PaperPlayer biorxiv genomics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.245258v1?rss=1

Authors: Hao, Y., Mabry, M. E., Edger, P., Freeling, M., Zheng, C., Jin, L., VanBuren, R., Colle, M., An, H., Abrahams, R. S., Qi, X., Barry, K., Daum, C., Shu, S., Schmutz, J., Sankoff, D., Barker, M. S., Lyons, E., Pires, J. C., Conant, G. C.

Abstract:

The members of the tribe Brassiceae share an ancient whole genome triplication (WGT), and plants in this tribe display extraordinarily high within-species morphological diversity. One proposed model for the formation of these hexaploid Brassiceae is that they result from a "two-step" pair of hybridizations. However, direct evidence supporting this model of formation has been lacking; meanwhile, the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. After adding this new genome to three others that are also descended from the ancient hexaploidy, we traced the history of gene loss after the WGT using a phylogenomic pipeline called POInT (the Polyploidy Orthology Inference Tool). This approach allowed us to confirm the two-step model of hexaploidy formation and to assign statistical confidence to our parental "subgenome" assignments for >90,000 individual genes. We show that each subgenome has a statistically distinguishable rate of homeolog losses. Moreover, our modeling allowed us to infer that there was a significant temporal gap between the two allopolyploidizations, with about one third of the total shared gene losses between the four analyzed Brassiceae species in the first two subgenomes prior to the arrival of the third subgenome. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, where subgenome origin drives homeolog loss propensities but where genes from different subgenomes function together without difficulty.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.248740v1?rss=1

Authors: Rahman, S. R., Cnaani, J., Kinch, L. N., Grishin, N. V., Hines, H. M.

Abstract:

Background: In the model bumble bee species B. terrestris, both males and females exhibit black coloration on the third thoracic and first metasomal segments. We discovered a fortuitous lab-generated mutant in which this typical black coloration is replaced by yellow. As this same color variant is found in several sister lineages to B. terrestris within the Bombus s.s. subgenus, this could be a result of ancestral allele sorting. Results: Utilizing a combination of RAD-Seq and whole-genome re-sequencing approaches, we localized the color-generating variant to a single SNP in the protein-coding sequence of a homeobox transcription factor, cut. Sanger sequencing confirmed fixation of this SNP between wildtype and yellow mutants. Protein domain analysis revealed this SNP to generate an amino acid change (Ala38Pro) that modifies the conformation of coiled-coil structural elements which lie outside the characteristic DNA binding domains. We found all Hymenopterans including B. terrestris sister lineages possess the non-mutant allele, indicating different mechanism(s) are involved in the same black to yellow transition in nature. Conclusions: Cut is a highly pleiotropic gene important for multiple facets of development, yet this mutation generated no noticeable external phenotypic effects outside of setal characteristics. Reproductive capacity was observed to be reduced, however, with queens being less likely to mate and produce female offspring, in a manner similar to workers. Our research implicates a novel developmental player in pigmentation, and potentially caste as well, thus contributing to a better understanding of the evolution of diversity in both of these processes.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.247122v1?rss=1

Authors: Heldrich, J., Markowitz, T. E., Vale-Silva, L. A., Hochwagen, A.

Abstract:

Meiotic chromosomes organize around a cohesin-dependent axial element, which promotes meiotic recombination and fertility. In the absence of cohesin, axial-element proteins instead accumulate in poorly understood genomic regions. Here, we show in S. cerevisiae that these regions are particularly enriched for axis proteins even on wild-type chromosomes and thus reflect a cohesin-independent recruitment mechanism. By contrast, other organizers of chromosome structure, including cohesin, condensin, and topoisomerases, are depleted from the same regions. This spatial patterning is observable before meiotic entry and therefore independent of meiotic recombination. Indeed, the regional density of gene-coding sequences is sufficient to predict a large fraction of cohesin-independent axis protein binding, suggesting that the gene-associated chromatin landscape plays a role in modulating axis protein deposition. The increased accumulation of axis proteins in these regions corresponds to a greater potential for initiation of recombination and progression to crossovers.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.235309v1?rss=1

Authors: Simbaqueba, J., Rodriguez, E. A., Burbano, D. M., Gonzalez, C., Caro, A.

Abstract:

The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali (Foph) is one of the most limiting factors for the production and export of cape gooseberry (Physalis peruviana) in Colombia. A previous study of the transcriptomic profile of a highly virulent strain of F. oxysporum in cape gooseberry plants, from a collection of 136 fungal isolates obtained from wilted cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of other F. oxysporum formae speciales (ff. spp.). This pathogenic strain was named Foph, due to its specificity for cape gooseberry hosts. Here, we sequenced the genome of Foph, using the Illumina MiSeq platform. We analyzed the assembled genome, focusing on the confirmation of the presence of homologues of SIX effectors and the identification of novel candidates of effector genes unique of Foph. By comparative and phylogenomic analyses based on single-copy orthologues, we identified that Foph is closely related to F. oxysporum ff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions between Foph and Fol, that contain effector genes and identified seven new effector gene candidates, specific to Foph strains. We also conducted a molecular characterization of a panel of 29 F. oxysporum additional stains associated to cape gooseberry crops isolated from different regions of Colombia. These results suggest the polyphyletic origin of Foph and the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified by sequencing and analyzing the genome of Foph, represent new sources involved in the interaction between Foph and cape gooseberry. These resources could be implemented to develop appropriate management strategies of the wilt disease caused by Foph in the cape gooseberry crop.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.244541v1?rss=1

Authors: Schneider, C., Woehle, C., Greve, C., D'Haese, C. A., Wolf, M., Janke, A., Balint, M., Hüttel, B.

Abstract:

Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in evolutionary sciences, ecology, systematics and in biodiversity-related applied fields such as environmental management and natural product research. Advances in DNA sequencing technologies make genome sequencing feasible for many non-genetic model species. However, genome sequencing today relies on large quantities of high quality, high molecular weight (HMW) DNA which is mostly obtained from fresh tissues. This is problematic for biodiversity genomics of Metazoa as most species are small and yield minute amounts of DNA. Furthermore, briging living specimens to the lab bench not realistic for the majority of species. Here we overcome those difficulties by sequencing two species of springtails (Collembola) from single specimens preserved in ethanol. We used a newly developed, genome-wide amplification-based protocol to generate PacBio libraries for HiFi long-read sequencing. The assembled genomes were highly continuous. They can be considered complete as we recovered over 95% of BUSCOs. Genome-wide amplification does not seem to bias genome recovery. Presence of almost complete copies of the mitochondrial genome in the nuclear genome were pitfalls for automatic assemblers. The genomes fit well into an existing phylogeny of springtails. A neotype is designated for one of the species, blending genome sequencing and creation of taxonomic references. Our study shows that it is possible to obtain high quality genomes from small, field-preserved sub-millimeter metazoans, thus making their vast diversity accessible to the fields of genomics.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.244624v1?rss=1

Authors: Canakoglu, A., Pinoli, P., Bernasconi, A., Alfonsi, T., Melidis, D. P., Ceri, S.

Abstract:

ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola, and Dengue. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.243840v1?rss=1

Authors: Sengupta, D., Choudhury, A., Fortes-Lima, C., Aron, S., Whitelaw, G., Bostoen, K., Gunnink, H., Chousou-Polydouri, N., Delius, P., Tollman, S., Casas, F. G.-O., Norris, S., Mashinya, F., Alberts, M., Hazelhurst, S., Schlebusch, C. M., Ramsay, M.

Abstract:

South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.244657v1?rss=1

Authors: Kellaway, S. G., Keane, P., Edginton-White, B., Kakkad, R., Kennett, E., Bonifer, C.

Abstract:

Mutations of the hematopoietic master regulator RUNX1 cause acute myeloid leukaemia, familial platelet disorder and other haematological malignancies whose phenotypes and prognoses depend upon the class of RUNX1 mutation. The biochemical behaviour of these oncoproteins and their ability to cause unique diseases has been well studied, but the genomic basis of their differential action is unknown. To address this question we compared integrated phenotypic, transcriptomic and genomic data from cells expressing four types of RUNX1 oncoproteins in an inducible fashion during blood development from embryonic stem cells. We show that each class of mutated RUNX1 deregulates endogenous RUNX1 function by a different mechanism, leading to specific alterations in developmentally controlled transcription factor binding and chromatin programming. The result is distinct perturbations in the trajectories of gene regulatory network changes underlying blood cell development that are consistent with the nature of the final disease phenotype. The development of novel treatments for RUNX1-driven diseases will therefore require individual consideration.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.243543v1?rss=1

Authors: Tian, L., Jabbari, J. S., Thijssen, R., Gouil, Q., Amarasinghe, S. L., Kariyawasam, H., Su, S., Dong, X., Law, C. W., Lucattini, A., Chung, J. D., Naim, T., Chan, A., Ly, C. H., Lynch, G. S., Ryall, J. G., Anttila, C. J. A., Peng, H., Anderson, M. A., Roberts, A. W., Huang, D. C. S., Clark, M. B., Ritchie, M. E.

Abstract:

Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level. Here we developed single-cell full-length transcript sequencing by sampling (FLT-seq), together with the computational pipeline FLAMES to overcome these issues and perform isoform discovery and quantification, splicing analysis and mutation detection in single cells. With FLT-seq and FLAMES, we performed the first comprehensive characterization of the full-length isoform landscape in single cells of different types and species and identified thousands of unannotated isoforms. We found conserved functional modules that were enriched for alternative transcript usage in different cell populations, including ribosome biogenesis and mRNA splicing. Analysis at the transcript-level allowed data integration with scATAC-seq on individual promoters, improved correlation with protein expression data and linked mutations known to confer drug resistance to transcriptome heterogeneity. Our methods reveal previously unseen isoform complexity and provide a better framework for multi-omics data integration.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.09.243402v1?rss=1

Authors: Patel, S., Howard, D., French, L.

Abstract:

Porphyromonas gingivalis, a keystone species in the development of periodontal disease, is a suspected cause of Alzheimer's disease. This bacterium is reliant on gingipain proteases, which cleave host proteins after arginine and lysine residues. To characterize gingipain susceptibility, we performed enrichment analyses of arginine and lysine proportion proteome-wide. Proteins in the SRP-dependent cotranslational protein targeting to membrane pathway were enriched for these residues and previously associated with periodontal and Alzheimer's disease. These ribosomal genes are up-regulated in prefrontal cortex samples with detected P. gingivalis sequences. Other differentially expressed genes have been previously associated with dementia (ITM2B, MAPT, ZNF267, and DHX37). For an anatomical perspective, we characterized the expression of the P. gingivalis associated genes in the mouse and human brain. This analysis highlighted the hypothalamus, cholinergic neurons, and the basal forebrain. Our results suggest markers of neural P. gingivalis infection and link the gingipain and cholinergic hypotheses of Alzheimer's disease.

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