Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis

Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

doi:10.1007/s00438-013-0755-7

Cited by 15 publications

(6 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…4 Gyoja and Satoh 2013. 5 Ledent et al 2002; Simionato et al 2007; Wang et al 2009; Liu and Zhao 2010; Liu et al 2013. 6 Simionato et al 2007; Gyoja et al 2012; Gyoja 2014.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates

Bao

Shimeld

2017

Genome Biology and Evolution

View full text Add to dashboard Cite

The gain and loss of genes encoding transcription factors is of importance to understanding the evolution of gene regulatory complexity. The basic helix–loop–helix (bHLH) genes encode a large superfamily of transcription factors. We systematically classify the bHLH genes from five mollusc, two annelid and one brachiopod genomes, tracing the pattern of bHLH gene evolution across these poorly studied Phyla. In total, 56–88 bHLH genes were identified in each genome, with most identifiable as members of previously described bilaterian families, or of new families we define. Of such families only one, Mesp, appears lost by all these species. Additional duplications have also played a role in the evolution of the bHLH gene repertoire, with many new lophotrochozoan-, mollusc-, bivalve-, or gastropod-specific genes defined. Using a combination of transcriptome mining, RT-PCR, and in situ hybridization we compared the expression of several of these novel genes in tissues and embryos of the molluscs Crassostrea gigas and Patella vulgata, finding both conserved expression and evidence for neofunctionalization. We also map the positions of the genes across these genomes, identifying numerous gene linkages. Some reflect recent paralog divergence by tandem duplication, others are remnants of ancient tandem duplications dating to the lophotrochozoan or bilaterian common ancestors. These data are built into a model of the evolution of bHLH genes in molluscs, showing formidable evolutionary stasis at the family level but considerable within-family diversification by tandem gene duplication.

show abstract

“…4 Gyoja and Satoh 2013. 5 Ledent et al 2002; Simionato et al 2007; Wang et al 2009; Liu and Zhao 2010; Liu et al 2013. 6 Simionato et al 2007; Gyoja et al 2012; Gyoja 2014.…”

Section: Discussionmentioning

confidence: 99%

“…2000; Ledent and Vervoort 2001; Liu and Zhao 2010), nonmodel vertebrates (Dang, Wang, Zhang, et al. 2011; Liu et al. 2013), Ciona intestinalis (Satou et al.…”

Section: Introductionunclassified

Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates

Bao

Shimeld

2017

Genome Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…Simionato et al [25] reported that gene family size does not generally reflect the evolutionary diversity of gene families, such as the tyrosine kinase family and the basic helix-loop-helix family [25][26][27]. Therefore, we tried to explore the difference in the OR gene numbers between marine and terrestrial mammals resulting from gene-specific duplications or increased numbers of gene gains and losses.…”

Section: Or Gene Numbers Of Marine Mammals Are Significantly Lower Thmentioning

confidence: 99%

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Liu

Shen

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

show abstract

“…Simionato et al [22] reported that gene family size does not generally reflect the evolutionary diversity of gene families, such as the tyrosine kinase family and the basic helix-loop-helix family [22][23][24]. Therefore, we tried to explore the difference in the OR gene numbers between marine and terrestrial mammals resulting from gene-specific duplications or increased numbers of gene gains and losses.…”

Section: Ogg Number Of Marine Mammals Is Significantly Lower Than Thamentioning

confidence: 99%

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Liu

Shen

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified and the factors that might underlie these variations are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had less OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous gene in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR genes compared with their related terrestrial lineages, which may be related to the weaker purifying selection. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

show abstract

Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis

Cited by 15 publications

References 60 publications

Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates

Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Contact Info

Product

Resources

About