Gene expression, chromosome heterogeneity and the fast-X effect in mammals
Linh-Phuong Nguyen, Nicolas Galtier, Benoit Nabholz
Biol Lett 2015 Feb;11(2):20150010. doi: 10.1098/rsbl.2015.0010
| Attribute | Value |
|---|---|
| Number of MSA | 4981 |
| MSA Format | FASTA |
| Stored as | .gz one file per alignment |
| Aligners used | Sourced from a database of MSAs |
| Filtering strategy | OrthoMAM v6, GBlocks |
| Tree | Yes, single species tree (tree.nwk) |
| Sequences/MSA | 6 [5:6] |
| Codons/MSA | 511 [154:1898] |
| Tree length/MSA | 0.21 [0.09:0.50] |
| Gaps/codon column | 0.34 [0.0:1.17] |
| Gaps/1000 codons sequence | 58.1 [0.0:203.0] |
| Taxonomic range | Mammals |
| Selection analyses run | Counting-based lineage dN/dS estimation |
The higher rate of non-synonymous over synonymous substitutions (dN/dS) of the X chromosome compared with autosomes is often interpreted as a consequence of X hemizygosity. However, other factors, such as gene expression, are also known to vary between X and autosomes. Analysing 4800 orthologues in six mammals, we found that gene expression levels, associated with GC content, fully account for the variation in dN/dS between X and autosomes with no detectable effect of hemizygosity. We also report an extensive variance in dN/dS and gene expression between autosomes.