Cenci ◽  
Mairenys Concepci&oacuten-Hernández ◽  
Geert Angenon ◽  
Mathieu Rouard
Keyword(s):  
Gene Family ◽  
Phylogenetic Analyses ◽  
Gene Families ◽  
Single Copy ◽  
Biotic And Abiotic Stresses ◽  
Large Gene ◽  
Classification Framework ◽  
Genes Encoding ◽  
History Of

GDSL-type esterase/lipase (GELP) enzymes have multiple functions in plants, spanning from developmental processes to the response to biotic and abiotic stresses. Genes encoding GELP belong to a large gene family with several tens to more than hundred members per species in angiosperms. Here, we applied iterative phylogenic analyses to identify 10 main clusters subdivided into 44 expert-curated reference orthogroups (OGs) using three monocot and five dicot genomes. Our results show that some GELP OGs expanded while others were maintained as single copy genes. This semi-automatic approach proves to be effective to characterize large gene families and provides a solid classification framework for the GELP members in angiosperms. The orthogroup-based reference will be useful to perform comparative studies, infer gene functions and better understand the evolutionary history of this gene family.

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