Genetic Diversity of Sodefrin-Variant Pheromones and Pheromone Responsiveness in Subspecies of the Japanese Sword-Tail Newt Cynops ensicauda
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Sequence Determination of cDNA Encoding Sodefrin or Its Variant Precursors or SPF Proteins
2.3. Phylogenetic Tree Reconstruction
2.4. Test for Biological Activity of Sodefrin, Sodefrin-Variant Peptides, and Imorin
3. Results
3.1. Analysis of Transcripts Encoding Sodefrin Precursor, Sodefrin-Variant Precursor, and SPF Proteins
3.2. Phylogenetic Analysis of the Sodefrin Precursor-Related Proteins
3.3. Evaluation of the Pheromonal Activity of Sodefrin, Sodefrin Variants and Imorin
3.4. Obtaining and Organizing the Amino Acid Sequences of Known Sodefrin or Sodefrin-Variant Precursor and SPF Proteins
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Group | Abbreviated Transcript Name | Accession | mRNA Length (Base) | Number of Amino Acid Residues | Total Number of Clones | Number of Clones per Individual | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Cynops ensicauda ensicauda | C. e. popei | ||||||||||||||||||||
A | B | C | D | E | F | G | H | A | B | C | D | E | F | G | H | ||||||
Sodefrin and Sodefrin-variant Precursor (S-SVP) | S-SVP subgroup | 316–625 | 102–205 | 55 | 6 | 6 | 5 | 5 | 6 | 5 | 4 | 4 | 4 | 2 | 1 | 1 | 3 | 1 | 1 | 1 | |
Sodefrin precursor | 577 | 189 | 11 | 6 | 3 | 1 | 1 | ||||||||||||||
Cee-sodefrin01-1 | LC861879 | 577 | 189 | 3 | 3 | ||||||||||||||||
Cee-sodefrin01-2 | LC861880 | 577 | 189 | 1 | 1 | ||||||||||||||||
Cee-sodefrin02-1 | LC861881 | 577 | 189 | 1 | 1 | ||||||||||||||||
Cee-sodefrin03-1 | LC861882 | 577 | 189 | 1 | 1 | ||||||||||||||||
Cee-sodefrin03-2 | LC861883 | 577 | 189 | 1 | 1 | ||||||||||||||||
Cee-sodefrin04-1 | LC861884 | 577 | 189 | 2 | 2 | ||||||||||||||||
Cee-sodefrin04-2 | LC861885 | 577 | 189 | 1 | 1 | ||||||||||||||||
Cee-sodefrin05-1 | LC861886 | 577 | 189 | 1 | 1 | ||||||||||||||||
[Gln8]sodefrin precursor | 316–625 | 102–205 | 36 | 3 | 4 | 4 | 6 | 5 | 4 | 4 | 3 | 1 | 1 | 1 | |||||||
Cee-[Gln8]sodefrin01-1 | LC861867 | 586 | 192 | 10 | 3 | 2 | 4 | 1 | |||||||||||||
Cee-[Gln8]sodefrin01-2 | LC861868 | 586 | 192 | 2 | 2 | ||||||||||||||||
Cee-[Gln8]sodefrin02-1 | LC861869 | 586 | 192 | 2 | 2 | ||||||||||||||||
Cee-[Gln8]sodefrin02-2 | LC861870 | 586 | 192 | 1 | 1 | ||||||||||||||||
Cee-[Gln8]sodefrin03-1 | LC861871 | 586 | 192 | 5 | 1 | 4 | |||||||||||||||
Cee-[Gln8]sodefrin04-1 | LC861872 | 316 | 102 | 1 | 1 | ||||||||||||||||
Cee-[Gln8]sodefrin05-1 | LC861873 | 586 | 192 | 1 | 1 | ||||||||||||||||
Cee-[Gln8]sodefrin05-2 | LC861874 | 586 | 192 | 1 | 1 | ||||||||||||||||
Cee-[Gln8]sodefrin06-1 | LC861875 | 586 | 192 | 3 | 2 | 1 | |||||||||||||||
Cee-[Gln8]sodefrin06-2 | LC861876 | 586 | 192 | 2 | 2 | ||||||||||||||||
Cee-[Gln8]sodefrin07-1 | LC861877 | 586 | 192 | 1 | 1 | ||||||||||||||||
Cee-[Gln8]sodefrin08-1 | LC861878 | 577 | 189 | 1 | 1 | 3 | 1 | 1 | |||||||||||||
Cep-[Gln8]sodefrin01-1 | LC861897 | 586 | 192 | 5 | |||||||||||||||||
Cep-[Gln8]sodefrin02-1 | LC861898 | 625 | 205 | 1 | 1 | ||||||||||||||||
Silefrin precursor | 529–586 | 173–192 | 8 | 4 | 2 | 1 | 1 | ||||||||||||||
Cep-silefrin01-1 | LC861899 | 586 | 192 | 4 | 4 | ||||||||||||||||
Cep-silefrin02-1 | LC861900 | 586 | 192 | 1 | 1 | ||||||||||||||||
Cep-silefrin03-1 | LC861901 | 586 | 192 | 1 | 1 | ||||||||||||||||
Cep-silefrin04-1 | LC861902 | 529 | 192 | 1 | 1 | ||||||||||||||||
Cep-silefrin05-1 | LC861903 | 586 | 173 | 1 | 1 | ||||||||||||||||
Sodefrin precursor-like factor (SPF) | SPF-ß subgroup | 374–539 | 124–179 | 73 | 2 | 2 | 3 | 3 | 2 | 3 | 4 | 4 | 4 | 6 | 7 | 7 | 5 | 7 | 7 | 7 | |
Cee-SPF-ß01-1 | LC861887 | 506 | 168 | 6 | 3 | 3 | |||||||||||||||
Cee-SPF-ß02-1 | LC861888 | 491 | 163 | 1 | 1 | ||||||||||||||||
Cee-SPF-ß03-1 | LC861889 | 506 | 168 | 4 | |||||||||||||||||
Cee-SPF-ß04-1 | LC861890 | 491 | 163 | 1 | 1 | 3 | |||||||||||||||
Cee-SPF-ß05-1 | LC861891 | 506 | 168 | 1 | 1 | 1 | |||||||||||||||
Cee-SPF-ß06-1 | LC861892 | 506 | 168 | 4 | 1 | 3 | |||||||||||||||
Cee-SPF-ß07-1 | LC861893 | 506 | 168 | 3 | 1 | 2 | |||||||||||||||
Cee-SPF-ß08-1 | LC861894 | 506 | 168 | 1 | 1 | ||||||||||||||||
Cee-SPF-ß09-1 | LC861895 | 506 | 168 | 1 | 1 | ||||||||||||||||
Cee-SPF-ß10-1 | LC861896 | 539 | 179 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß01-1 | LC861904 | 506 | 168 | 27 | 3 | 1 | 5 | 6 | 4 | 3 | 5 | ||||||||||
Cep-SPF-ß02-1 | LC861905 | 389 | 129 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß03-1 | LC861906 | 506 | 168 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß04-1 | LC861907 | 506 | 168 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß05-1 | LC861908 | 506 | 168 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß06-1 | LC861909 | 506 | 168 | 2 | 2 | ||||||||||||||||
Cep-SPF-ß07-1 | LC861910 | 506 | 168 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß08-1 | LC861911 | 389 | 129 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß09-1 | LC861912 | 539 | 179 | 6 | 3 | 1 | 2 | ||||||||||||||
Cep-SPF-ß09-2 | LC861913 | 539 | 179 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß09-3 | LC861914 | 539 | 179 | 1 | 1 | ||||||||||||||||
Cep-SPF-ß10-1 | LC861915 | 539 | 179 | 4 | 1 | 1 | 1 | 1 | |||||||||||||
Cep-SPF-ß10-2 | LC861916 | 539 | 179 | 3 | 3 |
Group | Abbreviated Transcript Name | Accession | mRNA Length (Base) | Number of Amino Acid Residues | Total Number of Clones | Number of Clones per Individual | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Cynops pyrrhogaster | |||||||||||||
A | B | C | D | E | F | G | H | ||||||
Sodefrin and Sodefrin-variant Precursor (S-SVP) | S-SVP subgroup | 460–577 | 150–189 | 52 | 4 | 8 | 5 | 7 | 8 | 7 | 7 | 6 | |
Sodefrin precursor | 460–577 | 150–189 | 28 | 4 | 5 | 1 | 3 | 5 | 3 | 4 | 3 | ||
Cp-sodefrin01-1 | LC861931 | 577 | 189 | 6 | 1 | 3 | 1 | 1 | |||||
Cp-sodefrin01-2 | LC861932 | 577 | 189 | 1 | 1 | ||||||||
Cp-sodefrin02-1 | LC861933 | 577 | 189 | 1 | 1 | ||||||||
Cp-sodefrin03-1 | LC861934 | 460 | 150 | 1 | 1 | ||||||||
Cp-sodefrin04-1 | LC861935 | 577 | 189 | 1 | 1 | ||||||||
Cp-sodefrin05-1 | LC861936 | 577 | 189 | 1 | 1 | ||||||||
Cp-sodefrin06-1 | LC861937 | 529 | 173 | 1 | 1 | ||||||||
Cp-sodefrin07-1 | LC861938 | 529 | 173 | 1 | 1 | ||||||||
Cp-sodefrin08-1 | LC861939 | 577 | 189 | 1 | 1 | ||||||||
Cp-sodefrin09-1 | LC861940 | 577 | 189 | 1 | 1 | ||||||||
Cp-sodefrin10-1 | LC861941 | 529 | 173 | 4 | 2 | 2 | |||||||
Cp-sodefrin10-2 | LC861942 | 529 | 173 | 2 | 1 | 1 | |||||||
Cp-sodefrin11-1 | LC861943 | 514 | 168 | 1 | 1 | ||||||||
Cp-sodefrin12-1 | LC861944 | 577 | 189 | 1 | 1 | ||||||||
Cp-sodefrin13-1 | LC861945 | 529 | 173 | 1 | 1 | ||||||||
Cp-sodefrin14-1 | LC861946 | 529 | 173 | 1 | 1 | ||||||||
Cp-sodefrin15-1 | LC861947 | 553 | 181 | 1 | 1 | ||||||||
Cp-sodefrin16-1 | LC861948 | 529 | 173 | 1 | 1 | ||||||||
Cp-sodefrin17-1 | LC861949 | 529 | 173 | 1 | 1 | ||||||||
[Asn10]sodefrin precursor | 577 | 189 | 24 | 3 | 4 | 4 | 3 | 4 | 3 | 3 | |||
Cp-[Asn10]sodefrin01-1 | LC861917 | 577 | 189 | 5 | 3 | 1 | 1 | ||||||
Cp-[Asn10]sodefrin01-2 | LC861918 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin02-1 | LC861919 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin03-1 | LC861920 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin04-1 | LC861921 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin05-1 | LC861922 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin05-2 | LC861923 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin06-1 | LC861924 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin07-1 | LC861925 | 577 | 189 | 4 | 2 | 2 | |||||||
Cp-[Asn10]sodefrin08-1 | LC861926 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin09-1 | LC861927 | 577 | 189 | 3 | 1 | 2 | |||||||
Cp-[Asn10]sodefrin09-2 | LC861928 | 577 | 189 | 2 | 2 | ||||||||
Cp-[Asn10]sodefrin10-1 | LC861929 | 577 | 189 | 1 | 1 | ||||||||
Cp-[Asn10]sodefrin11-1 | LC861930 | 577 | 189 | 1 | 1 | ||||||||
Sodefrin precursor-like factor (SPF) | SPF-ß subgroup | 422–539 | 140–179 | 12 | 4 | 3 | 1 | 1 | 1 | 2 | |||
Cp-SPF-ß01-1 | LC861950 | 539 | 179 | 2 | 1 | 1 | |||||||
Cp-SPF-ß02-1 | LC861951 | 539 | 179 | 1 | 1 | ||||||||
Cp-SPF-ß03-1 | LC861952 | 539 | 179 | 1 | 1 | ||||||||
Cp-SPF-ß04-1 | LC861953 | 539 | 179 | 1 | 1 | ||||||||
Cp-SPF-ß05-1 | LC861954 | 422 | 140 | 1 | 1 | ||||||||
Cp-SPF-ß06-1 | LC861955 | 539 | 179 | 1 | 1 | ||||||||
Cp-SPF-ß07-1 | LC861956 | 506 | 168 | 1 | 1 | ||||||||
Cp-SPF-ß08-1 | LC861957 | 506 | 168 | 1 | 1 | ||||||||
Cp-SPF-ß09-1 | LC861958 | 506 | 168 | 1 | 1 | ||||||||
Cp-SPF-ß10-1 | LC861959 | 506 | 168 | 1 | 1 | ||||||||
Cp-SPF-ß11-1 | LC861960 | 506 | 168 | 1 | 1 |
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Sodefrin or Sodefrin Variant Sequences to Be Contained | Amino Acid Sequences of Sodefrin or Sodefrin Variants | Number of Amino Acid Residues | Number of Isoforms | Total Number of Clones | Number of Clones per Individual ** | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A | B | C | D | E | F | G | H | ||||||
Cynops ensicauda ensicauda | Presence | SIPSKDALLK (sodefrin) | 189 | 5 | 11 | 6 | 3 | 1 | 1 | ||||
SIPSKDAQLK ([Gln8]sodefrin) | 102–192 | 8 | 30 | 3 | 4 | 4 | 6 | 5 | 4 | 4 | |||
Absence * | 163–179 | 10 | 23 | 2 | 2 | 3 | 3 | 2 | 3 | 4 | 4 | ||
Cynops ensicauda popei | Presence | SIPSKDAQLK ([Gln8]sodefrin) | 192–205 | 2 | 6 | 3 | 1 | 1 | 1 | ||||
SILSKDAQLK (silefrin) | 173–192 | 5 | 8 | 4 | 2 | 1 | 1 | ||||||
Absence | 129–179 | 10 | 50 | 4 | 6 | 7 | 7 | 5 | 7 | 7 | 7 | ||
Cynops pyrrhogaster | Presence | SIPSKDALLK (sodefrin) | 150–189 | 17 | 28 | 4 | 5 | 1 | 3 | 5 | 3 | 4 | 3 |
SIPSKDALLN ([Asn10]sodefrin) | 173–189 | 11 | 24 | 3 | 4 | 4 | 3 | 4 | 3 | 3 | |||
Absence | 140–179 | 11 | 12 | 4 | 3 | 1 | 1 | 1 | 2 |
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Nakada, T.; Toyoda, F.; Tominaga, A.; Mochida, K.; Yokosuka, M.; Kikuyama, S. Genetic Diversity of Sodefrin-Variant Pheromones and Pheromone Responsiveness in Subspecies of the Japanese Sword-Tail Newt Cynops ensicauda. Animals 2025, 15, 947. https://doi.org/10.3390/ani15070947
Nakada T, Toyoda F, Tominaga A, Mochida K, Yokosuka M, Kikuyama S. Genetic Diversity of Sodefrin-Variant Pheromones and Pheromone Responsiveness in Subspecies of the Japanese Sword-Tail Newt Cynops ensicauda. Animals. 2025; 15(7):947. https://doi.org/10.3390/ani15070947
Chicago/Turabian StyleNakada, Tomoaki, Fumiyo Toyoda, Atsushi Tominaga, Koji Mochida, Makoto Yokosuka, and Sakae Kikuyama. 2025. "Genetic Diversity of Sodefrin-Variant Pheromones and Pheromone Responsiveness in Subspecies of the Japanese Sword-Tail Newt Cynops ensicauda" Animals 15, no. 7: 947. https://doi.org/10.3390/ani15070947
APA StyleNakada, T., Toyoda, F., Tominaga, A., Mochida, K., Yokosuka, M., & Kikuyama, S. (2025). Genetic Diversity of Sodefrin-Variant Pheromones and Pheromone Responsiveness in Subspecies of the Japanese Sword-Tail Newt Cynops ensicauda. Animals, 15(7), 947. https://doi.org/10.3390/ani15070947