Genomic Era Research Articles

Genomic Mysteries of Giant Bacteria: Insights and Implications.

Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2-3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.

DecentTree: Scalable Neighbour-Joining for the Genomic Era.

Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10,000 sequences. Given the increasing pace of generating new sequence data, particularly in outbreaks of emerging diseases, and the already enormous existing databases of sequence data for which NJ is a useful approach, new implementations of existing methods are warranted. Here we present DecentTree, which provides highly optimised and parallel implementations of Neighbour-Joining and several of its variants. DecentTree is designed as a stand-alone application and a header-only library easily integrated with other phylogenetic software (e.g., it is integral in the popular IQ-TREE software). We show that DecentTree shows similar or improved performance over existing software (BIONJ, Quicktree, FastME, and RapidNJ), especially for handling very large alignments. For example, DecentTree is up to 6-fold faster than the fastest existing Neighbour-Joining software (e.g., RapidNJ) when generating a tree of 64,000 SARS-CoV-2 genomes. DecentTree is open source and freely available at https://github.com/iqtree/decenttree. All code and data used in this analysis are available on Github (https://github.com/asdcid/Comparison-of-neighbour-joining-software). Supplementary data are available at Bioinformatics online.

Red macroalgae in the genomic era.

Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how thisis expected to accelerate research in many domains of red algal biology in the coming years.

Expert Panel Curation of 113 Primary Mitochondrial Disease Genes for the Leigh Syndrome Spectrum.

Primary mitochondrial diseases (PMDs) are heterogeneous disorders caused by inherited mitochondrial dysfunction. Classically defined neuropathologically as subacute necrotizing encephalomyelopathy, Leigh syndrome spectrum (LSS) is the most frequent manifestation of PMD in children, but may also present in adults. A major challenge for accurate diagnosis of LSS in the genomic medicine era is establishing gene-disease relationships (GDRs) for this syndrome with >100 monogenic causes across both nuclear and mitochondrial genomes. The Clinical Genome Resource (ClinGen) Mitochondrial Disease Gene Curation Expert Panel (GCEP), comprising 40 international PMD experts, met monthly for 4 years to review GDRs for LSS. The GCEP standardized gene curation for LSS by refining the phenotypic definition, modifying the ClinGen Gene-Disease Clinical Validity Curation Framework to improve interpretation for LSS, and establishing a scoring rubric for LSS. The GDR with LSS across the nuclear and mitochondrial genomes was classified as definitive for 31 of 114 GDRs curated (27%), moderate for 38 (33%), limited for 43 (38%), and disputed for 2 (2%). Ninety genes were associated with autosomal recessive inheritance, 16 were maternally inherited, 5 were autosomal dominant, and 3 were X-linked. GDRs for LSS were established for genes across both nuclear and mitochondrial genomes. Establishing these GDRs will allow accurate variant interpretation, expedite genetic diagnosis of LSS, and facilitate precision medicine, multisystem organ surveillance, recurrence risk counseling, reproductive choice, natural history studies, and determination of eligibility for interventional clinical trials. ANN NEUROL 2023;94:696-712.

Diagnosis and Molecular Pathology of Lymphoblastic Leukemias and Lymphomas in the Era of Genomics and Precision Medicine: Historical Evolution and Current Concepts—Part 2: B-/T-Cell Acute Lymphoblastic Leukemias

The diagnosis and treatment of lymphoid neoplasms have undergone a continuously progressive positive change in the last three decades, with accelerated progress in the previous decade due to the advent of genomics in cancer diagnosis. Significantly, there has been an increasing emphasis on integrating molecular genetics with clinical, morphological, immunophenotypic, and cytogenetic evaluation for diagnosis. As we think of moving forward with further advances in the genomics era, it will be first helpful to understand our current state of knowledge and how we achieved it in the challenging and complex field of lymphoid neoplasms, which comprise very heterogeneous neoplastic diseases in children and adults, including clinically acute lymphoblastic leukemias (ALLs) arising from precursor lymphoid cells and clinically indolent and aggressive lymphomas arising from mature lymphoid cells. This work aims to provide an overview of the historical evolution and the current state of knowledge to anyone interested in the field of lymphoid neoplasms, including students, physicians, and researchers. Therefore, I have discussed this complex topic in three review manuscripts, designated Parts 1–3. In Part 1, I explain the basis of the diagnostic classification of lymphoid neoplasms and its evolution up to the current fifth edition of the World Health Organization classification of hematolymphoid neoplasms and the crucial importance of diagnostic tumor classifications in achieving and advancing patient care and precision medicine. In the second and third manuscripts, I discuss current diagnostic considerations for B-ALL and T-ALL (Part 2) and common indolent and aggressive mature leukemias/lymphomas (Part 3), including significant updates in the WHO 2022 classification, newly described entities, and concepts, including genetic predisposition to ALLs and lymphomas, and emphasizing throughout the essential integration of molecular genetics with clinical, morphologic, immunophenotypic, and cytogenetic evaluation, as required for the precise diagnosis of the type of lymphoma/leukemia in any patient.

The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location.

The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature of evolution. Examples of both adaptive and deleterious introgression exist in a variety of systems. What is unclear is how the fitness of an introgressing haplotype changes as species diverge or as the size of the introgressing haplotype changes. In a simple model, we show that introgression may more easily occur into parts of the genome which have not diverged heavily from a common ancestor. The key insight is that alleles from a shared genetic background are likely to have positive epistatic interactions, increasing the fitness of a larger introgressing block. In regions of the genome where few existing substitutions are disrupted, this positive epistasis can be larger than incompatibilities with the recipient genome. Further, we show that early in the process of divergence, introgression of large haplotypes can be favored more than introgression of individual alleles. This model is consistent with observations of a positive relationship between recombination rate and introgression frequency across the genome; however, it generates several novel predictions. First, the model suggests that the relationship between recombination rate and introgression may not exist, or may be negative, in recently diverged species pairs. Furthermore, the model suggests that introgression that replaces existing derived variation will be more deleterious than introgression at sites carrying ancestral variants. These predictions are tested in an example of introgression in Drosophila melanogaster, with some support for both. Finally, the model provides a potential alternative explanation to asymmetry in the direction of introgression, with expectations of higher introgression from rapidly diverged populations into slowly evolving ones.

Precision Medicine and Artificial Intelligence: Challenges and Potential in the Post-Human Genome Era

Precision Medicine and Artificial Intelligence: Challenges and Potential in the Post-Human Genome Era

ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data.

In the genomic era, data dissemination and visualization is an integral part of scientific publications and research projects involving international consortia producing massive genome-wide data sets, intra-organizational collaborations, or individual labs. However, creating custom supporting websites is oftentimes impractical due to the required programming effort, web server infrastructure, and data storage facilities, as well as the long-term maintenance burden. ZENBU-Reports (https://fantom.gsc.riken.jp/zenbu/reports) is a web application to create interactive scientific web portals by using graphical interfaces while providing storage and secured collaborative sharing for data uploaded by users. ZENBU-Reports provides the scientific visualization elements commonly used in supplementary websites, publications and presentations, presenting a complete solution for the interactive display and dissemination of data and analysis results during the full lifespan of a scientific project both during the active research phase and after publication of the results.

Roof of the world: Home and border in the genomic era

Himalaya and the Tibetan Plateau, known as the ‘land of snow’ and the ‘roof of the world’, is home to tens of millions of indigenous people who live with a staggering amount of biological diversity. In the past decade scientists have applied genomic tools and methods to substantially advance the understanding of phylogeography and genetic mechanisms behind high‐elevation adaptation of local biota. However, contributions from indigenous researchers and native institutions are underrepresented in this scientific endeavour. We point to the higher degree of indigenous contribution within the discipline of conservation biology and how recognizing the prominence of traditional ecological knowledge (TEK) could deliver keen molecular ecological insights. Since the Himalaya‐Tibet ecological interface spans five countries, comprehensive biogeographical and phylogeographical taxon sampling in the region requires multi‐national collaborations across indigenous lands as well as indigenous community participation at both national and international levels. For the next generation of indigenous molecular ecologists, researching and cataloguing the evolutionary history and genetic information of the Tibetan and Himalayan landscape is a race against the melting glacier. At the roof of the world, their scientific judgement and stewardship will have environmental impacts that percolate far beyond indigenous lands.

DNA Fingerprinting of Crops and Its Significance in Crop Improvement

One of the improvements made possible by the era of genomics is DNA fingerprinting. DNA fingerprinting can be used to detect a variety of genetic changes. In breeding programmes fingerprinting is used to improve productivity and performance. Variety differentiation was relied on morphological characteristics prior to the introduction of genomics and proteomics approaches. Although morphological markers have been used for decades, protein-based markers like isozymes were discovered in the middle of the twentieth century and used for fingerprinting and crop genetic variety assessments. But nowadays, the emergence of genome sequencing has led to the widespread use of genetic markers for crop fingerprinting. The discovery of DNA-based genetic markers has improved genetic research. For genetic diversity estimation, crop evolution, gene mapping and phylogeny, diploid/haploid crop appraisal, heterosis analysis, varietal identification by using marker assisted selection (MAS), highly polymorphic DNA markers are generated. The use of DNA markers for crop fingerprinting started with RFLPs that did not involve PCR and subsequently advanced to PCR amplifiable markers such as AFLPs, RAPDs, SSRs, ISSRs, SNPs, and GBS.This review will provide an outlook on several types of markers and their significance in DNA fingerprinting of crops and possible applications, as well as suggestions for further research.

Diagnosis and Molecular Pathology of Lymphoblastic Leukemias and Lymphomas in the Era of Genomics and Precision Medicine: Historical Evolution and Current Concepts—Part 1: Lymphoid Neoplasms

The diagnosis and treatment of lymphoid neoplasms have undergone a progressively positive change in the last three decades, with accelerated progress in the previous decade due to the advent of genomics in cancer diagnosis. Significantly, there has been an increasing emphasis on integrating molecular genetics with clinical, morphologic, immunophenotypic, and cytogenetic evaluation for diagnosis. As we consider moving forward with further advances in the genomics era, it is first helpful to understand our current state of knowledge and how we achieved it in the challenging and complex field of lymphoid neoplasms, which comprise very heterogeneous neoplastic diseases in children and adults, including clinically acute lymphoblastic leukemias (ALLs) arising from precursor lymphoid cells and clinically indolent and aggressive lymphomas arising from mature lymphoid cells. This work aims to provide an overview of the historical evolution and the current state of knowledge to anyone interested in the field of lymphoid neoplasms, including students, physicians, and researchers. Therefore, I have discussed this complex topic in three review manuscripts, designated Parts 1–3. In Part 1, I explain the basis of the diagnostic classification of lymphoid neoplasms and its evolution up to the current fifth edition of the World Health Organization (WHO) classification of hematolymphoid neoplasms and the crucial importance of diagnostic tumor classifications in achieving and advancing patient care and precision medicine. In the second and third manuscripts, I discuss current diagnostic considerations for B-ALL and T-ALL (Part 2) and common indolent and aggressive mature leukemias/lymphomas (Part 3), including significant updates in the WHO 2022 classification, newly described entities and concepts, including genetic predisposition to ALLs and lymphomas, and throughout emphasizing the essential integration of molecular genetics with clinical, morphologic (pathologic), immunophenotypic, and cytogenetic evaluation, as is required for precise diagnosis of the type of lymphoma/leukemia in any patient.

A PacBio Hi-Fi Genome Assembly of the Painter's Mussel Unio pictorum (Linnaeus, 1758).

The highly diverse group of freshwater mussels from order Unionida is found in the world's freshwater systems due to several fascinating evolutionary adaptations, including "parental care," and most notably, an obligatory parasitic phase in their early life cycle, called glochidia, which infests and uses fish for nutrition and dispersal. Freshwater mussels play essential ecological roles in freshwater habitats, including water filtration, sediment bioturbation, and nutrient cycling. However, these species are also highly threatened, being one of the faunal groups with the highest recorded extinction rate in the wild. Genomics methods have an incredible potential to promote biodiversity conservation, allowing the characterization of population health, identification of adaptive genetic elements, delineation of conservation units, and providing a framework for predictive assessments of the impact of anthropogenic threats and climate change. Unfortunately, only six freshwater mussel species have had their whole genomes sequenced to date, and only two of these are European species. Here, we present the first genome assembly of the Painter's Mussel, Unio pictorum (Linnaeus, 1758), the type species representative of the order and the most widespread species of the genus in Europe. We used long-read PacBio Hi-Fi sequencing reads to produce a highly contiguous assembly that will pave the way for the study of European freshwater mussels in the Genome Era.

A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History.

Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.

Metabolic Studies in Genomic Era

Metabolic Studies in Genomic Era

The Role of Genetic Counselling in Genomic Era

The Role of Genetic Counselling in Genomic Era

Sixth International Conference on Duckweed Research and Applications Presents Lemnaceae as a Model Plant System in the Genomics and Postgenomics Era.

The 6th International Conference on Duckweed Research and Applications (6th ICDRA) was organized at the Institute of Plant Genetics and Crop Plant Research (IPK) located in Gatersleben, Germany, from 29 May to 1 June 2022. The growing community of duckweed research and application specialists was noted with participants from 21 different countries including an increased share of newly integrated young researchers. The four-day conference focused on diverse aspects of basic and applied research together with practical applications of these tiny aquatic plants that could have an enormous potential for biomass production.

Global developmental delay and intellectual disability in the era of genomics: Diagnosis and challenges in resource limited areas

AimsTo report the diagnostic yield of clinical singleton whole exome sequencing (WES) performed among a group of Jordanian children presenting with global developmental delay /intellectual disability (GDD/ID), discuss the underlying identified genetic disorders and the challenges encountered. Patients and methodsThis retrospective medical record review study included 154 children who were diagnosed with GDD/ID at our clinic at Jordan University Hospital between 2016 and 2021, and whose diagnostic work up included WES. ResultsConsanguinity among parents was reported in 94/154 (61.0%) patients and history of other affected siblings in 35/154 (22.7%) patients.Pathogenic and likely pathogenic variants (solved cases) were reported in 69/154 (44.8%) patients, a variant of uncertain significance was reported in 54/154 (35.0%) and a negative result was reported in 31/154 (20.1%) cases.In the solved cases, autosomal recessive diseases were the most common (33/69; 47.8%). Metabolic disorders were identified in 20/69 (28.9%) patients, followed by developmental and epileptic encephalopathies (9/69; 13.0%) and MECP2 related disorders (7/69; 10.1%). Other single gene disorders were identified in 33/69; 47.8%) patients. ConclusionThis study had several limitations, as it was hospital-based and only including patients who were able to afford the test. Nevertheless, it yielded several important findings. In resource-limited countries, WES may be a reasonable approach. We discussed the challenges that clinicians meet in the context of shortage of resources.

Understanding and modeling human traits and diseases: Insights from the comparative genomics resources of Zoonomia

Understanding and modeling human traits and diseases: Insights from the comparative genomics resources of Zoonomia

Advances in Synthetic Biology of Fungi and Contributions to the Discovery of New Molecules.

The sequencing of fungal genomes is becoming increasingly accessible, with a wealth of data already available. In parallel, the prediction of the putative biosynthetic pathways responsible for the synthesis of potential new natural products is also increasing. The difficulty of translating computational analyses into available compounds is becoming evident, slowing down a process that was thought to be faster with the advent of the genomic era. Advances in gene techniques made it possible to genetically modify a wider range of organisms, including fungi typically considered recalcitrant to DNA manipulation. However, the possibility of screening many gene cluster products for new activities in a high-throughput manner remains unfeasible. Nonetheless, some updates on the synthetic biology of fungi could provide interesting insights that could help to achieve this goal in the future.

Not just a GIST: an unclassifiable neoplasm in the genomics era

Unclassifiable primary tumors despite adequate tissue for pathologic examination are quite rare. We present a case of a 72-year-old female who was found to have an abdominal mass after she reported to the emergency department with complaints of abdominal pain with spasms, bloating and nausea. Computed tomography scan demonstrated a 12.3 × 15.7 × 15.9 large multilobulated mass, abutting and compressing the stomach, compatible with neoplasm. She underwent esophagogastroduodenoscopy with findings concerning for gastrointestinal stromal tumor. The patient underwent en bloc resection of the mass. The neoplasm was unable to be classified on pathologic examination despite a comprehensive workup and multiple consultations with specialized pathologists from local institutions, as well as national specialists. Final pathology was unclassified malignant neoplasm displaying calretinin expression only. This presents a difficult clinical entity to treat. Even in the genomics era, there are tumors that cannot be even broadly classified on pathologic examination.