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Colugo, Galeopterus variegatus, Cynocephalus volans

ABSTRACT: Genomic analysis reveals remarkable hidden biodiversity within colugos, and the sister group to primates.

PROVIDER: PRJNA316732 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3683850_1.fastq.gz	Fastqsanger.gz
	SRR3683850_2.fastq.gz	Fastqsanger.gz
	SRR3683860_1.fastq.gz	Fastqsanger.gz
	SRR3683860_2.fastq.gz	Fastqsanger.gz
	SRR3683870_1.fastq.gz	Fastqsanger.gz

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Cynocephalus volans

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Project description:BackgroundA significant fraction of mammalian genomes is composed of endogenous retroviral (ERV) sequences that are formed by germline infiltration of various retroviruses. In contrast to other retroviral genera, lentiviruses only rarely form ERV copies. We performed a computational search aimed at identification of novel endogenous lentiviruses in vertebrate genomes.FindingsUsing the in silico strategy, we have screened 104 publicly available vertebrate genomes for the presence of endogenous lentivirus sequences. In addition to the previously described cases, the search revealed the presence of endogenous lentivirus in the genome of Malayan colugo (Galeopterus variegatus). At least three complete copies of this virus, denoted ELVgv, were detected in the colugo genome, and approximately one hundred solo LTR sequences. The assembled consensus sequence of ELVgv had typical lentivirus genome organization including three predicted accessory genes. Phylogenetic analysis placed this virus as a distinct subgroup within the lentivirus genus. The time of insertion into the dermopteran lineage was estimated to be more than thirteen million years ago.ConclusionsWe report the discovery of the first endogenous lentivirus in the mammalian order Dermoptera, which is a taxon close to the Primates. Lentiviruses have infiltrated the mammalian germline several times across millions of years. The colugo virus described here represents possibly the oldest documented endogenization event and its discovery can lead to new insights into lentivirus evolution. This is also the first report of an endogenous lentivirus in an Asian mammal, indicating a long-term presence of this retrovirus family in Asian continent.

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Cynocephalus volans isolate:mCynVol1

Project description:Cynocephalus volans (Philippine flying lemur) genome mCynVol1, primary haplotype

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Cynocephalus volans isolate:mCynVol1

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Galeopterus variegatus isolate:US047

Project description:Galeopterus variegatus isolate:US047 Genome sequencing and assembly

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A Hidden Human Proteome Encoded by the “Non-Coding” Genes

Project description:It has been a long debate whether the 98% “non-coding” fraction of human genome can encode functional proteins besides a “random noise” of translation. We used our established translatome sequencing (RNC-seq) to analyze human cells and found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes and thus might be translated into proteins (with more than 50 amino acids). These new protein-coding genes distributed universally in all human chromosomes. We then used various experimental methods including mass spectrometry, immunoblotting, subcellular localization and phenotype assessments to verify the existence of such a hidden human proteome encoded by purported lncRNAs that can express functional proteins. These new proteins deviate from the canonical proteins in various physical and chemical properties, and emerged mostly in primates during evolution. In sum, we experimentally evidenced a hidden human functional proteome encoded by purported lncRNAs, suggesting that the human genome has to be systematically re-annotated.

2022-02-25 | PXD005291 | Pride

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