The Human Y Chromosome: Small, Strange, and Possibly Disappearing

The research paper, published in Nature on 2023-08-23, is “The complete sequence of a human Y chromosome”. Here is the abstract:

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY , DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

The full text of the paper is behind Nature’s Teutonic paywall, but a preprint is available on bioRχiv, with full text [PDF].

It is remarkable that, twenty years after the Human Genome Project was “declared complete” in April 2003, the recalcitrant Y chromosome has now been reliably sequenced. But then, the Y chromosome has long been known as the locus for all kinds of trouble making.



I definitely like the’Y chromosome map’ with its captions. True science! Settled!


I was fascinated by the spiny rats and the duck billed platypus. These species’ reproduction isn’t by parthenogenesis. Also they arent like creatures which are hermaphroditic, but still require another creature to mate with. The species HAS two genders, with sexual dimorphism and differentiation, BUT it’s due to factors other than their chromosomal makeup? Like what? Hormone washing in the womb?
(I feel I didnt need to know this, at the present stage of our cultural agon, but…in all knowledge there is comfort, they say, so thanks for posting this,)


There are a variety of ways various species perform sex differentiation. Reptiles and some (teleost) fish, for example, have temperature-dependent sex determination in which the temperature at which the embryo incubates causes expression of different genes that start the cascade determining sex. Other species have different forms of environmental sex determination, which may be triggered by length of daylight, location where larvæ land, and pheromones released by other individuals of the species.

It doesn’t seem to be understood exactly how the Amami rats do it; here is an article that suggests it may have something to do with zinc finger transcripts that control gene expression during development.

Life finds a way.