Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2020 Nov 10;38(5):1715–1730. doi: 10.1093/molbev/msaa285

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

PMC Copyright notice

Fig. 4. — Gene family composition analysis. (A) Clustering of rodent genomes in a multidimensional space of molecular functions. The first two principal components are displayed, accounting for 20.14% and 11.34% of the variation, respectively. PC1 separates the capybara from the rest of the rodents based on the enrichment of gene families related to sensory perception and immune response. HYST, Hystricognathi clade; MRC, mouse-related clade; SRC, squirrel-related clade. Black portion of arrows indicates expansion of gene families within each PC. (B) Gene families related to growth control and tumor suppression that showed a significant expansion in the capybara (P-value < 0.05). The heatmap shows normalized gene counts of PANTHER molecular function categories for the 16 rodents. (C) Maximum likelihood phylogenetic tree of MAGEB5 gene family of capybara (24 MAGEB5 members) compared with rodents and rabbit, plus primate outgroups (human, gorilla, rhesus macaque, and squirrel monkey). The yellow clade contains capybara and guinea pig members, whereas the orange clade shows a monophyletic expansion of MAGEB5 genes in capybara. Bottom: Schematic representation of the organization of MAGEB5 copies throughout the capybara genome. Triangles represent position and transcriptional direction of each copy (colors match clades on phylogeny), and the “//” represent different scaffolds. Hhyd, Hydrochoerus hydrochaeris (capybara); Cpor, Cavia porcellus (guinea pig); Clan, Chinchilla lanigera (chinchilla); Odeg, Octodon degus (degu); Hgla, Heterocephalus glaber (naked mole rat); Mmus, Mus musculus (mouse); Rnor, Rattus norvegicus (rat); Mocr, Microtus ochrogaster (vole); Maur, Mesocricetus auratus (hamster); Pman, Peromyscus maniculatus (deer mouse); Ngal, Nannospalax galili (blind mole rat); Jjac, Jaculus jaculus (jerboa); Dord, Dipodomys ordii (kangaroo rat); Ccan, Castor canadensis (beaver); Itri, Ictidomys tridecemlineatus (squirrel); Mmar, Marmota marmota (marmot).