Biology subjects

Pan, J.

Publications and source records attributed to Pan, J..

4 recordsLinked to original sources

bioRxiv2018

Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

Asgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2 using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

microbiology↗

bioRxiv2018

Exercise-related genes analysis of Mongolian Horse - Abaga horse and Wushen horse

The Mongolian horses, as a neglected scientific resource, have excellent endurance and stress resistance to adapt to the cold and harsh plateau conditions. Intraspecific genetic diversity is mainly embodied in various genetic advantages of different branches of Mongolian horse. Abaga horse is better than Wushen horse in running speed, for example. Because people pay progressively attention to the athletic performance of horse, such as horse racing in Mongolias Naadam festival, we expect to guide the exercise-oriented breeding of horses through genomics research. We obtained the clean data of 630,535,376,400 bp through the entire genome second-generation sequencing for the whole blood of 4 Abaga horses and 10 Wushen horses. Based on the data analysis of single nucleotide polymorphism (SNP), we severally detected that 479 and 943 positively selected genes, particularly exercise-related, were mainly enriched on equine chromosome 4 in Abaga horses and Wushen horses, which implied that the chromosome 4 may be associated with the evolution of the Mongolian horse and athletic performance. Four hundred and forty genes of positive selection were enriched in 12 exercise-related pathways and narrowed in 21 exercise-related genes in Abaga horse, which were distinguished from Wushen horse. So, we speculated that the Abaga horse may have oriented genes for the motorial mechanism and 21 exercise-related genes also provided molecular genetic basis for exercise-directed breeding of Mongolian horse.

genomics↗

bioRxiv2018

Dynamic and causal contribution of parietal cortex to perceptual decisions during category learning

Making perceptual decisions to categorize unknown sensory stimuli is a fundamental cognitive function, known as category learning. The posterior parietal cortex (PPC), although has been intensively studied for its role in decision-making and other cognitive functions, its causal link with behavior remains controversial. Here we combine in vivo two-photon imaging, circuit manipulation and auditory psychophysics behavior in mice to probe the role of PPC and its connectivity with sensory cortex in decision-making during category learning. We show that PPC neuronal populations exhibit coding dynamics characteristic of category learning, showing representations for both new sensory stimuli and prior learned categories. Circuit-specific perturbations of PPC and its projections to auditory cortex impaired decision performance specifically for categorizing new auditory stimuli. These data reveal a dynamic and causal role of the parietal-auditory circuit in decision-making, integrating prior knowledge to guide categorical decisions on new sensory stimuli.

neuroscience↗

bioRxiv2018

Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as genotyping platform in Norway spruce

BackgroundGenomic selection (GS) can increase genetic gain by reducing the length of breeding cycle in forest trees. Here we genotyped 1370 control-pollinated progeny trees from 128 full-sib families in Norway spruce (Picea abies (L.) Karst.), using exome capture as a genotyping platform. We used 116,765 high quality SNPs to develop genomic prediction models for tree height and wood quality traits. We assessed the impact of different genomic prediction methods, genotype-by-environment interaction (GxE), genetic composition, size of the training and validation set, relatedness, and the number of SNPs on the accuracy and predictive ability (PA) of GS.\n\nResultsUsing G matrix slightly altered heritability estimates relative to pedigree-based method. GS accuracies were about 11-14% lower than those based on pedigree-based selection. The efficiency of GS per year varied from 1.71 to 1.78, compared to that of the pedigree-based model if breeding cycle length was halved using GS. Height GS accuracy decreased more than 30% using one site as training for GS prediction to the second site, indicating that GxE for tree height should be accommodated in model fitting. Using half-sib family structure instead of full-sib led a significant reduction in GS accuracy and PA. The full-sib family structure only needed 750 makers to reach similar accuracy and PA as 100,000 markers required for half-sib family, indicating that maintaining the high relatedness in the model improves accuracy and PA. Using 4000-8000 markers in full-sib family structure was sufficient to obtain GS model accuracy and PA for tree height and wood quality traits, almost equivalent to that obtained with all makers.\n\nConclusionsThe study indicates GS would be efficient in reducing generation time of a breeding cycle in conifer tree breeding program that requires a long-term progeny testing. Sufficient number of trees within-family (16 for growth and 12 for wood quality traits) and number of SNPs (8000) are required for GS with full-sib family relationship. GS methods had little impact on GS efficiency for growth and wood quality traits. GS model should incorporate G x E effect when a strong GxE is detected.

genetics↗