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. 2016 May;26(5):649-59.
doi: 10.1101/gr.199075.115. Epub 2016 Feb 25.

Discovery of a New Repeat Family in the Callithrix Jacchus Genome

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Free PMC article

Discovery of a New Repeat Family in the Callithrix Jacchus Genome

Miriam K Konkel et al. Genome Res. .
Free PMC article

Abstract

We identified a novel repeat family, termed Platy-1, in the Callithrix jacchus (common marmoset) genome that arose around the time of the divergence of platyrrhines and catarrhines and established itself as a repeat family in New World monkeys (NWMs). A full-length Platy-1 element is ∼100 bp in length, making it the shortest known short interspersed element (SINE) in primates, and harbors features characteristic of non-LTR retrotransposons. We identified 2268 full-length Platy-1 elements across 62 subfamilies in the common marmoset genome. Our subfamily reconstruction and phylogenetic analyses support Platy-1 propagation throughout the evolution of NWMs in the lineage leading to C. jacchus Platy-1 appears to have reached its amplification peak in the common ancestor of current day marmosets and has since moderately declined. However, identification of more than 200 Platy-1 elements identical to their respective consensus sequence, and the presence of polymorphic elements within common marmoset populations, suggests ongoing retrotransposition activity. Platy-1, a SINE, appears to have originated from an Alu element, and hence is likely derived from 7SL RNA. Our analyses illustrate the birth of a new repeat family and its propagation dynamics in the lineage leading to the common marmoset over the last 40 million years.

Figures

Figure 1.
Figure 1.
Platy-1 characteristics. (A) The structure of Platy-1 (turquoise). The element terminates in an A-tail (light turquoise) and is flanked by TSDs (purple). Flanking sequence is shown in dark gray. (B) The TSD distribution length across 424 elements. (C) The A-tail length distribution of all 424 Platy-1 elements as well as the length distribution of pristine A-tails. (D) The endonuclease cleavage site across all elements with TSDs is illustrated as a Weblogo (Crooks et al. 2004).
Figure 2.
Figure 2.
Platy-1 evolution in NWMs. The histogram shows the Platy-1 distribution based on the divergence from the consensus sequence of all 2268 full-length sequences. The subfamilies are color-coded based on subfamily affiliation and grouped together based on age. The divergence from the respective consensus sequence was retrieved from RepeatMasker and is shown on the x-axis. The y-axis shows the number of elements with the indicated divergence. The plot is generated with custom BioPython scripts and the Vega + D3 Vincent wrapper/package (Bostock et al. 2011) (http://github.com/wrobstory/vincent).
Figure 3.
Figure 3.
Platy-1 subfamily tree reconstruction. A neighbor-joining tree for all 62 Platy-1 subfamilies is shown. The excerpt (bottom left) shows a network analysis for younger subfamilies. The nodes for each subfamily represent the approximate size of each subfamily based on the number of full-length Platy-1 elements.
Figure 4.
Figure 4.
Platy-1 genomic distribution. The expected (yellow) and actual (purple) Platy-1 distributions across all chromosomes (excluding Chr Random and Chr Y) are illustrated. In addition, the density per megabase is shown for each chromosome. Due to omission of putative Platy-1 loci on Chr Random, 2221 full-length elements were included in this analysis.
Figure 5.
Figure 5.
Alignment of Platy-1 with 7SL RNA and Alu elements. Shown is a multiple sequence alignment using MUSCLE (Edgar 2004) followed by manual curation of the oldest Platy-1 subfamilies with 7SL RNA, a selection of Alu consensus sequences, and FLAM. The alignment is visualized with AliView (Larsson 2014). Dashes indicate absence of the sequence. Also illustrated are the A box (consensus sequence: TRGYnnAnnnG) and B box (consensus sequence: GWTCRAnnCc). The tail of the Platy-1 sequence aligned equally well to the regions prior to the middle A-rich region and the 3′ end of an Alu element. In the latter case, the deletion may have been caused by recombination between homologous sequences. This alignment assumes that the element terminates at the middle A-rich region. An alternate alignment is provided in Supplemental Figure S4.
Figure 6.
Figure 6.
Phylogenetic distribution of Platy-1. (A) Four agarose gel chromatographs of our locus-specific phylogenetic analyses. An upper fragment indicates presence of a Platy-1 insertion; a lower fragment, absence. The vertical lines from left to right separate the outgroups from NWMs, Atelidae from Cebidae, and Cebidae from Pitheciidae. The gel chromatographs show (from left to right): (A) 100 bp ladder; (B) TLE; (C) human; (D) common chimpanzee; (E) African green monkey; (F) woolly monkey; (G) spider monkey; (H) red howler monkey; (I) common marmoset; (J) pygmy marmoset; (K) tamarin; (L) capuchin monkey; (M) squirrel monkey; (N) owl monkey; (O) titi; (P) saki. (For more detailed information regarding the species used, please see Supplemental Table S1A.) The top gel image shows a Platy-1 insertion shared across all NWMs. The gel chromatograph below shows an insertion specific to Callithrichinae, which is followed by a marmoset-specific insertion. The gel chromatograph on the bottom shows a common marmoset-specific Platy-1 insertion. (B) The phylogenetic results for our informative loci are shown in a pie chart: (Marm) marmosets; (cM) common marmoset; (fp) false positive; (NWM) New World monkey; (Call) Callithrichinae; (Ceb) Cebidae.

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