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Phylogenetic analysis of achaete–scute complex genes in metazoans

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Abstract

Achaete–scute complex (ASC) genes play essential roles in regulating neurogenesis of metazoans. Various metazoan species have greatly different numbers of genes in ASCa, ASCb and ASCc families. To explore evolutionary mechanisms of metazoan ASC genes, Blast (basic local alignment search tool) searches and phylogenetic analyses were conducted to identify ASC genes in metazoan species and to infer phylogenetic relationship between various ASC genes. As a result, 2784 ASC genes were identified in 804 metazoan species. The phylogenetic tree constructed using 1237 unique bHLH motifs shows that metazoan ASCa, ASCb and ASCc families contain six (a1–a6), five (b1–b5) and three (c1–c3) bHLH genes, respectively. Further phylogenetic analyses suggest that ASC genes in metazoans are derived from a primitive c gene, those in insects are derived from c2 gene, and those in chordates are derived from a2 and a3 genes. Data of gene linkage demonstrate that insect a6 is derived from a4 but not from a5, and chordate a2 is ancestral to b5 only, whilst a3 is ancestral to both b3 and b5. It is concluded that current ASC gene families in metazoans were established through a series of sub- and/or neo-functionalization to duplicated ancestral ASC gene(s). These results provide good references for exploring evolutionary mechanisms of other bHLH genes in metazoans. Besides, gene subtyping is considered as an efficient method for evolutionary studies on closely related homologous genes.

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (Nos. 31872425 and 31861143051).

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Authors and Affiliations

  1. School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China

    Yong Wang, Qin-Liu He, Zhi-Peng Luo & Liu Yang

  2. Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China

    Guang-Dong Wang, Qin Yao & Ke-Ping Chen

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  1. Yong Wang
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Correspondence to Yong Wang.

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Supplementary file 1

Taxonomic information of 804 metazoan species and bHLH motifs of achaete–scute complex genes in various metazoan phyla. This Microsoft Excel file contains 18 worksheets, each of which stores survey data of a specific metazoan phylum. The worksheets are ordered in accordance with metazoan phyla shown in Table 2. Individual metazoan species is numbered using a capital letter (to indicate which phylum it belongs to) plus a number. For each species, hierarchical taxonomic information, ASC genes and their correspondent bHLH motifs, protein accession numbers and coding region(s) are listed. If coding regions of different ASC genes are on the same contig, “at # k” is added after the contig number to indicate relative locus of an ASC gene. P1 and P2 mean phase of the first and the second intron, in which p0, p1 and p2 stand for phase 0, phase 1 and phase 2, respectively. L1 and L2 mean length of the first and the second intron in base pairs. (PDF 271 kb)

Figure S1

Maximum-likelihood phylogenetic tree of metazoan achaete–scute complex genes. The tree was constructed using amino acids of 1237 unique metazoan bHLH motifs which are different with each other. Three bHLH motifs of Max (Myc associated factor x) protein from roundworm (C. elegans), fruit fly (D. melanogaster) and mouse (M. musculus) were used as outgroup. Max genes belong to higher-order group B in the bHLH superfamily. Since bHLH genes of group B are paraphyletic and closest to the ancestral bHLH type from which groups A, C, D, E, and F bHLH arise (Ledent and Vervoort 2001), they are frequently used as outgroup for phylogenetic analysis of bHLH genes. Tree branches are shown in different colors to indicate separate phyletic clades formed by different ASC gene subtypes. Sequence names are composed of species number and ASC gene version, both of which are listed in supplementary file 1. For simplicity, only bootstrap values of over 50% are shown in the tree, and branch lengths are not proportional to distances between sequences (XLSX 478 kb)

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Wang, Y., Wang, GD., He, QL. et al. Phylogenetic analysis of achaete–scute complex genes in metazoans. Mol Genet Genomics 295, 591–606 (2020). https://doi.org/10.1007/s00438-020-01648-y

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