Sex chromosome systems in Neotropical Primates: What have we learnt so far from cytogenetics and genomics?

Neotropical Primates (Platyrrhini) show great diversity in their life histories, ecology, behaviour and genetics. This diversity extends to their chromosome complements, both to autosomes and to sex chromosomes. In this contribution, we will review what is currently known about sex chromosomes in this group, both from cytogenetic and from genomic evidence. The X and Y chromosomes in Neotropical Primates, also known as New World Monkeys, have striking structural differences compared with Old World Monkeys when Catarrhini sex chromosomes are considered. The XY bivalent displays a different meiotic behaviour in prophase I, and their Y chromosome shows extensive genomic differences. Even though the most widespread sex chromosome system is the XX/XY and thus considered the ancestral one for Platyrrhini, modifications of this sexual system are observed within this group. Multiple sex chromosome systems originated from Y-autosome translocations were described in several genera (Aotus, Callimico and Alouatta). In the howler monkeys, genus Alouatta, an independent origin of the sexual systems in South American and Mesoamerican species was postulated. All the above-mentioned evidence suggests that the Y chromosome of Platyrrhini has a different evolutionary history compared with the Catarrhini Y. There is still much to understand regarding their sex chromosome systems.

A Genome-Wide Landscape of Retrocopies in Primate Genomes.

Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes.

Evolution of TRIM5alpha B30.2 (SPRY) domain in New World primates.

The tripartite motif 5 protein (TRIM5) has been extensively studied in view of its ability to restrict retroviruses in mammalian hosts. The B30.2 domain, encoded by exon 8 of TRIM5, contains the major restriction determinants. We have analyzed the genetic diversity of the TRIM5 B30.2 domain in a wide range of New World primates (NWP). The TRIM5 region encoding the B30.2 domain of 35 animals, representing all NWP families and 10 genera, was PCR-amplified, sequenced and analyzed at the amino acid level. Comparisons were carried out with available GenBank data; analyses were carried out with a dataset of 44 representative sequences of 32 NWP species and 15 genera, with a human B30.2 sequence as outgroup. A high genetic diversity was observed, both with respect to length and amino acid substitutions, mainly at the three variable regions of this domain associated with the restriction phenotype. Phylogenetic reconstructions based on B30.2 DNA differed from the consensus NWP topology due to positive selection along different lineages and definite codon positions, with robust evidence either with a complete or a pruned dataset. This was especially evident in codons 406 and 496, consistently demonstrated with all methods. Positive selection was virtually absent in all NWP species when analyzing intra-specific polymorphisms except for Saguinus labiatus. Our findings indicated that NWP TRIM5 proteins have been subjected to selection, probably by retroviruses and/or retroelements. We anticipate that the diversity of NWP TRIM5 is indicative of disparate retroviral restriction phenotypes representing a plentiful source of factors countering HIV infection.