Genomic insights into molecular adaptation to intertidal environments in the mangrove Aegiceras corniculatum

2021 ◽  
Author(s):  
Xiao Feng ◽  
Guohong Li ◽  
Shaohua Xu ◽  
Weihong Wu ◽  
Qipian Chen ◽  
...  
Keyword(s):  
Molecular Adaptation ◽  
Aegiceras Corniculatum ◽  
Intertidal Environments

scholarly journals A high-quality genome of the mangrove Aegiceras corniculatum aids investigation of molecular adaptation to intertidal environments

2020 ◽  
Author(s):  
Xiao Feng ◽  
Guohong Li ◽  
Shaohua Xu ◽  
Weihong Wu ◽  
Qipian Chen ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
High Salinity ◽  
Molecular Adaptation ◽  
Calcium Signal ◽  
High Quality ◽  
Protein Coding ◽  
Aegiceras Corniculatum ◽  
Protein Coding Genes ◽  
Salt Secretion ◽  
Intertidal Environments

AbstractMangroves have colonized extreme intertidal environments characterized by high salinity, hypoxia, and other abiotic stresses. During millions of years of evolution, mangroves have adapted to these habitats, evolving a series of highly specialized traits. Aegiceras corniculatum, a pioneer mangrove species that evolved salt secretion and crypto-vivipary, is an attractive ecological model to investigate molecular mechanisms underlying adaptation to intertidal environments. Here we report a high-quality reference genome of A. corniculatum using the PacBio SMRT sequencing technology, comprising 827 Megabases (Mb) and containing 32,092 protein-coding genes. The longest scaffold and N50 for the assembled genome are 13.76 Mb and 3.87 Mb. Comparative and evolutionary analyses revealed that A. corniculatum experienced a whole-genome duplication (WGD) event around 35 million years ago after the divergence between Aegiceras and Primula. We inferred that maintenance of cellular environmental homeostasis is an important adaptive process in A. corniculatum. The 14-3-3 protein-coding genes were retained after the recent WGD event, decoding a calcium signal to regulate Na+ homeostasis. A. corniculatum has more H+-ATPase coding genes, essential for the maintenance of low Na+ concentration in the cells, than its relatives. Photosynthesis and oxidative-phosphorylation pathways are overrepresented among significantly expanded gene families and might supply the energy needed for salt secretion. Genes involved in natural antioxidant biosynthesis, contributing to scavenging reactive oxygen species against high salinity, have also increased in copy number. We also found that all homologs of DELAY OF GERMINATION1 (DOG1), a pivotal regulator of seed dormancy, lost their heme-binding ability in A. corniculatum. This loss may contribute to crypto-vivipary. Our study provides a valuable resource to investigate molecular adaptation to extreme environments in mangroves.

Above- and below-ground biomasses of two species of mangrove on the Hawkesbury River estuary, New South Wales

1997 ◽  
Vol 48 (2) ◽  
pp. 147 ◽  
Author(s):  
Neil Saintilan
Keyword(s):  
New South ◽  
New South Wales ◽  
River Estuary ◽  
Avicennia Marina ◽  
Above Ground Biomass ◽  
Aegiceras Corniculatum ◽  
South Wales ◽  
Below Ground ◽  
Mangrove Communities ◽  
Intertidal Environments

Above- and below-ground biomasses of two species of mangrove, Avicennia marina and Aegiceras corniculatum, were estimated in a range of intertidal environments along the Hawkesbury River. Estimates of biomass of Avicennia communities in freshly accreted brackish substrata were in the order of 40 kg m–2, the highest figure ever recorded for temperate mangrove communities. The above-ground biomass communities of each species declined with increasing substratum salinity, whereas root/shoot ratios increased with increasing substratum salinity.

A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution

2019 ◽  
Vol 69 (4) ◽  
pp. 722-738 ◽  
Author(s):  
Christopher T Jones ◽  
Noor Youssef ◽  
Edward Susko ◽  
Joseph P Bielawski
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary History ◽  
Life History Trait ◽  
Molecular Adaptation ◽  
Simulation Studies ◽  
Site Model ◽  
Branch Site ◽  
A Site ◽  
Post Hoc

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

scholarly journals The Effects of Hill-Robertson Interference Between Weakly Selected Mutations on Patterns of Molecular Evolution and Variation

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 929-944 ◽  
Author(s):  
Gilean A T McVean ◽  
Brian Charlesworth
Keyword(s):  
Codon Bias ◽  
Molecular Adaptation ◽  
Weak Selection ◽  
Multiple Loci ◽  
Locus Model ◽  
Fitness Consequences ◽  
Novel Variants ◽  
Population Sizes ◽  
The Hill ◽  
Reversible Mutation

Abstract Associations between selected alleles and the genetic backgrounds on which they are found can reduce the efficacy of selection. We consider the extent to which such interference, known as the Hill-Robertson effect, acting between weakly selected alleles, can restrict molecular adaptation and affect patterns of polymorphism and divergence. In particular, we focus on synonymous-site mutations, considering the fate of novel variants in a two-locus model and the equilibrium effects of interference with multiple loci and reversible mutation. We find that weak selection Hill-Robertson (wsHR) interference can considerably reduce adaptation, e.g., codon bias, and, to a lesser extent, levels of polymorphism, particularly in regions of low recombination. Interference causes the frequency distribution of segregating sites to resemble that expected from more weakly selected mutations and also generates specific patterns of linkage disequilibrium. While the selection coefficients involved are small, the fitness consequences of wsHR interference across the genome can be considerable. We suggest that wsHR interference is an important force in the evolution of nonrecombining genomes and may explain the unexpected constancy of codon bias across species of very different census population sizes, as well as several unusual features of codon usage in Drosophila.

Pararhizobium mangrovi sp. nov., Isolated From Aegiceras corniculatum Stem

2021 ◽  
Author(s):  
Mi Li ◽  
Yonghong Liu ◽  
Kai Liu ◽  
Shuangyu Luo ◽  
Xiangxi Yi ◽  
...  
Keyword(s):  
Aegiceras Corniculatum

scholarly journals Diatoms of the intertidal environments of Willapa Bay, Washington, USA as a sea-level indicator

2021 ◽  
pp. 102033
Author(s):  
Isabel Hong ◽  
Benjamin P. Horton ◽  
Andrea D. Hawkes ◽  
Robert J. O'Donnell ◽  
Jason S. Padgett ◽  
...  
Keyword(s):  
Sea Level ◽  
Willapa Bay ◽  
Level Indicator ◽  
Intertidal Environments
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