Acta Scientific Microbiology

Research Article Volume 7 Issue 2

Sequence Evolution and Copy Number Variation in HINTW

Jeet Sawant* and Bengt Hannson

Department of Biology, Lund University, Sweden

*Corresponding Author: Jeet Sawant, Department of Biology, Lund University, Sweden.

Received: December 11, 2023; Published: January 18, 2024

Abstract

The mammalian Y and avian W chromosomes share several features including being repeat rich and gene poor. However, while Y holds several multicopy ampliconic genes, only a single ampliconic gene is known on W, HINTW. HINTW has a role in avian sex determination, evolves through gene conversion, and has a homolog on Z, HINTZ. Studies in Galliformes found more HINTW copies in young than old individuals, but whether a similar aging effect occurs in other birds remains unexplored. We aligned avian HINTZ and HINTW exon-III sequences and designed primers to study the number of HINTW copies in passerines. The primers successfully amplified HINTW in DNA extracted from red blood cells of species representatives of three passerine families, and using qPCR we estimated 9-15 HINTW copies among passerines, in closely related species from superfamily Sylvioidea, which is fewer than the 18-40 copies reported for Galliformes. Finally, we uncovered a significant loss of HINTW copies in red blood cells of aging great reed warblers, and that the gene loss accelerated in birds infected with malaria parasites. A further study on migratory species infected with malaria suggests further loss of gene copies hampering the reproductive success in the great reed warbler population.

Keywords: HINTW; Ampliconic; Gene Conversion; Gene copies; qPCR; Passerines; Malaria; Great Reed Warblers

References

  1. Szathmáry E. “Toward major evolutionary transitions theory 2.0”. Proceedings of the National Academy of Sciences 33 (2015): 10104-10111.
  2. Gray J C and Goddard M R. “Gene-flow between niches facilitates local adaptation in sexual populations”. Ecology Letters9 (2012): 955-962.
  3. van der Heide E M M., et al. “Sexual dimorphism in livestock species selected for economically important traits”. Journal of Animal Science9 (2016): 3684-3692.
  4. Tran HT., et al. “An estrogen sensor for poultry sex sorting1”. Journal of Animal Science 4 (2010): 1358-1364.
  5. Olanrewaju H A., et al. “Effect of light intensity adjusted for species- specific spectral sensitivity on blood physiological variables of male broiler chickens”. Poultry Science 3 (2019): 1090-1095.
  6. Warner D A and Shine R. “The adaptive significance of temperature-dependent sex determination in a reptile”. Nature7178 (2008): 566-568.
  7. Ospina-Álvarez N and Piferrer F. “Temperature-dependent sex determination in fish revisited: Prevalence, a single sex ratio response pattern, and possible effects of climate change”. PLoS ONE7 (2008): e2837.
  8. Gilbert SF. Developmental Biology, ed. Sunderland (MA): Sinauer (2000).
  9. Ghiselin M T. “The evolution of hermaphroditism among animals”. The Quarterly Review of Biology2 (1969): 189-208.
  10. Edenbrow M and Croft D P. “Kin and familiarity influence association preferences and aggression in the mangrove killifish Kryptolebias marmoratus”. Journal of Fish Biology3 (2012): 503-518.
  11. Bachtrog D. “Y-chromosome evolution: Emerging insights into processes of Y-chromosome degeneration”. In Nature Reviews Genetics 14.2 (2013): 113-124.
  12. Charlesworth B and Leon JA. “The Relation of Reproductive Effort to Age”. The American Naturalist 973 (1976): 449-459.
  13. Warren WC., et al. “Genome analysis of the platypus reveals unique signatures of evolution”. Nature 7192 (2008): 175-183.
  14. Gruetzner F., et al. “How did the platypus get its sex chromosome chain? A comparison of meiotic multiples and sex chromosomes in plants and animals”. Chromosoma 2 (2006): 75- 88.
  15. Deakin JE., et al. “The evolution of marsupial and monotreme chromosomes”. Cytogenetic and Genome Research2-4 (2012): 113-129.
  16. Chue J and Smith CA. “Sex determination and sexual differentiation in the avian model”. In FEBS Journal7 (2011): 1027-1034.
  17. Cui Z., et al. “High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis”. Heredity3 (2015): 206-215.
  18. Jiang X H and Qiu G F. “Female-only sex-linked amplified fragment length polymorphism markers support ZW/ZZ sex determination in the giant freshwater prawn Macrobrachium rosenbergii”. Animal Genetics6 (2013): 782-785.
  19. Parnes S., et al. “Sex determination in crayfish: are intersex Cherax quadricarinatus (Decapoda, Parastacidae) genetically females?”. Genetical Research2 (2003): 107-116.
  20. Ezaz T., et al. “The ZW sex microchromosomes of an Australian dragon lizard share no homology with those of other reptiles or birds”. Chromosome Research : An International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology8 (2009): 965-973.
  21. Blackmon H., et al. “Sex Determination, Sex Chromosomes, and Karyotype Evolution in Insects”. The Journal of Heredity1 (2021): 78-93.
  22. Ellegren H. “Evolution of the avian sex chromosomes and their role in sex determination”. Trends in Ecology and Evolution5 (2017): 188-192.
  23. Skaletsky H., et al. “The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes”. Nature6942 (2003): 825-837.
  24. Estermann M A., et al. “Insights into Gonadal Sex Differentiation Provided by Single-Cell Transcriptomics in the Chicken Embryo”. Cell Reports 1 (2020): 107491.
  25. Ayers K L., et al. “The molecular genetics of avian sex determination and its manipulation”. Genesis5 (2013): 325-336.
  26. Graves J A M. “Avian sex, sex chromosomes, and dosage compensation in the age of genomics”. Chromosome Research 1 (2014): 45-57.
  27. Delbridge M L., et al. “TSPY, the candidate gonadoblastoma gene on the human Y chromosome, has a widely expressed homologue on the X-implications for Y chromosome evolution”. Chromosome Research 12 (2004): 345-356.
  28. Stiglec R., et al. “A new look at the evolution of avian sex chromosomes”. Cytogenetic and Genome Research1-4 (2007): 103-109.
  29. Ellegren H. “Sex-chromosome evolution: Recent progress and the influence of male and female heterogamety”. In Nature Reviews Genetics 12.3 (2011): 157-166.
  30. Brockdorff N and Turner BM. “Dosage compensation in mammals”. Cold Spring Harbor Perspectives in Biology3 (2015).
  31. DiNapoli L and Capel B. “SRY and the Standoff in Sex Determination”. Molecular Endocrinology 1 (2021): 1-9.
  32. Tomaszkiewicz M., et al. “Y and W Chromosome Assemblies: Approaches and Discoveries”. In Trends in Genetics 33.4 (2017): 266-282.
  33. Ioannidis J., et al. “Primary sex determination in birds depends on DMRT1 dosage, but gonadal sex does not determine adult secondary sex characteristics”. 118.10 (2021): e2020909118.
  34. Omotehara T., et al. “Spatiotemporal expression patterns of doublesex and mab-3 related transcription factor 1 in the chicken developing gonads and Müllerian ducts”. Poultry Science4 (2014): 953-958.
  35. Charlesworth B., et al. “The evolution of restricted recombination and the accumulation of repeated DNA sequences”. Genetics 4 (1986): 947-962.
  36. White M A., et al. “Purifying selection maintains dosage-sensitive genes during degeneration of the threespine stickleback Y chromosome”. Molecular Biology and Evolution8 (2015): 1981-1995.
  37. Brashear W A., et al. “Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation”. Genome Research12 (2021): 1841-1851.
  38. Sun C., et al. “Role and function of the Hintw in early sex differentiation in chicken (Gallus gallus) embryo”. Animal Biotechnology (2021): 1-11.
  39. Séraphin B. “The HIT protein family: a new family of proteins present in prokaryotes, yeast and mammals”. DNA Sequence: The Journal of DNA Sequencing and Mapping3 (1992): 177-179.
  40. Brenner C., et al. “Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins NIH Public Access Author Manuscript”. In Nat Struct Biol 4.3 (1997).
  41. Hori T., et al. “Wpkci, Encoding an Altered Form of PKCI, Is Conserved Widely on the Avian W Chromosome and Expressed in Early Female Embryos: Implication of Its Role in Female Sex Determination”. In Molecular Biology of the Cell 11.10 (2000): 3645-3660.
  42. Smith CA., et al. “DMRT1 is upregulated in the gonads during female-to-male sex reversal in ZW chicken embryos”. Biology of Reproduction2 (2003): 560-570.
  43. Rogers T F., et al. “Multi-copy gene family evolution on the avian w chromosome”. In Journal of Heredity, 112.3 (2021): 250-259.
  44. Backström N., et al. “Gene conversion drives the evolution of HINTW, an ampliconic gene on the female-specific avian W chromosome”. Molecular Biology and Evolution10 (2005): 1992-1999.
  45. McCarroll S A and Altshuler DM. “Copy-number variation and association studies of human disease”. Nature Genetics7S (2007): S37-S42.
  46. Sharp A J., et al. “Segmental Duplications and Copy- Number Variation in the Human Genome”. American Journal of Human Genetics1 (2005): 78-88.
  47. Ceplitis H and Ellegren H. “Adaptive Molecular Evolution of HINTW, a Female-Specific Gene in Birds”. Molecular Biology and Evolution2 (2004): 249-254.
  48. Brenner S E. “Errors in genome annotation”. Trends in Genetics4 (1999): 132-133.
  49. Brenner C. “Hint, Fhit and GalT: Function, Structure, Evolution and Mechanism of Three Branches of the Histidine Triad Superfamily of Nucleotide Hydrolases and Transferases”. In Biochemistry 41.29 (2002).
  50. Handley LJ L., et al. “Evolutionary Strata on the Chicken Z Chromosome: Implications for Sex Chromosome Evolution”. Genetics1 (2004): 367-376.
  51. Sánchez L and Chaouiya C. “Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads”. Journal of the Royal Society Interface142 (2018).
  52. Rogers L J., et al. “Advantages of having a lateralized brain”. Proceedings of the Royal Society B: Biological Sciences 271 (2004): S420-S422.
  53. Zhang Z., et al. “Whole-genome resequencing reveals signatures of selection and timing of duck domestication”. GigaScience4 (2018).
  54. Fregin S., et al. “New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers”. BMC Evolutionary Biology1 (2012): 1-12.
  55. Sigeman H., et al. “Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration”. Molecular Biology and Evolution12 (2021): 5275-5291.
  56. Letunic I and Bork, P. (n.d.). Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
  57. Schoch CL., et al. “NCBI Taxonomy: A comprehensive update on curation, resources and tools’. In Database (2020).
  58. Nei M and Gojobori T. “Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions”. Molecular Biology And Evolution5 (1986): 418-426.
  59. Felsenstein J. “CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP. Evolution”. International Journal of Organic Evolution4 (1985): 783-791.
  60. Tamura K., et al. “MEGA11: Molecular Evolutionary Genetics Analysis Version 11”. Molecular Biology and Evolution7 (2021): 3022-3027.
  61. Edgar R C. “MUSCLE: multiple sequence alignment with high accuracy and high throughput’. Nucleic Acids Research5 (2004): 1792-1797.
  62. Saitou N and Nei M. “The neighbor-joining method: a new method for reconstructing phylogenetic trees”. Molecular Biology and Evolution4 (1987).
  63. Smith C A., et al. “Genetic evidence against a role for W-linked histidine triad nucleotide binding protein (HINTW) in avian sex determination”. The International Journal of Developmental Biology1 (2009): 59-67.
  64. Warren W C., et al. “Genome analysis of the platypus reveals unique signatures of evolution”. Nature7192 (2008): 175-183.
  65. O’Neill M., et al. “ASW: a gene with conserved avian W-linkage and female specific expression in chick embryonic gonad”. Development Genes and Evolution5 (2000): 243-249.

Citation

Citation: Jeet Sawant and Bengt Hannson. “Sequence Evolution and Copy Number Variation in HINTW".Acta Scientific Microbiology 7.2 (2024): 54-71.

Copyright

Copyright: © 2024 Jeet Sawant and Bengt Hannson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.




Metrics

Acceptance rate30%
Acceptance to publication20-30 days

Indexed In






News and Events


Contact US