Evolution and divergence of the mammalian SAMD9/SAMD9L gene family

Ana Lemos De Matos, Jia Liu, Douglas McFadden, Pedro J. Esteves

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Background: The physiological functions of the human Sterile Alpha Motif Domain-containing 9 (SAMD9) gene and its chromosomally adjacent paralogue, SAMD9-like (SAMD9L), currently remain unknown. However, the direct links between the deleterious mutations or deletions in these two genes and several human disorders, such as inherited inflammatory calcified tumors and acute myeloid leukemia, suggest their biological importance. SAMD9 and SAMD9L have also recently been shown to play key roles in the innate immune responses to stimuli such as viral infection. We were particularly interested in understanding the mammalian evolutionary history of these two genes. The phylogeny of SAMD9 and SAMD9L genes was reconstructed using the Maximum Likelihood method. Furthermore, six different methods were applied to detect SAMD9 and SAMD9L codons under selective pressure: the site-specific model M8 implemented in the codeml program in PAML software and five methods available on the Datamonkey web server, including the Single Likelihood Ancestor Counting method, the Fixed Effect Likelihood method, the Random Effect Likelihood method, the Mixed Effects Model of Evolution method and the Fast Unbiased Bayesian AppRoximation method. Additionally, the house mouse (Mus musculus) genome has lost the SAMD9 gene, while keeping SAMD9L intact, prompting us to investigate whether this loss is a unique event during evolution. Results: Our evolutionary analyses suggest that SAMD9 and SAMD9L arose through an ancestral gene duplication event after the divergence of Marsupialia from Placentalia. Additionally, selection analyses demonstrated that both genes have been subjected to positive evolutionary selection. The absence of either SAMD9 or SAMD9L genes from some mammalian species supports a partial functional redundancy between the two genes. Conclusions: To the best of our knowledge, this work is the first study on the evolutionary history of mammalian SAMD9 and SAMD9L genes. We conclude that evolutionary selective pressure has acted on both of these two genes since their divergence, suggesting their importance in multiple cellular processes, such as the immune responses to viral pathogens.

Original languageEnglish (US)
Article number121
JournalBMC Evolutionary Biology
Volume13
Issue number1
DOIs
StatePublished - Jun 17 2013
Externally publishedYes

Fingerprint

divergence
gene
genes
Mus musculus
immune response
methodology
family
myeloid leukemia
history
method
gene duplication
Bayesian theory
Metatheria
codons
tumor
ancestry
mutation
phylogeny
genome
pathogen

Keywords

  • Evolutionary history
  • Mammals
  • Positive selection
  • SAMD9
  • SAMD9-like

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics

Cite this

Evolution and divergence of the mammalian SAMD9/SAMD9L gene family. / Lemos De Matos, Ana; Liu, Jia; McFadden, Douglas; Esteves, Pedro J.

In: BMC Evolutionary Biology, Vol. 13, No. 1, 121, 17.06.2013.

Research output: Contribution to journalArticle

Lemos De Matos, Ana ; Liu, Jia ; McFadden, Douglas ; Esteves, Pedro J. / Evolution and divergence of the mammalian SAMD9/SAMD9L gene family. In: BMC Evolutionary Biology. 2013 ; Vol. 13, No. 1.
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abstract = "Background: The physiological functions of the human Sterile Alpha Motif Domain-containing 9 (SAMD9) gene and its chromosomally adjacent paralogue, SAMD9-like (SAMD9L), currently remain unknown. However, the direct links between the deleterious mutations or deletions in these two genes and several human disorders, such as inherited inflammatory calcified tumors and acute myeloid leukemia, suggest their biological importance. SAMD9 and SAMD9L have also recently been shown to play key roles in the innate immune responses to stimuli such as viral infection. We were particularly interested in understanding the mammalian evolutionary history of these two genes. The phylogeny of SAMD9 and SAMD9L genes was reconstructed using the Maximum Likelihood method. Furthermore, six different methods were applied to detect SAMD9 and SAMD9L codons under selective pressure: the site-specific model M8 implemented in the codeml program in PAML software and five methods available on the Datamonkey web server, including the Single Likelihood Ancestor Counting method, the Fixed Effect Likelihood method, the Random Effect Likelihood method, the Mixed Effects Model of Evolution method and the Fast Unbiased Bayesian AppRoximation method. Additionally, the house mouse (Mus musculus) genome has lost the SAMD9 gene, while keeping SAMD9L intact, prompting us to investigate whether this loss is a unique event during evolution. Results: Our evolutionary analyses suggest that SAMD9 and SAMD9L arose through an ancestral gene duplication event after the divergence of Marsupialia from Placentalia. Additionally, selection analyses demonstrated that both genes have been subjected to positive evolutionary selection. The absence of either SAMD9 or SAMD9L genes from some mammalian species supports a partial functional redundancy between the two genes. Conclusions: To the best of our knowledge, this work is the first study on the evolutionary history of mammalian SAMD9 and SAMD9L genes. We conclude that evolutionary selective pressure has acted on both of these two genes since their divergence, suggesting their importance in multiple cellular processes, such as the immune responses to viral pathogens.",
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