Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

2022 ◽  
pp. 107395
Author(s):  
Alissa M. Williams ◽  
Olivia G. Carter ◽  
Evan S. Forsythe ◽  
Hannah K. Mendoza ◽  
Daniel B. Sloan
Keyword(s):  
Gene Duplication ◽  
Rate Variation

scholarly journals Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates

2019 ◽  
Vol 36 (7) ◽  
pp. 1384-1404 ◽  
Author(s):  
Arthur Zwaenepoel ◽  
Yves Van de Peer
Keyword(s):  
Maximum Likelihood ◽  
Gene Duplication ◽  
Gene Tree ◽  
Probabilistic Approach ◽  
Species Tree ◽  
Rate Variation ◽  
Whole Genome ◽  
Tree Reconciliation ◽  
Gene Duplication And Loss ◽  
Loss Rates

Abstract Gene tree–species tree reconciliation methods have been employed for studying ancient whole-genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular, the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation-based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rates across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigated the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.

scholarly journals Gene duplication and rate variation in the evolution of non-photosynthetic pathways in plastids

2021 ◽  
Author(s):  
Alissa M Williams ◽  
Olivia G Carter ◽  
Evan S Forsythe ◽  
Hannah K Mendoza ◽  
Daniel B Sloan
Keyword(s):  
Gene Duplication ◽  
Fatty Acid Biosynthesis ◽  
Single Copy ◽  
Rate Variation ◽  
Sequence Evolution ◽  
Catalytic Core ◽  
Multiple Species ◽  
Insight Into ◽  
Paralogous Proteins

While the chloroplast (plastid) is known for its role in photosynthesis, it is also involved in many other biosynthetic pathways essential for plant survival. As such, plastids contain an extensive suite of enzymes required for non-photosynthetic processes. The evolution of the associated genes has been especially dynamic in flowering plants (angiosperms), including examples of gene duplication and extensive rate variation. We examined the role of ongoing gene duplication in two key plastid enzymes, the acetyl-CoA carboxylase (ACCase) and the caseinolytic protease (Clp), responsible for fatty acid biosynthesis and protein turnover, respectively. In plants, there are two ACCase complexes: a homomeric version present in the cytosol and a heteromeric version present in the plastid. Duplications of the nuclear-encoded homomeric ACCase gene and retargeting to the plastid have been previously reported in multiple species. We find that these retargeted copies of the homomeric ACCase gene exhibit elevated rates of sequence evolution, consistent with neofunctionalization and/or relaxation of selection. The plastid Clp complex catalytic core is composed of nine paralogous proteins that arose via ancient gene duplication in the cyanobacterial/plastid lineage. We show that further gene duplication occurred more recently in the nuclear-encoded core subunits of this complex, yielding additional paralogs in many species of angiosperms. Moreover, in six of eight cases, subunits that have undergone recent duplication display increased rates of sequence evolution relative to those that have remained single copy. We also compared rate patterns between pairs of Clp core paralogs to gain insight into post-duplication evolutionary routes. These results show that gene duplication and rate variation continue to shape the plastid proteome.

scholarly journals Ancient whole genome duplications and the evolution of the gene duplication and loss rate

2019 ◽  
Author(s):  
Arthur Zwaenepoel ◽  
Yves Van de Peer
Keyword(s):  
Maximum Likelihood ◽  
Gene Duplication ◽  
Loss Rate ◽  
Gene Tree ◽  
Probabilistic Approach ◽  
Species Tree ◽  
Rate Variation ◽  
Whole Genome ◽  
Tree Reconciliation ◽  
Gene Duplication And Loss

AbstractGene tree - species tree reconciliation methods have been employed for studying ancient whole genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rate across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigate the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.

Bios, bios data analyzer and the biotic features of galactic evolution, DNA sequences and heart rate variation

2003 ◽  
Author(s):  
Hector Sabelli ◽  
Arthur Sugerman ◽  
Lazar Kovacevic ◽  
Louis Kauffman
Keyword(s):  
Heart Rate ◽  
Dna Sequences ◽  
Galactic Evolution ◽  
Rate Variation ◽  
Heart Rate Variation

Increased glyoxalase-1 levels in Fkbp5 knock-out mice caused by Glo1 gene duplication

2013 ◽  
Vol 46 (06) ◽  
Author(s):  
LK Kollmannsberger ◽  
NC Gassen ◽  
A Bultmann ◽  
J Hartmann ◽  
P Weber ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Knock Out ◽  
Glyoxalase 1 ◽  
Knock Out Mice

Calculation of Heart Rate Variation Owing to the Effect of Electromagnetic Fields Waves (EMF)

2018 ◽  
Vol 10 (2) ◽  
pp. 48-53 ◽  
Author(s):  
Mohammed Yahya H. ◽  
◽  
Ali Adil Turki ◽  
Ali H. F. Alnasraui ◽  
Qasim shaker K ◽  
...  
Keyword(s):  
Heart Rate ◽  
Electromagnetic Fields ◽  
Rate Variation ◽  
Heart Rate Variation
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