PaperPlayer biorxiv genomics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.31.231381v1?rss=1

Authors: Weinstein, E. N., Marks, D. S.

Abstract:

Large-scale sequencing has revealed extraordinary diversity among biological sequences, produced over the course of evolution and within the lifetime of individual organisms. Existing methods for building statistical models of sequences often preprocess the data using multiple sequence alignment, an unreliable approach for many genetic elements (antibodies, disordered proteins, etc.) that is subject to fundamental statistical pathologies. Here we introduce a structured emission distribution (the MuE distribution) that accounts for mutational variability (substitutions and indels) and use it to construct generative and predictive hierarchical Bayesian models (H-MuE models). Our framework enables the application of arbitrary continuous-space vector models (e.g. linear regression, factor models, image neural-networks) to unaligned sequence data. Theoretically, we show that the MuE generalizes classic probabilistic alignment models. Empirically, we show that H-MuE models can infer latent representations and features for immune repertoires, predict functional unobserved members of disordered protein families, and forecast the future evolution of pathogens.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.222521v1?rss=1

Authors: Flossmann, G., Wurmser, C., Pausch, H., Tenghe, A., Dodenhoff, J., Dahinten, G., Goetz, K.-U., Russ, I., Fries, H.-R.

Abstract:

Background: Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means for identifying chromosomal regions harboring deleterious DNA-variants causing such phenotypes. We performed a GWAS to unravel the causes of incidental cases of atypically small vulvae in German Landrace gilts. Results: A case-control GWAS involving Illumina porcine SNP60 BeadChip-called genotypes of 17 gilts with atypically small vulvae and 1,818 control animals (fertile German Landrace sows) identified a significantly associated region on the X-chromosome (P = 8.81x10-43). Inspection of whole-genome sequencing data in the critical area allowed us to pinpoint a likely causal variant in the form of a nonsense mutation of bone morphogenetic protein-15 (Sscrofa11.1_X:g.44618787C>T, BMP15:p.R212X). The mutant allele occurs at a frequency of 6.2% in the German Landrace breeding population. Homozygous gilts exhibit underdeveloped, most likely not functional ovaries and are not fertile. Male carriers do not seem to manifest defects. Heterozygous sows produce 0.41{+/-}0.02 (P=4.5x10-83) piglets more than wildtype animals. However, the mutant allele's positive effect on litter size accompanies a negative impact on lean meat growth. Conclusion: Our results provide an example for the power of GWAS in identifying the genetic causes of a fuzzy phenotype and add to the list of natural deleterious BMP15 mutations that affect fertility in a dosage-dependent manner, the first time in a poly-ovulatory species. We advise eradicating the mutant allele from the German Landrace breeding population since the adverse effects on the lean meat growth outweigh the larger litter size in heterozygous sows.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.234112v1?rss=1

Authors: Herchcovici Levi, S., Arnon, L., Feldman, S., Alajem, A., Bavli, D., Sun, X., Buganim, Y., Ram, O.

Abstract:

Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying a retinoic acid-based protocol as a differentiation assay representing exit from pluripotency, we show that Esrrb, a key pluripotent factor is upregulated during G2/M phase and promptly downregulated during exit from pluripotency. Enhancer chromatin states and Esrrb ChIP-seq map expose Esrrb's association with differentiation genes, were in the context of retinoic acid, enhancers associated with differentiation program driving extraembryonic endoderm cells (XENs). We show that only G2/M ESCs were capable of differentiating into XENs, whereas cells in the G1 phase predominantly produce epiblast stem cells (EpiSCs). Furthermore, Cells engineered to overexpress Esrrb allowed G1 ESCs to produce XENs, while Esrrb knockout ESCs completely lost their potential to differentiate into XEN. Interestingly, this phenomenon is unique to the pluripotency state as sorting cells after initiation of differentiation resulted in a cell cycle-independent differentiation decisions. Cells in both G1 and G2/M phases contributed equally to EpiSC and XEN cellular lineages. Taken together, this study reveals an important functional link between Esrrb and cell-cycle states during exit from pluripotency. Our novel approach of applying single cell RNAseq in a cell cycle dependent manner can be further expand into other differentiation assays and expand our understanding of early differentiation events.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.235150v1?rss=1

Authors: Kunert-Graf, J. M., Sakhanenko, N. M., Galas, D. J.

Abstract:

We report here some anomalies discovered in the minor allele frequencies (MAFs) and some likely mismappings found in our analyses of UK Biobank dataset (UKB) and several other databases. We compared the MAFs present in the UKB to those measured in two other UK studies, ALSPAC and TwinsUK, and found a large set of SNPs for which the UKB MAFs are inconsistent. Additionally, even after accounting for population structure effects and other possible causes of spurious correlations, we found many SNPs that appear to be in interchromosomal linkage. Analyzing these interchromosomal linkages carefully, we found that they are all associated with identical sequences on different chromosomes, implying that these SNPs are simply mismapped. Some (but certainly not all) of the MAF disagreements appear to be the result of these mismappings. Our results, including lists of SNPs with inconsistent MAFs and/or apparent interchromosomal linkage, are freely available to download at: http://kunertgraf.com/data/biobank.html

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.233932v1?rss=1

Authors: Cardosa, S., Ogunkolade, W., Lowe, R., Savage, E., Mein, C. A., Boucher, B. J., Hitman, G. A.

Abstract:

Betel-nut consumption is the fourth most common addictive habit globally and there is good evidence to link it with obesity, type 2 diabetes and the metabolic syndrome. We adopted a genome-wide transcriptomic approach in a human monocyte cell line incubated with arecoline and its nitrosated products to identify gene expression changes relevant to obesity, type 2 diabetes and the metabolic syndrome. The THP1 monocyte cell line was incubated separately with arecoline and 3-methylnitrosaminopropionaldehyde (MNPA) in triplicate for 24 hours and pooled cDNA indexed paired-end libraries were sequenced (Illumina NextSeq 500). After incubation with arecoline and MNPA, 15 and 39 genes respectively had significant changes in their expression (q<0.05, log fold change 1.5). Eighteen of those genes have reported associations with type 2 diabetes and obesity in humans; of these genes there was strong evidence to implicate CLEC10A , MAPK8IP1 , NEGR1 , NQ01 and INHBE . In summary, these pilot studies have identified a large number of genes whose expression was changed significantly in human TPH1 cells following incubation with arecoline or with 3-methylnitrosaminopropionaldehyde. These findings suggest that further investigation of these genes in betel-quid chewers with obesity and/or type 2 diabetes is warranted.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.233718v1?rss=1

Authors: Maitra, A., Raghav, S., Dalal, A., Ali, F., Paynter, V. M., Paul, D., Biswas, N. K., Ghosh, A., Jani, K., Chinnaswamy, S., Pati, S., Sahu, A., Mitra, D., Bhat, M. K., Mayor, S., Sarin, A., The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium,, Shouche, Y. S., Seshasayee, A. S. N., Palakodeti, D., Bashyam, M. D., PARIDA, A., Das, S.

Abstract:

The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India. Given the importance of this information for public health response initiatives investigating transmission of COVID-19, the sequence data is being released in GISAID database. This information will improve our understanding on how the virus is spreading, ultimately helping to interrupt the transmission chains, prevent new cases of infection, and provide impetus to research on intervention measures. This will also provide us with information on evolution of the virus, genetic predisposition (if any) and adaptation to human hosts. One thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. A2a (20A/B/C) was found to be predominant, along with few parental haplotypes 19A/B. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Additionally, mutations in important regions of the viral genome with significant geographical clustering have also been observed. The temporal haplotype diversities landscape in each region appears to be similar pan India, with haplotype diversities peaking between March-May, while by June A2a (20A/B/C) emerged as the predominant one. Within haplotypes, different states appear to have different proportions. Temporal and geographic patterns in the sequences obtained reveal interesting clustering of mutations. Some mutations are present at particularly high frequencies in one state as compared to others. The negative estimate Tajimas D (D = -2.26817) is consistent with the rapid expansion of SARS-CoV-2 population in India. Detailed mutational analysis across India to understand the gradual emergence of mutants at different regions of the country and its possible implication will help in better disease management.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.02.232785v1?rss=1

Authors: Gleeson, J., Lane, T. A., Harrison, P. J., Haerty, W., Clark, M. B.

Abstract:

Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Therefore, a crucial requirement of RNA sequencing is identifying differential expression. The recent development of long-read direct RNA (dRNA) sequencing has the potential to overcome many limitations of short and long-read sequencing methods that require RNA fragmentation, cDNA synthesis or PCR. dRNA sequences native RNA and can encompass an entire RNA in a single read. However, its ability to identify differential gene and isoform expression in complex organisms is poorly characterised. Using a mixture of synthetic controls and human SH-SY5Y cell differentiation into neuron-like cells, we show that dRNA sequencing accurately quantifies RNA expression and identifies differential expression of genes and isoforms. We generated ~4 million dRNA reads with a median length of 991 nt. On average, reads covered 74% of SH-SY5Y transcripts and 29% were full-length. Measurement of expression and fold changes between synthetic control RNAs confirmed accurate quantification of genes and isoforms. Differential expression of 231 genes, 291 isoforms, plus 27 isoform switches were detected between undifferentiated and differentiated SH-SY5Y cells and samples clustered by differentiation state at the gene and isoform level. Genes upregulated in neuron-like cells were associated with neurogenesis. We further identified >30,000 expressed transcripts including thousands of novel splice isoforms and transcriptional units. Our results establish the ability of dRNA sequencing to identify biologically relevant differences in gene and isoform expression and perform the key capabilities of expression profiling methodologies.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.31.193243v1?rss=1

Authors: fang, Z.-Z., Lin-Wang, K., Dai, H., Zhou, D.-R., Jiang, C.-C., Espley, R. V., Lin, Y.-J., Pan, S.-L., Ye, X.-F.

Abstract:

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum 'Sanyueli' (P. salicina Lindl.), which is known to have a low-chill requirement. The assembled genome size was 308.06 Mb, with a contig N50 of 815.7 kb. A total of 30,159 protein-coding genes was predicted from the genome and 56.42% (173.39 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in 'Sanyueli' revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of 'Sanyueli' was significantly lower than that in the dormant flower buds of the high chill requiring 'Furongli' plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of 'Sanyueli' plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.30.230102v1?rss=1

Authors: Li, M., Xu, Y., Kang, L., Shen, Z., Li, X., Wu, W., Ma, W., Fang, C., Yang, F., Jiang, X., Gong, S., Zhang, L.

Abstract:

Background: In response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples. Methods: Eighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization. Results: By examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period. Conclusions: The hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.01.232496v1?rss=1

Authors: Liu, Y., Yang, M., Deng, Y., Su, G., Archibald Enninful, A., Guo, C. C., Tebaldi, T., Zhang, D., Kim, D., Bai, Z., Norris, E., Pan, A., Li, J., Xiao, Y., Halene, S., Fan, R.

Abstract:

We present DBiTseq Deterministic Barcoding in Tissue for spatial omics sequencing for comapping of mRNAs and proteins in a formaldehyde fixed tissue slide via NGS sequencing. Parallel microfluidic channels were used to deliver DNA barcodes to the surface of a tissue slide and crossflow of two sets of barcodes A1 to A50 and B1 to B50 followed by ligation in situ yielded a 2D mosaic of tissue pixels, each containing a unique full barcode AB. Application to mouse embryos revealed major tissue types in early organogenesis as well as fine features like microvasculature in a brain and pigmented epithelium in an eye field. Gene expression profiles in 10um pixels conformed into the clusters of single cell transcriptomes, allowing for rapid identification of cell types and spatial distributions. DBiT seq can be adopted by researchers with no experience in microfluidics and may find applications in a range of fields including developmental biology, cancer biology, neuroscience, and clinical pathology.

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