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Sunday, April 03, 2022

A complete human genome sequence (2022)

The first complete human genome sequence has finally been published.

This is my first post on the complete telomere-to-telomere sequence of the human genome in cell line CHM13 (T2T-CHM13). There were six papers in the April 1st edition of Science. My posts on all six papers are listed at the bottom of this post.

There's a lot of detail in this paper but the bottom line isn't much different from what the preprint said last May (2021) [see Telomere-to-telomere sequencing of a complete human genome]. The authors now report that they discovered 1,956 new genes: 99 protein-coding genes and 1,857 noncoding genes. This brings the total number of protein-coding genes to 19,969. Nurk et al. claim that there are 43,525 noncoding genes. Call me skeptical.

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A.V., Mikheenko, A., Vollger, M.R., Altemose, N., Uralsky, L. and Gershman, A. et al. (2021) The complete sequence of a human genome. Science 376:44-53. [doi: 10.1126/science.abj6987]

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Much of the newly sequenced regions corresponds to the functional part of the genome: centromeres, telomeres, and ribosomal RNA genes. It doesn't change the conclusion that 90% of our genome is junk. The paper doesn't mention the controversy over function vs junk and that's in line with the standard adopted in 2014 where these workers avoid any direct mention of the controversy.

Warning: Science has come up with some strange PDF viewing program that takes forever to load and doesn't allow you to print the entire document at once. Printing is very slow on my printer. You can't save the PDF and view it in your own viewer even if you have a subscription to the magazine.

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