Abstract
Homeobox genes cloned from the purple sea star Pisaster ochraceus (Phylum Echinodermata/Class Asteroidea) were used along with related sequences available from members of other representative animal phyla to generate molecular phylogenies for Distal-less/Dlx, Hox5, Hox7, and Hox9/10 homeobox genes. Phylogenetic relationships were inferred based on the predicted 60 amino acid homeodomain, using amino acid (AA) and nucleotide (NT) models as well as the recently developed codon substitution models of sequence evolution. The resulting phylogenetic trees were mostly congruent with the consensus species-tree, grouping these newly identified genes with those isolated from other Asteroidea. This analysis also allowed a preliminary comparison of the performance of codon models with that of NT and AA evolutionary models in the inference of homeobox phylogeny. We found that, overall, the NT models displayed low reliability in recovering major clades at the Superphylum/Phylum level, and that codon models were slightly more dependable than AA models. Remarkably, in the majority of cases, codon substitution models seemed to outperform both AA and NT models at both the Class level and homeobox paralogy-group level of classification.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 359-365 |
| Number of pages | 7 |
| Journal | Development Genes and Evolution |
| Volume | 225 |
| Issue number | 6 |
| DOIs | |
| State | Published - Nov 1 2015 |
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Keywords
- Asteroidea
- Codon model
- Distal-less
- Dlx
- Echinoderm
- Gbx
- Hemichordate
- Homeobox
- Hox
- Phylogeny
- Pisaster
- Rx
- Sea star
- Transcription factor
ASJC Scopus subject areas
- Developmental Biology
- Genetics
Cite this
Molecular phylogeny of four homeobox genes from the purple sea star Pisaster ochraceus. / Matassi, Giorgio; Imai, Janice Hitomi; Di Gregorio, Anna.
In: Development Genes and Evolution, Vol. 225, No. 6, 01.11.2015, p. 359-365.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Molecular phylogeny of four homeobox genes from the purple sea star Pisaster ochraceus
AU - Matassi, Giorgio
AU - Imai, Janice Hitomi
AU - Di Gregorio, Anna
PY - 2015/11/1
Y1 - 2015/11/1
N2 - Homeobox genes cloned from the purple sea star Pisaster ochraceus (Phylum Echinodermata/Class Asteroidea) were used along with related sequences available from members of other representative animal phyla to generate molecular phylogenies for Distal-less/Dlx, Hox5, Hox7, and Hox9/10 homeobox genes. Phylogenetic relationships were inferred based on the predicted 60 amino acid homeodomain, using amino acid (AA) and nucleotide (NT) models as well as the recently developed codon substitution models of sequence evolution. The resulting phylogenetic trees were mostly congruent with the consensus species-tree, grouping these newly identified genes with those isolated from other Asteroidea. This analysis also allowed a preliminary comparison of the performance of codon models with that of NT and AA evolutionary models in the inference of homeobox phylogeny. We found that, overall, the NT models displayed low reliability in recovering major clades at the Superphylum/Phylum level, and that codon models were slightly more dependable than AA models. Remarkably, in the majority of cases, codon substitution models seemed to outperform both AA and NT models at both the Class level and homeobox paralogy-group level of classification.
AB - Homeobox genes cloned from the purple sea star Pisaster ochraceus (Phylum Echinodermata/Class Asteroidea) were used along with related sequences available from members of other representative animal phyla to generate molecular phylogenies for Distal-less/Dlx, Hox5, Hox7, and Hox9/10 homeobox genes. Phylogenetic relationships were inferred based on the predicted 60 amino acid homeodomain, using amino acid (AA) and nucleotide (NT) models as well as the recently developed codon substitution models of sequence evolution. The resulting phylogenetic trees were mostly congruent with the consensus species-tree, grouping these newly identified genes with those isolated from other Asteroidea. This analysis also allowed a preliminary comparison of the performance of codon models with that of NT and AA evolutionary models in the inference of homeobox phylogeny. We found that, overall, the NT models displayed low reliability in recovering major clades at the Superphylum/Phylum level, and that codon models were slightly more dependable than AA models. Remarkably, in the majority of cases, codon substitution models seemed to outperform both AA and NT models at both the Class level and homeobox paralogy-group level of classification.
KW - Asteroidea
KW - Codon model
KW - Distal-less
KW - Dlx
KW - Echinoderm
KW - Gbx
KW - Hemichordate
KW - Homeobox
KW - Hox
KW - Phylogeny
KW - Pisaster
KW - Rx
KW - Sea star
KW - Transcription factor
UR - http://www.scopus.com/inward/record.url?scp=84947617138&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84947617138&partnerID=8YFLogxK
U2 - 10.1007/s00427-015-0516-1
DO - 10.1007/s00427-015-0516-1
M3 - Article
C2 - 26432455
AN - SCOPUS:84947617138
VL - 225
SP - 359
EP - 365
JO - Development Genes and Evolution
JF - Development Genes and Evolution
SN - 0949-944X
IS - 6
ER -