Dataset Information

Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis.

ABSTRACT:

Background

Human brain development is a complicated process. When normal growth and development of brain or central nervous system is impaired, it leads to neurodevelopemental disorders (NDDs). Autosomal Recessive Primary Microcephaly (MCPH) is one of those, for which seven loci (MCPH1-MCPH7) with the corresponding genes (MCPH1, WDR62, CDK5RAP2, CEP152, ASPM, CENPJ, and STIL) have been reported so far. An important field of study is to find out diversity among organisms due to evolution. How species are related to each other can be inferred through finding evolutionary relationship between organisms in the form of ancestors and descendents.

Methods

MEGA5 was used for phylogenetic tree reconstruction. Pair-wise and multiple alignment was built through ClustalW algorithm. Neighbor joining (NJ) and maximum parsimony (MP) methods were used for tree reconstruction. Bootstrap analysis was done to check the reliability of trees. Synteny analysis was performed using Ensemble synteny view in ensemble database and genome synteny viewer (GSV).

Results

Evolutionary time for single gene trees showed that CENPJ (0.02) evolving rapidly while CDK5RAP2 (0.1) evolving with least rate as compare to other genes. All trees were reconciling the species divergence time. Chimpanzee was inferred as closest specie of Human. In MCPH combined tree, five duplications were observed. Four duplications were before and one was after vertebrate and invertebrate divergence. Two genes MCPH1 and WDR62 were closely related with each other. Synteny analysis indicated that maximum conservation of Human was with Chimpanzee. Highly conserved synteny was observed for Human and Chimpanzee in case of CENPJ with no deletion.

Conclusion

It has been hypothesized that due to having closest relationship, mutations can affect Chimpanzee likewise as these affect Human. Conservation shows that apart from sequence similarity, function of MCPH genes in closely related species is also same and this function disrupts as a result of mutation and hence leads to the diseased state. Huge genomic and proteomic data is available today which enables us to perform In Silico analysis. Our cost and time effective analysis has opened many insights into disease understanding and it will definitely provide a way towards accurate diagnosis.

SUBMITTER: Rauf S

PROVIDER: S-EPMC4015606 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis.

Rauf Sobiah S Mir Asif A

Theoretical biology & medical modelling 20131022

<h4>Background</h4>Human brain development is a complicated process. When normal growth and development of brain or central nervous system is impaired, it leads to neurodevelopemental disorders (NDDs). Autosomal Recessive Primary Microcephaly (MCPH) is one of those, for which seven loci (MCPH1-MCPH7) with the corresponding genes (MCPH1, WDR62, CDK5RAP2, CEP152, ASPM, CENPJ, and STIL) have been reported so far. An important field of study is to find out diversity among organisms due to evolution. ...[more]

PMID: 24148351

Similar Datasets

Project description:Cetacean brain size expansion is an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. Here, all exons of the seven primary microcephaly (MCPH) genes that play key roles in size regulation during brain development were investigated in representative cetacean lineages.Sequences of MCPH2-7 genes were intact in cetaceans but frameshift mutations and stop codons was identified in MCPH1. Extensive positive selection was identified in four of six intact MCPH genes: WDR62, CDK5RAP2, CEP152, and ASPM. Specially, positive selection at CDK5RAP2 and ASPM were examined along lineages of odontocetes with increased encephalization quotients (EQ) and mysticetes with reduced EQ but at WDR62 only found along odontocete lineages. Interestingly, a positive association between evolutionary rate (?) and EQ was identified for CDK5RAP2 and ASPM. Furthermore, we tested the binding affinities between Calmodulin (CaM) and ASPM IQ motif in cetaceans because only CaM combined with IQ, can ASPM perform the function in determining brain size. Preliminary function assay showed binding affinities between CaM and IQ motif of the odontocetes with increased EQ was stronger than for the mysticetes with decreased EQ. In addition, evolution rate of ASPM and CDK5RAP2 were significantly related to mean group size (as one measure of social complexity).Our study investigated the genetic basis of cetacean brain size evolution. Significant positive selection was examined along lineages with both increased and decreased EQ at CDK5RAP2 and ASPM, which is well matched with cetacean complex brain size evolution. Evolutionary rate of CDK5RAP2 and ASPM were significantly related to EQ, suggesting that these two genes may have contributed to EQ expansion in cetaceans. This suggestion was further indicated by our preliminary function test that ASPM might be mainly linked to evolutionary increases in EQ. Most strikingly, our results suggested that cetaceans evolved large brains to manage complex social systems, consisting with the 'social brain hypothesis', as evolutionary rate of ASPM and CDK5RAP2 were significantly related to mean group size.

Dataset Information

Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis.

Background

Methods

Results

Conclusion

Publications

Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets