scholarly journals Rapid Turnover of Life-Cycle-Related Genes in the Brown Algae

2018 ◽  
Author(s):  
A.P. Lipinska ◽  
M.L. Serrano-Serrano ◽  
Akira F. Peters ◽  
K. Kogame ◽  
J Mark Cock ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Brown Algae ◽  
Phenotypic Diversity ◽  
Expression Patterns ◽  
Life Cycles ◽  
Sexual Life ◽  
High Turnover ◽  
Life Cycle Stages ◽  
Eukaryotic Group

ABSTRACTBackgroundSexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free living, and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures in each of the life cycle generations. Here, we have analysed the nature and extent of genome-wide generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations, in order to assess the potential role of generation-specific selection in shaping patterns of gene expression and divergence.ResultsWe show that the proportion of the transcriptome that is generation-biased is associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also a key role for newly emerged, lineage-specific genes in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes exhibit changes in their patterns of expression.ConclusionOur analysis uncovers the characteristics, expression patterns and evolution of generation-biased genes and underline the selective forces that shape this previously underappreciated source of phenotypic diversity.

scholarly journals Analysis of Pir Gene Expression Across the Plasmodium Life Cycle

2021 ◽  
Author(s):  
Timothy S. Little ◽  
Deirdre A. Cunningham ◽  
Audrey Vandomme ◽  
Carlos Talavera Lopez ◽  
Sarah I. Amis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Antigenic Variation ◽  
Expression Patterns ◽  
Plasmodium Species ◽  
Data Sets ◽  
Life Cycle Stages ◽  
Determine Function ◽  
Gene Expression Studies ◽  
Functional Investigation

Abstract Background Plasmodium interspersed repeat ( pir ) is the largest multigene family in the genomes of most Plasmodium species. A variety of functions for the PIR proteins which they encode have been proposed, including antigenic variation, immune evasion, sequestration and rosetting. However, direct evidence for these is lacking. The repetitive nature of the family has made it difficult to determine function experimentally. However, there has been some success in using gene expression studies to suggest roles for some members in virulence and chronic infection. Methods Here we examined pir gene expression across the life cycle of P. berghei using publicly available RNAseq data-sets, and at high resolution in the intraerythrocytic development cycle using new data from P. chabaudi . Results Expression of pir genes is greatest in stages of the parasite which invade and reside in red blood cells. The marked exception is that liver merozoites and male gametocytes produce a very large number of pir gene transcripts, notably compared to female gametocytes, which produce relatively few. Within the asexual blood stages different subfamilies peak at different times, suggesting further functional distinctions. Representing a subfamily of its own, the highly conserved ancestral pir gene warrants further investigation due to its potential tractability for functional investigation. It is highly transcribed in multiple life cycle stages and across most studied Plasmodium species and thus is likely to play an important role in parasite biology. Conclusions By identifying distinct expression patterns for different pir genes and subfamilies we hope to provide a basis for the design of future experiments to uncover their function.

scholarly journals The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites

2019 ◽  
Vol 18 (5) ◽  
pp. 302-313 ◽  
Author(s):  
Steven Abel ◽  
Karine G Le Roch
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Chromatin Structure ◽  
Expression Patterns ◽  
Large Body ◽  
Gene Families ◽  
Dimensional Structure ◽  
Parasite Life Cycle ◽  
Life Cycle Stages ◽  
Parasite Plasmodium Falciparum

AbstractDue to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence points toward chromatin structure and epigenetic factors mediating the changes in gene expression associated with parasite life cycle stages. These attributes may be critically important for immune evasion, host cell invasion and development of the parasite in its two hosts, the human and the Anopheles vector. Thus, the factors involved in the maintenance and regulation of chromatin and epigenetic features represent potential targets for antimalarial drugs. In this review, we discuss the mechanisms in P. falciparum that regulate chromatin structure, nucleosome landscape, the 3-dimensional structure of the genome and additional distinctive features created by parasite-specific genes and gene families. We review conserved traits of chromatin in eukaryotes in order to highlight what is unique in the parasite.

scholarly journals Analysis of pir gene expression across the Plasmodium life cycle

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Timothy S. Little ◽  
Deirdre A. Cunningham ◽  
Audrey Vandomme ◽  
Carlos Talavera Lopez ◽  
Sarah Amis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Antigenic Variation ◽  
Expression Patterns ◽  
Data Sets ◽  
Life Cycle Stages ◽  
Determine Function ◽  
Repetitive Nature ◽  
Gene Expression Studies ◽  
Functional Investigation

Abstract Background Plasmodium interspersed repeat (pir) is the largest multigene family in the genomes of most Plasmodium species. A variety of functions for the PIR proteins which they encode have been proposed, including antigenic variation, immune evasion, sequestration and rosetting. However, direct evidence for these is lacking. The repetitive nature of the family has made it difficult to determine function experimentally. However, there has been some success in using gene expression studies to suggest roles for some members in virulence and chronic infection. Methods Here pir gene expression was examined across the life cycle of Plasmodium berghei using publicly available RNAseq data-sets, and at high resolution in the intraerythrocytic development cycle using new data from Plasmodium chabaudi. Results Expression of pir genes is greatest in stages of the parasite which invade and reside in red blood cells. The marked exception is that liver merozoites and male gametocytes produce a very large number of pir gene transcripts, notably compared to female gametocytes, which produce relatively few. Within the asexual blood stages different subfamilies peak at different times, suggesting further functional distinctions. Representing a subfamily of its own, the highly conserved ancestral pir gene warrants further investigation due to its potential tractability for functional investigation. It is highly transcribed in multiple life cycle stages and across most studied Plasmodium species and thus is likely to play an important role in parasite biology. Conclusions The identification of distinct expression patterns for different pir genes and subfamilies is likely to provide a basis for the design of future experiments to uncover their function.

scholarly journals Evidence for complex life cycle constraints on salamander body form diversification

2017 ◽  
Vol 114 (37) ◽  
pp. 9936-9941 ◽  
Author(s):  
Ronald M. Bonett ◽  
Andrea L. Blair
Keyword(s):  
Life Cycle ◽  
Phenotypic Diversity ◽  
Life Cycles ◽  
Complex Life Cycle ◽  
Body Form ◽  
Life Cycle Stages ◽  
Biphasic Life Cycle ◽  
Evolution Of Life ◽  
Adult Body ◽  
Life Cycle Evolution

Metazoans display a tremendous diversity of developmental patterns, including complex life cycles composed of morphologically disparate stages. In this regard, the evolution of life cycle complexity promotes phenotypic diversity. However, correlations between life cycle stages can constrain the evolution of some structures and functions. Despite the potential macroevolutionary consequences, few studies have tested the impacts of life cycle evolution on broad-scale patterns of trait diversification. Here we show that larval and adult salamanders with a simple, aquatic-only (paedomorphic) life cycle had an increased rate of vertebral column and body form diversification compared to lineages with a complex, aquatic-terrestrial (biphasic) life cycle. These differences in life cycle complexity explain the variations in vertebral number and adult body form better than larval ecology. In addition, we found that lineages with a simple terrestrial-only (direct developing) life cycle also had a higher rate of adult body form evolution than biphasic lineages, but still 10-fold lower than aquatic-only lineages. Our analyses demonstrate that prominent shifts in phenotypic evolution can follow long-term transitions in life cycle complexity, which may reflect underlying stage-dependent constraints.

Autonomy and integration in complex parasite life cycles

Parasitology ◽  
2016 ◽  
Vol 143 (14) ◽  
pp. 1824-1846 ◽  
Author(s):  
DANIEL P. BENESH
Keyword(s):  
Life Cycle ◽  
Holistic Approach ◽  
Life Cycles ◽  
Complex Life Cycle ◽  
Functional Specialization ◽  
Life Stages ◽  
Free Living ◽  
New Host ◽  
Complex Life Cycles ◽  
Life Cycle Stages

SUMMARYComplex life cycles are common in free-living and parasitic organisms alike. The adaptive decoupling hypothesis postulates that separate life cycle stages have a degree of developmental and genetic autonomy, allowing them to be independently optimized for dissimilar, competing tasks. That is, complex life cycles evolved to facilitate functional specialization. Here, I review the connections between the different stages in parasite life cycles. I first examine evolutionary connections between life stages, such as the genetic coupling of parasite performance in consecutive hosts, the interspecific correlations between traits expressed in different hosts, and the developmental and functional obstacles to stage loss. Then, I evaluate how environmental factors link life stages through carryover effects, where stressful larval conditions impact parasites even after transmission to a new host. There is evidence for both autonomy and integration across stages, so the relevant question becomes how integrated are parasite life cycles and through what mechanisms? By highlighting how genetics, development, selection and the environment can lead to interdependencies among successive life stages, I wish to promote a holistic approach to studying complex life cycle parasites and emphasize that what happens in one stage is potentially highly relevant for later stages.

scholarly journals Endocrine Control of Life-Cycle Stages: A Constraint on Response to the Environment?

The Condor ◽  
2000 ◽  
Vol 102 (1) ◽  
pp. 35-51 ◽  
Author(s):  
Jerry D. Jacobs ◽  
John C. Wingfield
Keyword(s):  
Life History ◽  
Life Cycle ◽  
Control Systems ◽  
Life Cycles ◽  
Environmental Cues ◽  
Endocrine Control ◽  
Theoretical Approaches ◽  
Life Cycle Stages ◽  
Wide Range ◽  
Breeding Seasons

Abstract Most organisms live in seasonal environments that fluctuate on a predictable schedule and sometimes unpredictably. Individuals must, therefore, adjust so as to maximize their survival and reproductive success over a wide range of environmental conditions. In birds, as in other vertebrates, endocrine secretions regulate morphological, physiological, and behavioral changes in anticipation of future events. The individual thus prepares for predictable fluctuations in its environment by changing life-cycle stages. We have applied finite-state machine theory to define and compare different life-history cycles. The ability of birds to respond to predictable and unpredictable regimes of environmental variation may be constrained by the adaptability of their endocrine control systems. We have applied several theoretical approaches to natural history data of birds to compare the complexity of life cycles, the degree of plasticity of timing of stages within the cycle, and to determine whether endocrine control mechanisms influence the way birds respond to their environments. The interactions of environmental cues on the timing of life-history stages are not uniform in all populations. Taking the reproductive life-history stage as an example, arctic birds that have short breeding seasons in severe environments appear to use one reliable environmental cue to time reproduction and they ignore other factors. Birds having longer breeding seasons exhibit greater plasticity of onset and termination and appear to integrate several environmental cues. Theoretical approaches may allow us to predict how individuals respond to their environment at the proximate level and, conversely, predict how constraints imposed by endocrine control systems may limit the complexity of life cycles.

scholarly journals Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gilbert O. Silveira ◽  
Murilo S. Amaral ◽  
Helena S. Coelho ◽  
Lucas F. Maciel ◽  
Adriana S. A. Pereira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Schistosoma Mansoni ◽  
Reference Genes ◽  
Large Scale ◽  
Developmental Stages ◽  
Adult Males ◽  
Histone H4 ◽  
Expression Levels ◽  
Life Cycle Stages

AbstractReverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is the most used, fast, and reproducible method to confirm large-scale gene expression data. The use of stable reference genes for the normalization of RT-qPCR assays is recognized worldwide. No systematic study for selecting appropriate reference genes for usage in RT-qPCR experiments comparing gene expression levels at different Schistosoma mansoni life-cycle stages has been performed. Most studies rely on genes commonly used in other organisms, such as actin, tubulin, and GAPDH. Therefore, the present study focused on identifying reference genes suitable for RT-qPCR assays across six S. mansoni developmental stages. The expression levels of 25 novel candidates that we selected based on the analysis of public RNA-Seq datasets, along with eight commonly used reference genes, were systematically tested by RT-qPCR across six developmental stages of S. mansoni (eggs, miracidia, cercariae, schistosomula, adult males and adult females). The stability of genes was evaluated with geNorm, NormFinder and RefFinder algorithms. The least stable candidate reference genes tested were actin, tubulin and GAPDH. The two most stable reference genes suitable for RT-qPCR normalization were Smp_101310 (Histone H4 transcription factor) and Smp_196510 (Ubiquitin recognition factor in ER-associated degradation protein 1). Performance of these two genes as normalizers was successfully evaluated with females maintained unpaired or paired to males in culture for 8 days, or with worm pairs exposed for 16 days to double-stranded RNAs to silence a protein-coding gene. This study provides reliable reference genes for RT-qPCR analysis using samples from six different S. mansoni life-cycle stages.

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