scholarly journals Molecular evolution of GDP-L-galactose phosphorylase (GGP), a key regulatory gene in plant ascorbate biosynthesis

2019 ◽  
Author(s):  
Junjie Tao ◽  
Zhuan Hao ◽  
Chunhui Huang
Keyword(s):  
Molecular Evolution ◽  
Plant Species ◽  
Regulatory Gene ◽  
Purifying Selection ◽  
Plant Evolution ◽  
Rapid Expansion ◽  
Evolutionary Patterns ◽  
Site Model ◽  
Early Stages ◽  
Evolutionary Innovation

Abstract Background Ascorbic acid (AsA) is a multi-functional molecule and plays essential roles in maintaining the normal life activities of living organisms. Although widely present in plants, the concentration of AsA varies greatly in different plant species. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood in previous works. However, the molecular evolutionary patterns of the gene remain unclear.Results In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, including angiosperms, gymnosperms, lycophytes, bryophytes and chlorophytes, and their phylogenetic relationships, gene duplication and molecular evolution analyses were investigated. Phylogenetic analysis showed that GGP exists widely in various plants, and five major duplication events and several taxon-specific duplications were found, which led to the rapid expansion of GGP genes in seed plants, especially in angiosperms. The structure of GGP genes were more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins have a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that plant GGP genes was predominated by strong purifying selection, indicating the functional importance and conservativeness of plant GGP genes during evolution. Most of the branches under positive selection identified by branch-site model were mainly in the chlorophytes lineage, indicating the evolutionary innovation of GGP genes also mainly occurred in the early stages of plant evolution and episodic diversifying selection contributed to the evolution of plant GGP genes.Conclusions The molecular evolutionary patterns of GGP were first systematically explored in this study. The conservative function of GGP and its rapid expansion in angiosperms may be one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.

scholarly journals Molecular evolution of GDP-L-galactose phosphorylase, a key regulatory gene in plant ascorbate biosynthesis

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Junjie Tao ◽  
Zhuan Hao ◽  
Chunhui Huang
Keyword(s):  
Molecular Evolution ◽  
Abiotic Stress Tolerance ◽  
Regulatory Gene ◽  
Purifying Selection ◽  
Plant Evolution ◽  
Rapid Expansion ◽  
Whole Genome ◽  
Evolutionary Patterns ◽  
Whole Genome Duplications ◽  
Genome Duplications

Abstract Ascorbic acid (AsA) is a widespread antioxidant in living organisms, and plays essential roles in the growth and development of animals and plants as well as in the response to abiotic stress tolerance. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood; however, the molecular evolutionary patterns of the gene remain unclear. In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, and the phylogenetic relationships, gene duplication and molecular evolution analyses of the genes were systematically investigated. Results showed that GGP genes are present throughout the plant kingdom and five shared whole-genome duplications and several lineage-specific whole-genome duplications were found, which led to the rapid expansion of GGPs in seed plants, especially in angiosperms. The structure of GGP genes was more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins had a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that GGP genes were predominated by purifying selection, indicating that the gene is functionally conserved due to its vital importance in AsA biosynthesis. Most of the branches under positive selection identified by the branch-site model were mainly in the chlorophytes lineage, indicating episodic diversifying selection may contribute to the evolution of GGPs, especially in the chlorophyte lineage. The conserved function of GGP and its rapid expansion in angiosperms maybe one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.

scholarly journals Molecular evolution of the plant R regulatory gene family.

Genetics ◽  
1994 ◽  
Vol 138 (3) ◽  
pp. 849-854
Author(s):  
M D Purugganan ◽  
S R Wessler
Keyword(s):  
Molecular Evolution ◽  
Gene Family ◽  
Plant Species ◽  
Regulatory Gene ◽  
Nonsynonymous Substitution ◽  
R Genes ◽  
Nucleotide Substitutions ◽  
Variable Regions ◽  
Helix Loop Helix ◽  
Regulatory Loci

Abstract Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-terminal and C-terminal domains; mean replacement rates for these conserved regions are 1.02 x 10(-9) nonsynonymous nucleotide substitutions per site per year. More than one-half of the protein, however, is diverging rapidly, with nonsynonymous substitution rates of 4.08 x 10(-9) substitutions per site per year. Detailed analysis of R homologs within the grasses (Poaceae) confirm that these variable regions are indeed evolving faster than the flanking conserved domains. Both nucleotide substitutions and small insertion/deletions contribute to the diversification of the variable regions within these regulatory genes. These results demonstrate that large tracts of sequence in these regulatory loci are evolving at a fairly rapid rate.

Molecular evolution of candidate sour taste receptor gene PKD1L3 in mammals

Genome ◽  
2011 ◽  
Vol 54 (11) ◽  
pp. 890-897 ◽  
Author(s):  
Dazhi Chen ◽  
Ping Li ◽  
Wenhu Guo ◽  
Fang Ye ◽  
Jian Wu ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Receptor Gene ◽  
Mammalian Species ◽  
Taste Receptor ◽  
Purifying Selection ◽  
Evolutionary Patterns ◽  
Sour Taste ◽  
Selection Force ◽  
Stimulus Recognition

The PKD1L3 gene encodes an ion channel protein that can interact with the PKD2L1 protein to form a candidate sour taste receptor. In the present study, we have analyzed the evolutionary patterns of PKD1L3 genes from 10 mammalian species. The results showed that PKD1L3 genes have evolved under a dominant purifying selection force. However, for some branches and sites, PKD1L3 genes were detected to have been operated by positive selection. Moreover, some of these positive evolutionary sites are likely to participate in acid stimulus recognition. In rodents, PKD1L3 genes evolved more rapidly than other mammalian lineages. Combined with other functional research reports, our results suggest that rodents may not be the most appropriate model for functional research on the PKD1L3 gene.

scholarly journals Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals

2016 ◽  
Vol 113 (21) ◽  
pp. E2983-E2992 ◽  
Author(s):  
Pierre Boudinot ◽  
Stanislas Mondot ◽  
Luc Jouneau ◽  
Luc Teyton ◽  
Marie-Paule Lefranc ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Purifying Selection ◽  
Cell Receptor ◽  
Nkt Cells ◽  
Evolutionary Patterns ◽  
Mait Cells ◽  
Mhc Genes ◽  
Class 1 ◽  
Complementarity Determining Regions

Whereas major histocompatibility class-1 (MH1) proteins present peptides to T cells displaying a large T-cell receptor (TR) repertoire, MH1Like proteins, such as CD1D and MR1, present glycolipids and microbial riboflavin precursor derivatives, respectively, to T cells expressing invariant TR-α (iTRA) chains. The groove of such MH1Like, as well as iTRA chains used by mucosal-associated invariant T (MAIT) and natural killer T (NKT) cells, respectively, may result from a coevolution under particular selection pressures. Herein, we investigated the evolutionary patterns of the iTRA of MAIT and NKT cells and restricting MH1Like proteins: MR1 appeared 170 Mya and is highly conserved across mammals, evolving more slowly than other MH1Like. It has been pseudogenized or independently lost three times in carnivores, the armadillo, and lagomorphs. The corresponding TRAV1 gene also evolved slowly and harbors highly conserved complementarity determining regions 1 and 2. TRAV1 is absent exclusively from species in which MR1 is lacking, suggesting that its loss released the purifying selection on MR1. In the rabbit, which has very few NKT and no MAIT cells, a previously unrecognized iTRA was identified by sequencing leukocyte RNA. This iTRA uses TRAV41, which is highly conserved across several groups of mammals. A rabbit MH1Like gene was found that appeared with mammals and is highly conserved. It was independently lost in a few groups in which MR1 is present, like primates and Muridae, illustrating compensatory emergences of new MH1Like/Invariant T-cell combinations during evolution. Deciphering their role is warranted to search similar effector functions in humans.

Angiosperm origin and early stages of seed plant evolution deduced from rRNA sequence comparisons

1991 ◽  
Vol 32 (3) ◽  
pp. 253-261 ◽  
Author(s):  
A. V. Troitsky ◽  
Yu. F. Melekhovets ◽  
G. M. Rakhimova ◽  
V. K. Bobrova ◽  
K. M. Valiejo-Roman ◽  
...  
Keyword(s):  
Plant Evolution ◽  
Seed Plant ◽  
Rrna Sequence ◽  
Sequence Comparisons ◽  
Early Stages

scholarly journals Molecular Phylogenetics and Evolutionary Analysis of a Highly Recombinant Begomovirus, Cotton Leaf Curl Multan Virus and Associated Satellites

2021 ◽  
Author(s):  
Tahir Farooq ◽  
Muhammad Umar ◽  
Xiaoman She ◽  
Yafei Tang ◽  
Zifu He
Keyword(s):  
Molecular Phylogenetics ◽  
Management Strategies ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Cotton Leaf ◽  
Evolutionary Analysis ◽  
Cotton Production ◽  
Evolutionary Patterns ◽  
Satellite Sequences ◽  
Leaf Curl

Abstract Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite’s virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite (CLCuMuA) and Cotton leaf curl Multan betasatellite (CLCuMuB) populations arising from distinct regions exhibit high mutation rates. Though evolutionary linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.

scholarly journals Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise

2018 ◽  
Author(s):  
Russell A. Ligon ◽  
Christopher D. Diaz ◽  
Janelle L. Morano ◽  
Jolyon Troscianko ◽  
Martin Stevens ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Functional Integration ◽  
Empirical Support ◽  
Evolutionary Patterns ◽  
Evolutionary Innovation ◽  
Birds Of Paradise ◽  
Analytical Approaches

Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group - the birds-of-paradise - exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit - the courtship phenotype. Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness - functional overlap and interdependency - promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations.Author SummaryAnimals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits - like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary time-scales. Positive covariation among ornament classes suggests that selection is acting on correlated suites of traits - a composite courtship phenotype - and that this integration may be partially responsible for the extreme variation we see in birds-of-paradise.

Introduction

2007 ◽  
Author(s):  
Earl B. Alexander ◽  
Roger G. Coleman ◽  
Todd Keeler-Wolfe ◽  
Susan P. Harrison
Keyword(s):  
North America ◽  
Plant Species ◽  
Plant Communities ◽  
Special Interest ◽  
Deep Understanding ◽  
Plant Evolution ◽  
Ultramafic Rocks ◽  
Serpentine Soils ◽  
Distinctive Features ◽  
Very High

Ultramafic, or colloquially “serpentine,” rocks and soils have dramatic effects on the vegetation that grows on them. Many plants cannot grow in serpentine soils, leaving distinctive suites of plants to occupy serpentine habitats. Plants that do grow on serpentine soils may be stunted, and plant distributions are commonly sparse relative to other soils in an area. Plant communities on serpentine soils are usually distinctive, even if one does not recognize the plant species. Because of these distinctive features, ultramafic rocks and serpentine soils are of special interest to all observers of landscapes. Geology underlies both conceptually and literally the distinctive vegetation on serpentine soils. The occurrence of special floras on particular substrates within particular regions makes rocks and soils of key significance to plant evolution and biogeography. Sophisticated interpretations of these interrelationships require a combined knowledge of geology, soils, and botany that few people possess. Even highly specialized professionals generally lack the requisite expertise in all three disciplines. The science of ecology, which in principle concerns interactions among all aspects of the environment, seldom incorporates a deep understanding of rocks and soils. Some scientists have attempted to bridge this gap through creating a discipline known as geoecology (Troll 1971, Huggett 1995), which forms the basis for our interdisciplinary exploration of serpentine rocks and soils in western North America. The term “serpentine” is applied in a general sense to all ultramafic rocks, soils developed from them, and plants growing on them. Ultramafic rocks are those with very high magnesium and iron concentrations. The word serpentine is derived from the Latin word serpentinus, meaning “resembling a serpent, or a serpent’s skin,” because many serpentine rocks have smooth surfaces mottled in shades of green to black. The distinctive chemistry of ultramafic rocks and serpentine soils restricts the growth of many plants and makes them refuges for plants that thrive in serpentine habitats, including serpentine endemics (species that are restricted to these soils) and other species that have evolved means of tolerating these habitats. Often the means of tolerance include visible adaptations such as slow growth and relatively thick, spiny foliage.

scholarly journals Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

Calreticulin molecular evolution: a strong purifying and episodic diversifying selection result

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Rigers Bakiu
Keyword(s):  
Molecular Evolution ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Amino Acid Sequences ◽  
Over Expression ◽  
Diversifying Selection ◽  
Pathological Conditions ◽  
Weight Protein ◽  
Low Molecular Weight Protein

AbstractCalreticulin (CRT) is a low molecular weight protein present in vertebrates, invertebrates and higher plants. Its multiple functions have been demonstrated. It plays an important role as a chaperone and Ca2+ buffer inside sarcoplasmic/endoplasmic reticulum (SR/ER), and outside the ER in many physiological/pathological processes. Recently it has been observed that CRT over-expression or its absence is linked to various pathological conditions, such as malignant evolution and progression, and these facts really increased its study interests. Using an evolution approach CRT was further characterized. Several Bayesian phylogenetic analyses were performed using coding and amino acid sequences. CRT molecular evolution was investigated for the presence of negative or/and positive selection using HyPhy package. The results indicated that the purifying selection might have operated over the whole CRT primary structure. Although, an episodic diversifying selection was also found on the analyzed CRT sequences.

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