Genome Sequencing Technologies Research Articles

Delivering paediatric precision medicine: Genomic and environmental considerations along the causal pathway of childhood neurodevelopmental disorders.

Precision medicine refers to treatments that are targeted to an individual's unique characteristics. Precision medicine for neurodevelopmental disorders (such as cerebral palsy, attention‐deficit/hyperactivity disorder, obsessive–compulsive disorder, Tourette syndrome, and autism spectrum disorder) in children has predominantly focused on advances in genomic sequencing technologies to increase our ability to identify single gene mutations, diagnose a multitude of rare neurodevelopmental disorders, and gain insights into pathogenesis. Although targeting specific gene variants with high penetrance will help some children with rare disease, this approach will not help most children with neurodevelopmental disorders. A ‘pathway’ driven approach targeting the cumulative influence of psychosocial, epigenetic, or cellular factors is likely to be more effective. To optimize the therapeutic potential of precision medicine, we present a biopsychosocial integrated framework to examine the ‘gene–environment neuroscience interaction’. Such an approach would be supported through harnessing the power of big data, transdiagnostic assessment, impact and implementation evaluation, and a bench‐to‐bedside scientific discovery agenda with ongoing clinician and patient engagement.What this paper adds Precision medicine has predominantly focused on genetic risk factors.The impact of environmental risk factors, particularly inflammatory, metabolic, and psychosocial risks, is understudied.A holistic biopsychosocial model of neurodevelopmental disorder causal pathways is presented.The model will provide precision medicine across the full spectrum of neurodevelopmental disorders.

Genetic basis of speciation and adaptation: from loci to causative mutations.

Does evolution proceed in small steps or large leaps? How repeatable is evolution? How constrained is the evolutionary process? Answering these long-standing questions in evolutionary biology is indispensable for both understanding how extant biodiversity has evolved and predicting how organisms and ecosystems will respond to changing environments in the future. Understanding the genetic basis of phenotypic diversification and speciation in natural populations is key to properly answering these questions. The leap forward in genome sequencing technologies has made it increasingly easier to not only investigate the genetic architecture but also identify the variant sites underlying adaptation and speciation in natural populations. Furthermore, recent advances in genome editing technologies are making it possible to investigate the functions of each candidate gene in organisms from natural populations. In this article, we discuss how these recent technological advances enable the analysis of causative genes and mutations and how such analysis can help answer long-standing evolutionary biology questions.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.

Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data.

Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.

The Burden and Benefits of Knowledge: Ethical Considerations Surrounding Population-Based Newborn Genome Screening for Hearing.

Recent advances in genomic sequencing technologies have expanded practitioners’ utilization of genetic information in a timely and efficient manner for an accurate diagnosis. With an ever-increasing resource of genomic data from progress in the interpretation of genome sequences, clinicians face decisions about how and when genomic information should be presented to families, and at what potential expense. Presently, there is limited knowledge or experience in establishing the value of implementing genome sequencing into newborn screening. Herein we provide insight into the complexities and the burden and benefits of knowledge resulting from genome sequencing of newborns.

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology.

Advances in genome sequencing technologies have unlocked new possibilities in identifying disease-associated and causative genetic markers, which may in turn enhance disease diagnosis and improve prognostication and management strategies. With the capability of examining genetic variations ranging from single-nucleotide mutations to large structural variants, whole-genome sequencing (WGS) is an increasingly adopted approach to dissect the complex genetic architecture of neurologic diseases. There is emerging evidence for different structural variants and their roles in major neurologic and neurodevelopmental diseases. This review first describes different structural variants and their implicated roles in major neurologic and neurodevelopmental diseases, and then discusses the clinical relevance of WGS applications in neurology. Notably, WGS-based detection of structural variants has shown promising potential in enhancing diagnostic power of genetic tests in clinical settings. Ongoing WGS-based research in structural variations and quantifying mutational constraints can also yield clinical benefits by improving variant interpretation and disease diagnosis, while supporting biomarker discovery and therapeutic development. As a result, wider integration of WGS technologies into health care will likely increase diagnostic yields in difficult-to-diagnose conditions and define potential therapeutic targets or intervention points for genome-editing strategies.

Systemic Therapy of Metastatic Pancreatic Adenocarcinoma: Current Status, Challenges, and Opportunities.

Simple SummaryPancreatic ductal adenocarcinoma (PDAC) is a common type of cancer originating from the pancreatic glands and is characterized by a rapidly progressive course and a dismal prognosis. Currently, chemotherapy is the cornerstone of treatment that has modest efficacy. Targeted treatment options are rapidly evolving with the growing understanding of pathobiological underpinnings of tumorigenesis, progression, and treatment resistance mechanisms. Combination strategies targeting multiple signaling pathways supporting tumor growth and propagation are active areas of contemporary research that will likely transform the treatment paradigm of pancreatic cancer.Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by nonspecific presenting symptoms, lack of a screening test, rapidly progressive clinical course, and presentation with an advanced-stage disease in the majority of patients. PDAC is essentially a systemic disease irrespective of the initial stage, as most patients with non-metastatic PDAC undergoing curative-intent treatment eventually experience metastatic relapse. Currently, cytotoxic chemotherapy remains the cornerstone of treatment in patients with advanced disease. However, the current standard treatment with multiagent chemotherapy has modest efficacy and results in median overall survival (OS) of less than a year and a 5-year OS of about 10%. The pathobiology of PDAC poses many challenges, including a unique tumor microenvironment interfering with drug delivery, intratumoral heterogeneity, and a strongly immunosuppressive microenvironment that supports cancer growth. Recent research is exploring a wide range of novel therapeutic targets, including genomic alterations, tumor microenvironment, and tumor metabolism. The rapid evolution of tumor genome sequencing technologies paves the way for personalized, targeted therapies. The present review summarizes the current chemotherapeutic treatment paradigm of advanced PDAC and discusses the evolving novel targets that are being investigated in a myriad of clinical trials.

Microbiota in Goat Buck Ejaculates Differs Between Breeding and Non-breeding Seasons.

Changes in semen microbiota are associated with alterations to sperm quality and fertility. However, the microbiota from most livestock species has not yet been studied. Goats are seasonal breeders, but semen microbiota has never been described in this species, and it is unknown how seasonality affects it. Our study objective is 2-fold: to describe the microbiota in goat buck ejaculates and to determine if it differs between breeding and non-breeding seasons. Semen from six males of the Murciano-Granadina breed was collected during both seasons. Two replicates were performed per male and season on different days. The microbiota was characterized by genomic sequencing technology. Sperm quality was also evaluated. Repetition was not significant for the studied variables. Sperm velocities were higher for the breeding than for the non-breeding season. The ejaculates from both seasons also differed in the proportion of apoptotic spermatozoa. The five dominant phyla were Firmicutes, Proteobacteria, Fusobacteria, Actinobacteria, and Bacteroidetes during the breeding season and Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria during the non-breeding season. The dominant genus during both seasons was Ureaplasma. Differences in microbial community structure (the beta diversity) were found. A decrease in the relative abundance of the genus Faecalibacterium and an increase in the genera Sphingomonas and Halomonas were observed in the ejaculates collected during the breeding season. Sphingomonas and Faecalibacterium abundance favorably and unfavorably correlated with sperm quality, respectively. In conclusion, the semen microbiota from goat bucks varies between breeding and non-breeding seasons, and the microbiota remains stable for 7 days within a season. In addition, the genera Sphingomonas and Faecalibacterium could be possible biomarkers of semen quality in goat bucks. These results contribute to an in-depth understanding of the effects of reproductive seasonality on goat buck ejaculates.

Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States

This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety.

Multiplex PCR method for simultaneous identification of Xanthii Fructus and its adulterants

The purpose of this study is to establish a molecular method to identify Xanthii Fructus and two adulterants, the fruits of Xanthium mongolicum and X. italicum. Xanthii Fructus is the fruit of X. sibiricum, which is a Chinese herbal medicine used clinically to treat allergic rhinitis. The fruits of X. mongolicum and X. italicum have strong morphological similarities with Xanthii Fructus, while their safety of medication cannot be guaranteed. The genomes of X. sibiricum, X. mongolicum, and X. italicum were sequenced, which generated sequences of 2.21, 2.24, and 2.54 Gb, respectively. Based on the 76 specific contigs screened out by BLASTN and Bowtie 2, the corresponding primers were designed by Primer 5.0. Three pairs of primers with stable amplification efficiency and good reproducibility were screened out to establish a multiplex PCR method based on the PCR amplification results. Further, the annealing temperature, the amount of DNA template, the number of cycles, different DNA polymerases, and different PCR thermal cyclers were optimized. Fragments of 262 bp and 458 bp from X. sibiricum, 260, 454, and 927 bp from X. mongolicum, and 260 bp and 926 bp from X. italicum were amplified under the following conditions: the annealing temperature of 52 ℃, 35 cycles, 30 ng template DNA. Then, the established method was used to detect 18 samples of X. sibiricum, 17 samples of X. mongolicum, and 12 samples of X. italicum. The results showed that all the samples had positive results, which were consistent with the morphological identification results, thus proving the stability and reliability of the established method. Combining genome sequencing technology and multiplex PCR method to identify Xanthii Fructus and its adulterants can not only obtain the difference in genetic background but also facilitate the design of reliable primers. The multiplex PCR have high specificity and repeatability, providing a new method for the molecular identification of Xanthii Fructus.

Optimizing the clinical management of EGFR-mutant advanced non-small cell lung cancer: a literature review.

Background and ObjectiveDespite several steps forward in the treatment of epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC), however there are still pending issues and upcoming challenges requiring adequate addressing in order to optimize the clinical management of metastatic patients harboring molecular alterations within the EGFR gene. This review aims to summarize the most recent findings regarding the diagnostic testing and therapeutic strategies of EGFR-mutant advanced NSCLC.MethodsLiterature search was conducted using MEDLINE/PubMed, EMBASE, Scopus and Cochrane Library databases, up to December 2021. Relevant studies in English language published between 2004 and 2021 were selected.Key Content and FindingsThe increased detection of uncommon EGFR mutations in the real-word practice along with the clinical development of novel selective inhibitors, highlighted the issue of an adequate selection of the best EGFR-tyrosine-kinase inhibitor (TKI) to the right patient mutation. The advent of osimertinib in first-line has dramatically changed the spectrum of molecular mechanisms underlying both innate and acquired resistance to the EGFR-TKI therapy, accelerating the clinical investigation of novel genomic-driven sequential strategies as well as upfront targeted combinations. The recent approval of potent, selective inhibitors targeting the EGFR exon-20 insertions, renewed interest toward this patients’ subset, questioning the diagnostic accuracy of old-standard genomic sequencing technologies and pushing the implementations of next-generation sequencing (NGS)-based molecular profiling in the real word practice scenario.ConclusionsThis review provides evidence-based answers to the aforementioned challenges aiming to optimize the clinical management of metastatic patients harboring molecular alterations within the EGFR gene.

GFI1 KO can develop allergic reaction independently from IL5 and ILC2 cells

Abstract The number of people living with a chronic inflammatory lung disease, such as asthma, is constantly increasing. The development of resistance to existing therapies and the fact that exposure to air pollution and particular matter are continuously increasing have made asthma a major health problem worldwide. We have observed that in mice lacking the transcriptional factor GFI1 (short for “Growth factor independent 1”) where ILC2 are not functional and IL5 is almost absent, a severe asthmatic inflammatory reaction can still be provoked with increased numbers of eosinophils in the airways. This finding strongly suggests that pathways other than those initiated by IL5/IL5R and ILC2 cells exist that play a major role in severe allergic asthma. We hypothesize that the situation in GFI1 KO mice reflects what it is observed in asthmatic patients that are resistant to the recent therapies. We further posit that GFI1 KO mice is a tool to discover new pathways involved in asthmatic reactions different from the known and established mechanisms involving IL5. We are using this unique mouse model (Gfi1 deficient mice) and high throughput genomic sequencing technologies with a specific bioinformatics approach to identify new molecules pathways mediating the inflammatory reaction in asthma. We expect to reveal new molecular signaling pathways that cause lung inflammation during an allergic asthma reaction, specifically those regulating eosinophil recruitment and activities. Our first results show that GFI1 KO seem to be able to support an allergic reaction though IL17 pathway and Th17 cells. We anticipate to identify of molecular targets, which could be used to develop new, more effective therapies for patients with severe allergic asthma.

Alisol B23‐Acetate Targets SHH Signaling in MED12 Knockdown Breast Cancer Cells to Inhibit Oncogenesis

Breast cancer currently ranks second in leading causes of death in women in the United States. It is estimated that one in eight women will develop breast cancer over the course of their life, so finding treatment options for this disease is critical. Current treatment strategies include chemotherapy, radiation, and surgery, all of which can cause harmful side effects that can be damaging to the patient’s overall health. Furthermore, these strategies are not always effective, so personalized treatment has become an area of interest to those who are searching for alternative treatment options. With the current genome sequencing technology that is available, researchers are able to identify specific locations in the DNA that could be a potential target area for treatment. One of those locations is the Mediator subunit MED12 that has been shown to be mutated in up to 67% of breast cancer tumors. Our results from previous experiments show mutations in MED12 promote GLI3‐dependent Sonic Hedgehog (SHH) signaling, thus indicating that tumor cells could potentially use this pathway to proliferate when MED12 is mutated. With these findings we hypothesize that MED12 mutations promote hyperactivated SHH signaling in breast cancer cells and that the compound Alisol B 23‐acetate (AB23A), a natural triterpenoid, can target SHH signaling in these cells to suppress oncogenesis. To study the effects of MED12 mutation, the MCF‐7 breast cancer cell line was infected with a lentivirus carrying a shRNA targeted against MED12. Most MED12 mutations in breast cancer cells lead to a loss of function in the protein, so we presume that a knockdown of MED12 would lead to similar presentation that is seen in tumors. To test for the effects of this knockdown on cell growth, proliferation assays were conducted which confirmed that MED12 knockdown promotes oncogenesis. Quantitative PCR was then conducted to determine the effects of MED12 on GLI3 target genes. Our results show that when MED12 is knocked down, there is an increase in the expression of GLI3 target genes. Next, MTT assays were performed to determine the effects of AB23A on both MCF‐7 control and MCF‐7 MED12 knockdown cells. These results indicate that AB23A does not affect the viability of MCF‐7 control cells but does promote cell death in MCF‐7 MED12 knockdown cells. Furthermore, through quantitative PCR analysis, we found that AB23A specifically promotes downregulation of GLI3 target genes, thus indicating that this compound likely targets the GLI3‐dependent SHH signaling pathway. Overall, these results provide insight into AB23A as a potential therapeutic treatment for breast cancer with MED12 mutations.

CRISPR/Cas9-Based Genome Editing and Its Application in Aspergillus Species.

Aspergillus, a genus of filamentous fungi, is extensively distributed in nature and plays crucial roles in the decomposition of organic materials as an important environmental microorganism as well as in the traditional fermentation and food processing industries. Furthermore, due to their strong potential to secrete a large variety of hydrolytic enzymes and other natural products by manipulating gene expression and/or introducing new biosynthetic pathways, several Aspergillus species have been widely exploited as microbial cell factories. In recent years, with the development of next-generation genome sequencing technology and genetic engineering methods, the production and utilization of various homo-/heterologous-proteins and natural products in Aspergillus species have been well studied. As a newly developed genome editing technology, the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system has been used to edit and modify genes in Aspergilli. So far, the CRISPR/Cas9-based approach has been widely employed to improve the efficiency of gene modification in the strain type Aspergillus nidulans and other industrially important and pathogenic Aspergillus species, including Aspergillus oryzae, Aspergillus niger, and Aspergillus fumigatus. This review highlights the current development of CRISPR/Cas9-based genome editing technology and its application in basic research and the production of recombination proteins and natural products in the Aspergillus species.

Multi-Omics Techniques for Soybean Molecular Breeding.

Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.

Construction of a high-density genetic map and identification of QTLs related to agronomic and physiological traits in an interspecific (Gossypium hirsutum\u2009\xd7\u2009Gossypium barbadense) F2 population

BackgroundAdvances in genome sequencing technology, particularly restriction-site associated DNA sequence (RAD-seq) and whole-genome resequencing, have greatly aided the construction of cotton interspecific genetic maps based on single nucleotide polymorphism (SNPs), Indels, and other types of markers. High-density genetic maps can improve accuracy of quantitative trait locus (QTL) mapping, narrow down location intervals, and facilitate identification of the candidate genes.ResultIn this study, 249 individuals from an interspecific F2 population (TM-1 and Hai7124) were re-sequenced, yielding 6303 high-confidence bin markers spanning 5057.13 cM across 26 cotton chromosomes. A total of 3380 recombination hot regions RHRs were identified which unevenly distributed on the 26 chromosomes. Based on this map, 112 QTLs relating to agronomic and physiological traits from seedling to boll opening stage were identified, including 15 loci associated with 14 traits that contained genes harboring nonsynonymous SNPs. We analyzed the sequence and expression of these ten candidate genes and discovered that GhRHD3 (GH_D10G0500) may affect fiber yield while GhGPAT6 (GH_D04G1426) may affect photosynthesis efficiency.ConclusionOur research illustrates the efficiency of constructing a genetic map using binmap and QTL mapping on the basis of a certain size of the early-generation population. High-density genetic map features high recombination exchanges in number and distribution. The QTLs and the candidate genes identified based on this high-density genetic map may provide important gene resources for the genetic improvement of cotton.

Plotsr: visualizing structural similarities and rearrangements between multiple genomes.

SummaryThird-generation genome sequencing technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands new tools for visualizing their structural properties. Here, we present plotsr, an efficient tool to visualize structural similarities and rearrangements between genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualization with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density).Availability and implementationplotsr is implemented as a python package and uses the standard matplotlib library for plotting. It is freely available under the MIT license at GitHub (https://github.com/schneebergerlab/plotsr) and bioconda (https://anaconda.org/bioconda/plotsr).Supplementary information Supplementary data are available at Bioinformatics online.

Moving from 'fully' to 'appropriately' informed consent in genomics: The PROMICE framework.

Genomic sequencing technologies (GS) pose novel challenges not seen in older genetic technologies, making traditional standards for fully informed consent difficult or impossible to meet. This is due to factors including the complexity of the test and the broad range of results it may identify. Meaningful informed consent is even more challenging to secure in contexts involving significant time constraints and emotional distress, such as when rapid genomic testing (RGS) is performed in neonatal intensive care units. In this article, we propose that informed consent matters not for its own sake, but because obtaining it furthers a range of morally important goals, such as promoting autonomy, well‐being, and trust in medicine. These goals form the basis of a new framework [PROmoting Morally Important Consent Ends (PROMICE)] for assessing the ethical appropriateness of various informed consent models. We illustrate this framework with two examples: (a) a tiered and layered consent model for obtaining consent for GS, and (b) consent for RGS in critically ill newborns. We conclude that appropriately—rather than fully—informed consent provides the correct standard for genomic medicine and research.

16p13.11p11.2 triplication syndrome: a new recognizable genomic disorder characterized by optical genome mapping and whole genome sequencing.

Highly identical segmental duplications (SDs) account for over 5% of the human genome and are enriched in the short arm of the chromosome 16. These SDs are susceptibility factors for recurrent chromosomal rearrangements mediated by non-allelic homologous recombination (NAHR). Chromosomal microarray analysis (CMA) has been widely used as the first-tier test for individuals with developmental disabilities and/or congenital anomalies and several genomic disorders involving the 16p-arm have been identified with this technique. However, the resolution of CMA and the limitations of short-reads whole genome sequencing (WGS) technology do not allow the full characterization of the most complex chromosomal rearrangements. Herein, we report on two unrelated patients with a de novo 16p13.11p11.2 triplication associated with a 16p11.2 duplication, detected by CMA. These patients share a similar phenotype including hypotonia, severe neurodevelopmental delay with profound speech impairment, hyperkinetic behavior, conductive hearing loss, and distinctive facial features. Short-reads WGS could not map precisely any of the rearrangement's breakpoints that lie within SDs. We used optical genome mapping (OGM) to determine the relative orientation of the triplicated and duplicated segments as well as the genomic positions of the breakpoints, allowing us to propose a mechanism involving recombination between allelic SDs and a NAHR event. In conclusion, we report a new clinically recognizable genomic disorder. In addition, the mechanism of these complex chromosomal rearrangements involving SDs could be unraveled by OGM.

BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins.

Pesticidal proteins derived from the bacterium Bacillus thuringiensis, have provided the bases for a diverse array of pest management tools ranging from natural products used in organic agriculture, to modern biotechnological approaches. With advances in genome sequencing technologies and protein structure determination, an increasing number of pesticidal proteins from myriad bacterial species have been identified. The Bacterial Pesticidal Protein Resource Center (BPPRC) has been established to provide informational and analytical resources on the wide range of pesticidal proteins derived from bacteria that have potential utility for arthropod management. In association with a revised nomenclature for these proteins, BPPRC contains a database that allows users to browse and download sequences. Users can search the database for the best matches to sequences of interest and can incorporate their own sequences into basic informatic analyses. These analyses include the ability to draw and export guide trees from either whole protein sequences or, in the case of the three-domain Cry proteins, from individual domains. The associated website also provides a portal for users to submit protein sequences for naming. The BPPRC provides a single authoritative source of information to which all stakeholders can be referred including academics, government regulatory bodies and research and development personnel in the industrial sector. The database provides information on more than 1060 pesticidal proteins derived from 13 species of bacteria, including insecticidal activities for a subset of these proteins. Database URL: www.bpprc.org and www.bpprc-db.org/

Biotechnological Advancements in Coriander (Coriandrum sativum L.)

Coriander (Coriandrum sativum L.), one of the oldest essential oil-bearing spice and medicinal plants in the world, is widely used in folk medicine and seasoning in food. Thanks to its phytochemicals that have various bioactivity, recently, lots of studies have been conducted on coriander breeding. Classical breeding studies led to the development of new varieties over time. These studies could not accelerate the improvements in some of the plant parameters such as essential oil yield, biotic-abiotic stress resistance, and some other quality characteristics. In this respect, it is very important to conduct basic research on modern breeding programs to determine the yield and quality performance of coriander. Although coriander cultivation is carried out in different parts of the world today, genetic studies on coriander breeding are limited. Studies conducted with genome sequencing technology and molecular markers, the genetic diversity and population structure of the coriander were investigated, and a certain amount of progress was obtained for coriander breeding. This review aims to highlight the importance of coriander biotechnological advancements for coriander breeding. In the light of this information, biotechnological solutions can be enhanced coriander breeding. The review will provide more practical information for coriander researchers.