Multiple FGF4 Retrocopies Recently Derived within Canids

Two transcribed retrocopies of the fibroblast growth factor 4 (FGF4) gene have previously been described in the domestic dog. An FGF4 retrocopy on chr18 is associated with disproportionate dwarfism, while an FGF4 retrocopy on chr12 is associated with both disproportionate dwarfism and intervertebral disc disease (IVDD). In this study, whole-genome sequencing data were queried to identify other FGF4 retrocopies that could be contributing to phenotypic diversity in canids. Additionally, dogs with surgically confirmed IVDD were assayed for novel FGF4 retrocopies. Five additional and distinct FGF4 retrocopies were identified in canids including a copy unique to red wolves (Canis rufus). The FGF4 retrocopies identified in domestic dogs were identical to domestic dog FGF4 haplotypes, which are distinct from modern wolf FGF4 haplotypes, indicating that these retrotransposition events likely occurred after domestication. The identification of multiple, full length FGF4 retrocopies with open reading frames in canids indicates that gene retrotransposition events occur much more frequently than previously thought and provide a mechanism for continued genetic and phenotypic diversity in canids.

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Darwin’s Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds

Genome Biology and Evolution ◽

10.1093/gbe/evaa027 ◽

2020 ◽

Vol 12 (3) ◽

pp. 136-150

Author(s):

George Pacheco ◽

Hein van Grouw ◽

Michael D Shapiro ◽

Marcus Thomas P Gilbert ◽

Filipe Garrett Vieira

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phenotypic Diversity ◽

Genotyping By Sequencing ◽

Columba Livia ◽

Whole Genome Sequencing Data ◽

Evolutionary Relationships ◽

Whole Genome ◽

Sequencing Data ◽

Domestic Species

Abstract Through its long history of artificial selection, the rock pigeon (Columba livia Gmelin 1789) was forged into a large number of domestic breeds. The incredible amount of phenotypic diversity exhibited in these breeds has long held the fascination of scholars, particularly those interested in biological inheritance and evolution. However, exploiting them as a model system is challenging, as unlike with many other domestic species, few reliable records exist about the origins of, and relationships between, each of the breeds. Therefore, in order to broaden our understanding of the complex evolutionary relationships among pigeon breeds, we generated genome-wide data by performing the genotyping-by-sequencing (GBS) method on close to 200 domestic individuals representing over 60 breeds. We analyzed these GBS data alongside previously published whole-genome sequencing data, and this combined analysis allowed us to conduct the most extensive phylogenetic analysis of the group, including two feral pigeons and one outgroup. We improve previous phylogenies, find considerable population structure across the different breeds, and identify unreported interbreed admixture events. Despite the reduced number of loci relative to whole-genome sequencing, we demonstrate that GBS data provide sufficient analytical power to investigate intertwined evolutionary relationships, such as those that are characteristic of animal domestic breeds. Thus, we argue that future studies should consider sequencing methods akin to the GBS approach as an optimal cost-effective approach for addressing complex phylogenies.

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Systematic analysis of the PTEN 5′ leader identifies a major AUU initiated proteoform

Open Biology ◽

10.1098/rsob.150203 ◽

2016 ◽

Vol 6 (5) ◽

pp. 150203 ◽

Cited By ~ 20

Author(s):

Ioanna Tzani ◽

Ivaylo P. Ivanov ◽

Dmitri E. Andreev ◽

Ruslan I. Dmitriev ◽

Kellie A. Dean ◽

...

Keyword(s):

Pi3k Pathway ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Sequencing Data ◽

Human Tumour ◽

Systematic Analysis ◽

Human Genes ◽

Abundant Evidence ◽

Upstream Open Reading Frames ◽

Reading Frames

Abundant evidence for translation within the 5′ leaders of many human genes is rapidly emerging, especially, because of the advent of ribosome profiling. In most cases, it is believed that the act of translation rather than the encoded peptide is important. However, the wealth of available sequencing data in recent years allows phylogenetic detection of sequences within 5′ leaders that have emerged under coding constraint and therefore allow for the prediction of functional 5′ leader translation. Using this approach, we previously predicted a CUG-initiated, 173 amino acid N-terminal extension to the human tumour suppressor PTEN. Here, a systematic experimental analysis of translation events in the PTEN 5′ leader identifies at least two additional non-AUG-initiated PTEN proteoforms that are expressed in most human cell lines tested. The most abundant extended PTEN proteoform initiates at a conserved AUU codon and extends the canonical AUG-initiated PTEN by 146 amino acids. All N-terminally extended PTEN proteoforms tested retain the ability to downregulate the PI3K pathway. We also provide evidence for the translation of two conserved AUG-initiated upstream open reading frames within the PTEN 5′ leader that control the ratio of PTEN proteoforms.

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Pan-cancer proteogenomic analysis reveals long and circular noncoding RNAs encoding peptides

NAR Cancer ◽

10.1093/narcan/zcaa015 ◽

2020 ◽

Vol 2 (3) ◽

Author(s):

Ghofran Othoum ◽

Emily Coonrod ◽

Sidi Zhao ◽

Ha X Dang ◽

Christopher A Maher

Keyword(s):

Noncoding Rnas ◽

Open Reading Frames ◽

Circular Rnas ◽

Sequencing Data ◽

Transcriptomic Sequencing ◽

Cancer Types ◽

Functional Peptides ◽

Pan Cancer ◽

Coding Potential ◽

Reading Frames

Abstract Recent studies show that annotated long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) encode for stable, functional peptides that contribute to human development and disease. To systematically discover lncRNAs and circRNAs encoding peptides, we performed a comprehensive integrative analysis of mass spectrometry-based proteomic and transcriptomic sequencing data from >900 patients across nine cancer types. This enabled us to identify 19,871 novel peptides derived from 8,903 lncRNAs. Further, we exploited open reading frames overlapping the backspliced region of circRNAs to identify 3,238 peptides that are uniquely derived from 2,834 circRNAs and not their corresponding linear RNAs. Collectively, our pan-cancer proteogenomic analysis will serve as a resource for evaluating the coding potential of lncRNAs and circRNAs that could aid future mechanistic studies exploring their function in cancer.

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