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Sequence variability at three MHC loci of finless porpoises (Neophocaena phocaenoides)

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Abstract

Major histocompatibility complex (MHC) class II DQB and DRA genes and class I gene of finless porpoises (Neophocaena phocaenoides) were investigated by single-strand conformation polymorphism and sequence analysis. The DRA, DQB, and MHC-I loci each contained 5, 14, and 34 unique sequences, respectively, and considerable sequence variation was found at the MHC-I and DQB loci. Gene duplication was manifested as three to five distinct sequences at each of the DQB and MHC-I loci from some individuals, and these sequences at each of the two loci separately clustered into four groups (cluster A, B, C, and D) based on the phylogenetic trees. Phylogenetic reconstruction revealed a trans-species pattern of evolution. Relatively high rates of non-synonymous (d N) vs synonymous (d S) substitution in the peptide-binding region (PBR) suggested balancing selection for maintaining polymorphisms at the MHC-I and DQB loci. In contrast, one single locus with little sequence variation was detected in the DRA gene, and no non-synonymous substitutions in the PBR indicated no balancing selection on this gene.

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Acknowledgments

This study was supported through the National Natural Science Foundation Commission of China Grants, No.30270212, No.30470253, and No.30670294 and “Qinglan Project” of Jiangsu Province awarded to Dr. Guang Yang. The authors thank Anli Gao, Xin-Rong Xu, Hua Chen, and Qing Chang for collecting samples during the years, and members of the Institute of Genetic Resources, Nanjing Normal University, for their contributions to this paper.

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  1. Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 122 Ninghai Road, Nanjing, 210097, China

    Shixia Xu, Peng Sun, Kaiya Zhou & Guang Yang

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  1. Shixia Xu
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  2. Peng Sun
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Correspondence to Guang Yang.

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Xu, S., Sun, P., Zhou, K. et al. Sequence variability at three MHC loci of finless porpoises (Neophocaena phocaenoides). Immunogenetics 59, 581–592 (2007). https://doi.org/10.1007/s00251-007-0223-9

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