scholarly journals Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes

2005 ◽  
Vol 34 (1) ◽  
pp. 147-158 ◽  
Author(s):  
Jerome C. Regier ◽  
Heather M. Wilson ◽  
Jeffrey W. Shultz
Keyword(s):  
Phylogenetic Analysis ◽  
Nuclear Protein ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Phylogenetic analysis of the corbiculate bee tribes based on 12 nuclear protein-coding genes (Hymenoptera: Apoidea: Apidae)

Apidologie ◽  
2008 ◽  
Vol 39 (1) ◽  
pp. 163-175 ◽  
Author(s):  
Atsushi Kawakita ◽  
John S. Ascher ◽  
Teiji Sota ◽  
Makoto Kato ◽  
David W. Roubik
Keyword(s):  
Phylogenetic Analysis ◽  
Nuclear Protein ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 115
Author(s):  
Yuxin Hu ◽  
Weiyue Xing ◽  
Zhengyu Hu ◽  
Guoxiang Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Phylogenetic Relationship ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Volvocine Algae

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

Phylogeny of Decapoda using two nuclear protein-coding genes: Origin and evolution of the Reptantia

2008 ◽  
Vol 48 (1) ◽  
pp. 359-368 ◽  
Author(s):  
L.M. Tsang ◽  
K.Y. Ma ◽  
S.T. Ahyong ◽  
T.-Y. Chan ◽  
K.H. Chu
Keyword(s):  
Nuclear Protein ◽  
Protein Coding ◽  
Origin And Evolution ◽  
Protein Coding Genes

scholarly journals The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Ruoran Li ◽  
Xuli Jia ◽  
Jing Zhang ◽  
Shangang Jia ◽  
Tao Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Brown Algae ◽  
Linear Analysis ◽  
The Other ◽  
Genomic Evolution ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Plastid Genomes ◽  
The Family ◽  
Generation Sequencing

Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.

EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 689-691 ◽  
Author(s):  
Yoon-Seong Jeon ◽  
Kihyun Lee ◽  
Sang-Cheol Park ◽  
Bong-Soo Kim ◽  
Yong-Joon Cho ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Relevant Information ◽  
Biological Information ◽  
Sequence Alignments ◽  
Protein Coding ◽  
Structure Information ◽  
Biologically Relevant ◽  
Molecular Sequence ◽  
Protein Coding Genes

EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-generated multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionalities for editing rRNA alignments using secondary structure information. In addition, it supports simultaneous editing of both DNA sequences and their translated protein sequences for protein-coding genes. EzEditor is, to our knowledge, the first sequence editing software designed for both rRNA- and protein-coding genes with the visualization of biologically relevant information and should be useful in molecular phylogenetic studies. EzEditor is based on Java, can be run on all major computer operating systems and is freely available from http://sw.ezbiocloud.net/ezeditor/.

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