Biology subjects

Zhang, Y.-P.

Publications and source records attributed to Zhang, Y.-P..

5 recordsLinked to original sources

bioRxiv2018

Canine transmissible venereal tumor genome reveals ancient introgression from coyotes to arctic sled dogs

Dear Editor,\n\nAncient genome-sequencing studies have extensively refined our understanding of the genetic histories and adaptive evolution of humans1, as well as the domestic process of livestock and crops2. Recent studies about ancient and modern canids all indicate that canids have intricate histories, and lots of canine populations disappeared during evolution3-6. Thus, ancient genomes from canine fossils are in high demand to clarify canine evolution and the processes leading to dog domestication. Canine transmissible venereal tumor (CTVT), the oldest known somatic cell line, is a living fossil, originating from cancer cells transmitted from a host to other canids during the mating process7. Clonal origin analyses hints that the original dog infected with CTVT (CTVT founder) came from an ancient sled dog or wolf population ...

evolutionary biology↗

bioRxiv2018

Insulin Signaling-independent Activation of DAF-16 Shapes the Transcriptome during Normal Aging

The roles and regulatory mechanisms of transriptome changes during aging are unclear. It has been proposed that the transcriptome suffers decay during aging owing to age-associated down-regulation of transcription factors. In this study, we characterized the role of a transcription factor DAF-16, which is a highly conserved lifespan regulator, in the normal aging process of Caenorhabditis elegans. We found that DAF-16 translocates into the nucleus in aged wild-type worms and activates the expression of hundreds of genes in response to age-associated cellular stress. Most of the age-dependent DAF-16 targets are different from the canonical DAF-16 targets downstream of insulin signaling, indicating that activation of DAF-16 during aging is not due to reduced insulin signaling from DAF-2. Further analysis showed that it is due to the loss of proteostasis during aging, at least in part. We also found that without daf-16, dramatic gene expression changes occur as early as on adult day 2, indicating that DAF-16 acts to stabilize the transcriptome during normal aging. Our results thus reveal that normal aging is not simply a process in which the gene expression program descends into chaos due to loss of regulatory activities; rather, there is active transcriptional regulation that fights aging.

systems biology↗

bioRxiv2017

Allopatric divergence, local adaptation, and multiple Quaternary refugia in a long-lived tree (Quercus spinosa) from subtropical China

O_LIThe complex geography and climatic changes occurring in subtropical China during the Tertiary and Quaternary might have provided substantial opportunities for allopatric speciation. To gain further insight into these processes, we reconstruct the evolutionary history of Quercus spinosa, a common evergreen tree species mainly distributed in this area.\nC_LIO_LIForty-six populations were genotyped using four chloroplast DNA regions and 12 nuclear microsatellite loci to assess genetic structure and diversity, which was supplemented by divergence time and diversification rate analyses, environmental factor analysis, and ecological niche modeling of the species distributions in the past and at present.\nC_LIO_LIThe genetic data consistently identified two lineages: the western Eastern Himalaya-Hengduan Mountains lineage and the eastern Central-Eastern China lineage, mostly maintained by populations environmental adaptation. These lineages diverged through climate/orogeny-induced vicariance during the Neogene and remained separated thereafter. Genetic data strongly supported the multiple refugia (per se, interglacial refugia) or refugia within refugia hypotheses to explain Q. spinosa phylogeography in subtropical China.\nC_LIO_LIQ. spinosa population structure highlighted the importance of complex geography and climatic changes occurring in subtropical China during the Neogene in providing substantial opportunities for allopatric divergence.\nC_LI

evolutionary biology↗

bioRxiv2016

Evolutionary history of the brown rat: out of southern East Asia and selection

The brown rat (Rattus norvegicus) is found wherever humans live and transmits many diseases, and its breeding produced the laboratory rat used widely in medical research. Here, we sequenced whole genomes from 118 rats to explore the origin and dispersal routes of the brown rat and the domestication of the laboratory rat. We showed that brown rats migrated about 3600 years ago from southern East Asia, rather than Northern Asia as formerly suggested, to the Middle East and then to Europe and Africa. Many genes involved in the immune system experienced positive selection in the wild brown rat, while genes involved in the nervous system and energy metabolism showed evidence of artificial selection during the domestication of laboratory strains. Our findings demystify the puzzling origin and migration of brown rats and reveal the impact of evolution and domestication on this animal.

evolutionary biology↗

bioRxiv2016

An improved de novo pipeline for enrichment of high diversity mitochondrial genomes from Amphibia to high-throughput sequencing

We present an improved de novo pipeline by combining long-range polymerase chain reaction (LR-PCR) and capture hybridization for enriching mitochondrial DNA to high-throughput sequencing. We test a new set of primers and hybridizing long-range library (LR-HY) with 112 mitochondrial genomes (MtG) representing three orders, 12 families, 54 genera, and 106 species of Amphibia. The primers are used for obtaining wide taxonomic MtG amplicons to sequence directly and/or make probes for closely related species. LR-HY is compared to standard hybridization. The primers successfully amplify 82 MtGs from all three order, all families, 92.6% (50/54) of the genera, and 74.5% (79/106) of the species, despite some DNA degradation and gene rearrangement. We observe a significantly negative correlation between sequence depth and gene variation. The pattern of highly variable regions is separately distributed in different regions within the length of < 4 kb in the 33-pooled sample. We demonstrate that using 2 kb libraries generate deeper sequence coverage in the highly variable loci than using 400 bp libraries. In total, the pipeline successfully recovers 83 complete and 14 almost complete MtGs from 53 of 54 genera, including 14 MtGs had rearranged protein-coding genes. This universal primers combined with LR-HY is an efficient way to enrich complete MtGs across the entire Amphibia.

genomics↗