Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates.
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.
Department of Zoology, University of Oxford, United Kingdom.|Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Zhejiang, China.
Yongbo
Y
Bao
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.|Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.|National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
Fei
F
Xu
Department of Zoology, University of Oxford, United Kingdom.
Sebastian M
SM
Shimeld
D000818:Animals; D000845:Annelida / Q000235:genetics; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D020440:Gene Duplication / Q000235:genetics; D015870:Gene Expression; D016678:Genome; D007438:Introns / Q000235:genetics; D007448:Invertebrates / Q000235:genetics; D008974:Mollusca / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny
D051792:Basic Helix-Loop-Helix Proteins
annelid; bHLH gene; gene duplication; mollusc; transcription factor