GeCoAgent: A Conversational Agent for Empowering Genomic Data Extraction and Analysis

With the availability of reliable and low-cost DNA sequencing, human genomics is relevant to a growing number of end-users, including biologists and clinicians. Typical interactions require applying comparative data analysis to huge repositories of genomic information for building new knowledge, taking advantage of the latest findings in applied genomics for healthcare. Powerful technology for data extraction and analysis is available, but broad use of the technology is hampered by the complexity of accessing such methods and tools. This work presents GeCoAgent, a big-data service for clinicians and biologists. GeCoAgent uses a dialogic interface, animated by a chatbot, for supporting the end-users’ interaction with computational tools accompanied by multi-modal support. While the dialogue progresses, the user is accompanied in extracting the relevant data from repositories and then performing data analysis, which often requires the use of statistical methods or machine learning. Results are returned using simple representations (spreadsheets and graphics), while at the end of a session the dialogue is summarized in textual format. The innovation presented in this article is concerned with not only the delivery of a new tool but also our novel approach to conversational technologies, potentially extensible to other healthcare domains or to general data science.

Draft Genome Sequence of Bryobacteraceae Strain F-183

Here, we report a draft genome sequence of a bacterial strain, F-183, isolated from a duckweed frond. Strain F-183 belongs to the family Bryobacteraceae of the phylum Acidobacteria , and its genomic information would contribute to understanding the ecophysiology of this abundant but rarely characterized phylum.

Whole-Genome Sequence of Entomortierella parvispora E1425, a Mucoromycotan Fungus Associated with Burkholderiaceae -Related Endosymbiotic Bacteria

Some mucoromycotan fungi establish symbiotic associations with endohyphal bacteria. Here, the genome of Entomortierella parvispora E1425 (synonymously known as Mortierella parvispora E1425), which harbors a cultured Burkholderiaceae -related endobacterium (BRE) designated Mycoavidus sp. Strain B2-EB, was sequenced. We provide genomic information to elucidate fungal-BRE symbiotic features.

Transcription–Replication Coordination

Transcription and replication are the two most essential processes that a cell does with its DNA: they allow cells to express the genomic content that is required for their functions and to create a perfect copy of this genomic information to pass on to the daughter cells. Nevertheless, these two processes are in a constant ambivalent relationship. When transcription and replication occupy the same regions, there is the possibility of conflicts between transcription and replication as transcription can impair DNA replication progression leading to increased DNA damage. Nevertheless, DNA replication origins are preferentially located in open chromatin next to actively transcribed regions, meaning that the possibility of conflicts is potentially an accepted incident for cells. Data in the literature point both towards the existence or not of coordination between these two processes to avoid the danger of collisions. Several reviews have been published on transcription–replication conflicts, but we focus here on the most recent findings that relate to how these two processes are coordinated in eukaryotes, considering advantages and disadvantages from coordination, how likely conflicts are at any given time, and which are their potential hotspots in the genome.

The phylogenomic landscape of the genus Serratia

The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We show that Serratia is a diverse genus which displays striking plasticity and ability to adapt to its environment, including a highly-varied portfolio of plasmids, and provide evidence of different patterns of gene flow across the genus. This work provides an essential platform for understanding the emergence of clinical and other lineages of Serratia.

A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests

Background Orius laevigatus, a minute pirate bug, is a highly effective beneficial predator of crop pests including aphids, spider mites and thrips in integrated pest management (IPM) programmes. No genomic information is currently available for O. laevigatus, as is the case for the majority of beneficial predators which feed on crop pests. In contrast, genomic information for crop pests is far more readily available. The lack of publicly available genomes for beneficial predators to date has limited our ability to perform comparative analyses of genes encoding potential insecticide resistance mechanisms between crop pests and their predators. These mechanisms include several gene/protein families including cytochrome P450s (P450s), ATP binding cassette transporters (ABCs), glutathione S-transferases (GSTs), UDP-glucosyltransferases (UGTs) and carboxyl/cholinesterases (CCEs). Methods and findings In this study, a high-quality scaffold level de novo genome assembly for O. laevigatus has been generated using a hybrid approach with PacBio long-read and Illumina short-read data. The final assembly achieved a scaffold N50 of 125,649 bp and a total genome size of 150.98 Mb. The genome assembly achieved a level of completeness of 93.6% using a set of 1658 core insect genes present as full-length genes. Genome annotation identified 15,102 protein-coding genes - 87% of which were assigned a putative function. Comparative analyses revealed gene expansions of sigma class GSTs and CYP3 P450s. Conversely the UGT gene family showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily level between O. laevigatus and some of its targeted crop pests. A target site mutation in ryanodine receptors (I4790M, PxRyR) which has strong links to diamide resistance in crop pests and had previously only been identified in lepidopteran species was found to also be present in hemipteran species, including O. laevigatus. Conclusion and significance This assembly is the first published genome for the Anthocoridae family and will serve as a useful resource for further research into target-site selectivity issues and potential resistance mechanisms in beneficial predators. Furthermore, the expansion of gene families often linked to insecticide resistance may be an indicator of the capacity of this predator to detoxify selective insecticides. These findings could be exploited by targeted pesticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably, environmentally-friendly and effectively control pests without impacting beneficial predator populations.

Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis

The Candidate Phyla Radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and often lack ribosomal proteins L1, L9, and/or L30, which are basically ubiquitous in ordinary (non-CPR) bacteria. Here, we comprehensively analyzed the genomic information of CPR bacteria and identified their unique properties. In the distribution of protein lengths in CPR bacteria, the peak was at around 100–150 amino acids, whereas the position of the peak varies in the range of 100–300 amino acids in free-living non-CPR bacteria, and at around 100–200 amino acids in most symbiotic non-CPR bacteria. These results show that CPR bacteria have smaller proteins on average, like symbiotic non-CPR bacteria. We found that ribosomal proteins L28, L29, L32, and L33 are also deleted in CPR bacteria, in a lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins in CPR differ, in part, from those of non-CPR bacteria, with missing regions or specific added region. We also found that several regions of the 16S, 23S, and 5S rRNAs are lacking in CPR bacteria and that the total predicted length of the three rRNAs in CPR bacteria is smaller than that in non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than in free-living non-CPR bacteria, with simplified surface structures.

Genome structure and diversity among Cynanchum wilfordii accessions

Background Cynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information. Results We collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events. Conclusions Cw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.

Doenças associadas à Xylella fastidiosa no Brasil

Based on genomic information, the Xylella fastidiosa bacterium is classified into three main subspecies: fastidiosa, multiplex and pauca. These different subspecies are naturally transmitted through vector insects, known as sharpshooters, which feed on the sap of xylem vessels of plants, where the bacteria colonize. Mainly due to the obstruction in the transport of water and mineral salts in these conducting vessels, the X. fastidiosa bacterium causes serious diseases in different cultures of economic interest. In Brazil, this phytopathogen was detected for the first time in plum trees, a crop in which the multiplex subspecies is responsible for the disease known as plum leaf scald. Subsequently, the pauca subspecie was associated with citrus variegated chlorosis in sweet orange orchards in São Paulo State. In the same state, the pauca subspecie was also found in coffee plants causing atrophy of the coffee tree branches, a disease whose damage has not been quantified yet. Recently, the pauca subspecie has also been found in olive trees, causing the olive quick decline syndrome, reported in the southeast region, especially in the Serra da Mantiqueira region. In this review, specific aspects of these diseases were focused, as well as measures that can be adopted as management.