The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain

Both virulent and live-attenuated porcine reproductive and respiratory syndrome virus (PRRSV) strains can establish persistent infection in lymphoid tissues of pigs. To investigate the mechanisms of PRRSV persistence, we performed a transcriptional analysis of inguinal lymphoid tissue collected from pigs experimentally infected with an attenuated PRRSV strain at 46 days post infection. A total of 6404 differentially expressed genes (DEGs) were detected of which 3960 DEGs were upregulated and 2444 DEGs were downregulated. Specifically, genes involved in innate immune responses and chemokines and receptors associated with T-cell homing to lymphoid tissues were down regulated. As a result, homing of virus-specific T-cells to lymphoid tissues seems to be ineffective, evidenced by the lower frequencies of virus-specific T-cell in lymphoid tissue than in peripheral blood. Genes associated with T-cell exhaustion were upregulated. Likewise, genes involved in the anti-apoptotic pathway were upregulated. Collectively, the data suggested that the live-attenuated PRRSV strain establishes a pro-survival microenvironment in lymphoid tissue by suppressing innate immune responses, T-cell homing, and preventing cell apoptosis

Genome structure and evolutionary history of frankincense producing \u3ci\u3eBoswellia sacra\u3c/i\u3e

Boswellia sacra Flueck (family Burseraceae) tree is wounded to produce frankincense. We report its de novo assembled genome (667.8 Mb) comprising 18,564 high-confidence protein-encoding genes. Comparing conserved single-copy genes across eudicots suggest \u3e97% gene space assembly of B. sacra genome. Evolutionary history shows B. sacra gene-duplications derived from recent paralogous events and retained from ancient hexaploidy shared with other eudicots. The genome indicated a major expansion of Gypsy retroelements in last 2 million years. The B. sacra genetic diversity showed four clades intermixed with a primary genotype—dominating most resin-productive trees. Further, the stemtranscriptome revealed that wounding concurrently activates phytohormones signaling, cell wall fortification, and resin terpenoid biosynthesis pathways leading to the synthesis of boswellic acid—a key chemotaxonomic marker of Boswellia. The sequence datasets reported here will serve as a foundation to investigate the genetic determinants of frankincense and other resin-producing species in Burseraceae

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

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Taxonomic delimitation and the evolutionary history of the Australasian Lautusoid group of Senecio (Asteraceae)

Taxonomic delimitation can be a challenging task for systematists, because of the dynamic and complex evolutionary processes that shape patterns of biodiversity. Yet, it is an essential aspect of biology, because it defines units of evolutionary significance, which form the basis for studying all aspects of biodiversity. In this thesis, I studied the taxonomic delimitation and evolutionary history of the Australasian Lautusoid group of Senecio at the infrageneric, species, and infraspecific level. Members of the Lautusoid group are morphologically very diverse and occupy a wide array of habitats. Moreover, the Lautusoid group has a large diversity of chromosome profiles compared to other Australasian Senecio, which indicates the possible occurrence of hybridization in its evolutionary history. These patterns of diversity make it an attractive system for various evolutionary and ecological studies. Despite these interesting characteristics and the inclusion of members of the Lautusoid group in a number of taxonomic treatments, it is not known how many and which species form the Lautusoid group. To determine the delimitation of the Lautusoid group and to investigate the origin of Lautusoid species with higher chromosome numbers, a molecular phylogenetic study was carried out. The results of this study indicate that the group is a morphologically and phylogenetically distinct Senecio lineage with an Australasian distribution. These results also highlight the important role of hybrid speciation in the evolutionary history of the Lautusoid group by identifying allopolyploid hybrids between members of the Lautusoid group and members of other Australasian lineages. An allopolyploid species complex that was found to be affiliated with the Lautusoid group, S. glaucophyllus, was the focus of subsequent studies. Senecio glaucophyllus and a morphologically similar informally named taxon, S. aff. glaucophyllus, were examined to determine if they are distinct species. The results confirm that the two taxa are indeed morphologically and genetically distinct. However, against expectation, this study revealed that S. aff. glaucophyllus is the true S. glaucophyllus and that the plants that were called S. glaucophyllus belong to a species that is presently unnamed. This taxon, tentatively called S. “pseudoglaucophyllus”, aligns with S. glaucophyllus sensu Ornduff excluding S. glaucophyllus Cheeseman. In order to revisit the current classification of recognizing four infraspecific groups for S. “pseudoglaucophyllus” and to propose taxonomic recommendations, studies that look into its morphological and genetic diversity were performed. The results of these studies show that patterns of morphological variation in S. “pseudoglaucophyllus” are not congruent with patterns of genetic variation and that neither supports the current classification in which four infraspecific groups are recognized. Because infraspecific taxon boundaries cannot be unambiguously determined for S. “pseudoglaucophyllus”, this species is therefore best regarded as a single variable New Zealand species for which infraspecific groups should not be formally recognized

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain

Both virulent and live-attenuated porcine reproductive and respiratory syndrome virus (PRRSV) strains can establish persistent infection in lymphoid tissues of pigs. To investigate the mechanisms of PRRSV persistence, we performed a transcriptional analysis of inguinal lymphoid tissue collected from pigs experimentally infected with an attenuated PRRSV strain at 46 days post infection. A total of 6404 differentially expressed genes (DEGs) were detected of which 3960 DEGs were upregulated and 2444 DEGs were downregulated. Specifically, genes involved in innate immune responses and chemokines and receptors associated with T-cell homing to lymphoid tissues were down regulated. As a result, homing of virus-specific T-cells to lymphoid tissues seems to be ineffective, evidenced by the lower frequencies of virus-specific T-cell in lymphoid tissue than in peripheral blood. Genes associated with T-cell exhaustion were upregulated. Likewise, genes involved in the anti-apoptotic pathway were upregulated. Collectively, the data suggested that the live-attenuated PRRSV strain establishes a pro-survival microenvironment in lymphoid tissue by suppressing innate immune responses, T-cell homing, and preventing cell apoptosis

The delimitation and evolutionary history of the Australasian lautusoid group of Senecio (Asteraceae: Senecioneae)

Senecio (Asteraceae: Senecioneae) is one of the largest genera of flowering plants and its infrageneric delimitation has been impeded by its large size (> 1000 species), large morphological variation and widespread incongruence between phylogenies derived from different datasets. As part of efforts to improve our understanding of the evolutionary relationships among infrageneric Senecio groups, nuclear (nrITS, ETS) and plastid (psbA-trnH, trnL and trnL-F) DNA sequence data were used to study the delimitation of the Australasian Lautusoid group of Senecio. These data were also used to understand the evolutionary origins of polyploid species that have been placed in this informally recognized group. The results of our phylogenetic analyses indicate that Australasian Senecio compose four separate and distantly related lineages, which are here informally named the Disciform s.str., Lautusoid, Odoratus s.l., and Quadridentatus groups. A new delimitation of the Lautusoid group is presented that includes species previously placed in this group based on morphological similarities, as well as some that were previously assigned to other informally recognized Senecio groups. This brings the total number of confirmed members of the Lautusoid group to 15 species. Six allopolyploid species were identified that resulted from hybridization between members of the Lautusoid group and species of the three other Australasian Senecio lineages. Our findings indicate that hybridization has played an important role in the evolutionary diversification of Australasian Senecio and provide a framework for further studies into their evolutionary history