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Characterization of the domestic goat γδ T cell receptor gene loci and gene usage

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Abstract

Goats and cattle diverged 30 million years ago but retain similarities in immune system genes. Here, the caprine T cell receptor (TCR) gene loci and transcription of its genes were examined and compared to cattle. We annotated the TCR loci using an improved genome assembly (ARS1) of a highly homozygous San Clemente goat. This assembly has already proven useful for describing other immune system genes including antibody and leucocyte receptors. Both the TCRγ (TRG) and TCRδ (TRD) loci were similarly organized in goats as in cattle and the gene sequences were highly conserved. However, the number of genes varied slightly as a result of duplications and differences occurred in mutations resulting in pseudogenes. WC1+ γδ T cells in cattle have been shown to use TCRγ genes from only one of the six available cassettes. The structure of that Cγ gene product is unique and may be necessary to interact with WC1 for signal transduction following antigen ligation. Using RT-PCR and PacBio sequencing, we observed the same restriction for goat WC1+ γδ T cells. In contrast, caprine WC1+ and WC1− γδ T cell populations had a diverse TCRδ gene usage although the propensity for particular gene usage differed between the two cell populations. Noncanonical recombination signal sequences (RSS) largely correlated with restricted expression of TCRγ and δ genes. Finally, caprine γδ T cells were found to incorporate multiple TRD diversity gene sequences in a single transcript, an unusual feature among mammals but also previously observed in cattle.

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Acknowledgments

We would like to thank Dr. Amy Burnside, Institute of Applied Life Sciences at the University of Massachusetts Amherst, for assistance with the flow cytometry and Ms. Alice Newth, Livestock Learning Center at the University’s Hadley Farm, for being accommodating and assisting with blood collection. The USDA is an equal opportunity provider and employer. The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.

Funding

This work was funded by the US Department of Agriculture, National Institute for Food and Agriculture’s Agriculture and Food Research initiative (AFRI-NIFA-USDA) grant no. 2015-06970. DB was supported by USDA appropriated project 509031000-026-00-D. TS was supported by USDA appropriated project 3040-31000-100-00-D.

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  1. Alexandria Gillespie and Al Yirsaw are co-first authors of this paper.

Authors and Affiliations

  1. Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA

    Alexandria Gillespie, Al Yirsaw, Michael Turley, Janice C. Telfer & Cynthia L. Baldwin

  2. College of Information and Computer Sciences, University of Massachusetts, 140 Governors Drive, Amherst, MA, 01003, USA

    Karthick P. Gunasekaran

  3. United States Department of Agriculture, Agricultural Research Service, United States Meat Animal Research Center, Clay Center, NE, 68933, USA

    Timothy P. Smith

  4. United States Department of Agriculture, Agricultural Research Service, United States Dairy Forage Research Center, Madison, WI, 53706, USA

    Derek M. Bickhart

  5. Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK

    Timothy Connelley

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  1. Alexandria Gillespie
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  2. Al Yirsaw
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Contributions

AG and AY are co-first authors; they obtained and analyzed the genome annotation and gene sequence data; KG trained the computer program for genome annotation and chromosome mapping; TS and DB were involved in sequencing and assembling the caprine genome used here; MT constructed software programs to analyze the PacBio data; TC, JT, and CB conceived of the project, obtained funding, and supervised it. All authors contributed to writing the manuscript and constructing figures.

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Correspondence to Cynthia L. Baldwin.

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All work involving obtaining blood samples from cattle, goats, and sheep was approved by the University of Massachusetts’ Animal Care and Use Committee.

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Supplementary file1 (DOCX 24 KB)

251_2021_1203_MOESM2_ESM.pptx

Supplementary file2: Fig. S1 Deduced amino acid alignment of TRGC5 cassette’s genes (a) Location of the caprine and bovine TRG genes at two loci on chromosome 4 (substantial gap indicated as a double slash). The caprine TRG1 locus is inverted. Although the structures are similar between the species it is notable that there are several duplication or deletion events including the addition of the C8 cassette in the caprine TRG2 locus. (b) Deduced amino acid sequence alignment of genes in the bovine and caprine TRGC5 cassette using ClustalW. Dashes (-) are gaps introduced for maximal alignment. Dots (.) represent the same nucleotide as shown for the first sequence. A prefix of c indicates caprine while b indicates bovine sequences. Pseudogenes are indicated by φ. Fig S2 All TCR genes of caprine and bovine aligned Deduced amino acid sequence alignment using ClustalW of bovine and caprine TCR genes. (a) TRGV, (b) TRGC, and (c) TRDV. Dashes (-) are gaps introduced for preferred alignment. Dots (.) represent the same nucleotide as shown for the first sequence. Fig. S3 Phylogenetic tree of caprine and bovine TRDV genes TRDV genes were lined up with ClustalW using default parameters and displayed in a neighbor-joining phylogenetic tree. Bovine sequences follow naming conventions from previous annotations (Connelley et al 2014, Damani-Yokota et al 2018, Herzig et al 2010). Lines indicate the 11 subclades of bovine TRDV1 genes previously defined (Herzig et al 2010). A prefix of c indicates caprine while b indicates bovine sequences. (PPTX 10094 KB)

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Gillespie, A., Yirsaw, A., Gunasekaran, K.P. et al. Characterization of the domestic goat γδ T cell receptor gene loci and gene usage. Immunogenetics 73, 187–201 (2021). https://doi.org/10.1007/s00251-021-01203-y

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