Reference Genome Research Articles

Association of Single-Nucleotide Variants in ACE2 with the Persistence of Positive qPCR Test for SARS-CoV-2 in Healthcare Professionals During the First Wave of the COVID-19 Pandemic.

The persistence of qPCR positivity for SARS-CoV-2 in individuals who recovered from COVID-19 raised several questions regarding viral transmission, with a special interest in healthcare professionals who may pose a risk of transmitting SARS-CoV-2. This issue highlights the necessity for identifying the genetic risk factors associated with persistent SARS-CoV-2 infection. A promising target for achieving this goal is the angiotensin-converting enzyme 2 (ACE2) gene, which has been associated with clinical characteristics of COVID-19 infection, such as severity. The analysis of samples from the first wave of the COVID-19 pandemic represents the initial response of the immune human system against this new virus, without the effect of vaccination or the presence of multiple strains. The aim of this study was to analyze the association of genetic variants in ACE2 with persistent SARS-CoV-2 infection. We conducted a case-control study, including 151 healthcare workers who tested positive for SARS-CoV-2 by qPCR during the first wave of the COVID-19 pandemic, and who were followed up until their results were negative. ACE2 was sequenced through Sanger sequencing. The sequence was compared against a reference sequence and variants identified. Four ACE2 variants were associated with persistent SARS-CoV-2 qPCR positivity. Three of the variants with an effect on the resulting protein were associated with increased risk of persistent SARS-CoV-2 qPCR positivity, NG_012575.2:g.35481 C>T, NG_012575.2:g.35483 G>T and NG_012575.2:g.35498 G>T. On the other hand, the rs2285666 (NG_012575.2:g.14934 G>A) was associated with a higher risk for persistent SARS-CoV-2 qPCR positivity in women and rs4646150 (NG_012575.2:g.25701 G>A) in men. The NG_012575.2:g.35498 G>T variant represents an amino acid change with a possibly harmful effect on ACE2 function. Our results suggest that ACE2 variants might be useful for identifying the population at higher risk for developing persistent SARS-CoV-2-positive qPCR results. This knowledge can be helpful for designing health policies for protecting healthcare professionals and, in consequence, users of health services.

Jan and mini-Jan, a model system for potato functional genomics.

Potato ( Solanum tuberosum ) is the third most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags relative to other major food crops due primarily to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan', which possesses all essential characteristics for facile functional genomics studies. Jan has a high level of homozygosity after seven generations of self-pollination. Jan is vigorous and highly fertile with outstanding tuber traits, high regeneration rates, and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated genes, and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two "mini-Jan" lines with compact and dwarf plant stature using CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes related to growth. Mini-Jan mutants are fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan provide an outstanding model system that can be leveraged for gene editing and functional genomics research in potato.

Enhancing aluminium resistance in wheat ( Triticum aestivum L.) by exploring for novel genes in the wheat genome

Abstract Aluminium (Al 3+ ) toxicity is a major constraint to crop production worldwide and is considered second only to drought for its importance as an agronomic challenge. A common practice to manage the impact is the application of lime but this is expensive, and it can take years for the lime to be effective in ameliorating the subsoil acidity. Plant species with a natural ability to adapt to Al 3+ toxicity offer an option to maintain production while amelioration efforts continue, especially in low-rainfall areas where yield responses to lime is less profitable. In wheat ( Triticum aestivum L.), the genes conferring Al 3+ resistance have been extensively researched over the years through classical inheritance, cytogenetic, quantitative trait locus (QTL) and genome-wide association studies, and transcriptional analyses. As a focal point for this discussion, we assembled a total of 212 QTL from research papers published between 2006 and 2024, and their physical positions were projected on the sequenced genome of the moderately Al 3+ -resistant hexaploid wheat variety, Chinese Spring. The markers were distributed across the 21 wheat chromosomes, with the highest numbers on chromosomes 3B, 4D and 7A and the lowest on chromosomes 3D and 5D. The physical mapping of significantly associated markers onto the reference genome map uncovered novel candidate genes. These include wheat aluminium-induced (Wali) genes, the ATP-binding cassette (ABC) transporters, phytosulfokine receptor (PSKR), PIN-formed (PIN, auxin transporter), NAC (NAC domain), WRKY (WRKY domain) and natural resistance-associated macrophage proteins (NRAMP). These were discussed to provide a contextual review of gaps that can be exploited in enhancing Al 3+ resistance in wheat, which can lead to the discovery of novel genes and the development of improved cultivars.

Differences in constitutive gene expression of cytochrome P450 enzymes and ATP-binding cassette transporter gene expression between a susceptible and a highly macrocyclic lactone-resistant Haemonchus contortus isolate in the absence of drug-inducible expression

BackgroundAnthelmintic resistance in ruminants is a widespread problem that has a severe impact on productivity and animal welfare. The helminth Haemonchus contortus is generally considered the most important parasite in small ruminants due to its high pathogenicity and the widespread occurrence of anthelmintic resistance in it. Although the molecular mechanisms associated with resistance against the anthelmintics benzimidazoles (BZs) and levamisole are relatively well understood, the resistance mechanisms against the widely used anthelmintic macrocyclic lactones (MLs) ivermectin (IVM) and moxidectin (MOX) remain poorly understood. Detoxifying enzymes and xenobiotic transporters have been frequently proposed to play a role in ML resistance in multiple organisms, including nematodes.MethodsThe reference genome of H. contortus was screened for cytochrome P450 genes (cyp genes) by using the Basic Local Alignment Search Tool, and maximum-likelihood phylogenetic analysis was used to assign the sequences to gene families. Fourth-stage larvae of the susceptible (McMaster) and the ML-resistant (Berlin-selected) H. contortus isolates were generated in vitro and compared regarding basal expression levels of cyp genes and ATP-binding cassette (ABC) transporters by using RNA sequencing. The resistant isolate was further incubated with 100 nM IVM or MOX for 3, 6 and 12 h, and the effects of incubation time and drugs were evaluated.ResultsTwenty-five cyp genes were identified in the H. contortus genome and assigned to 13 different families. The ML-resistant isolate showed significantly higher and lower constitutive expression of 13 and four cyp genes, respectively. Out of the 50 ABC transporter genes, only six showed significantly higher expression in the ML-resistant isolate, while 12 showed lower expression. The fold changes were in general low (range 0.44–5.16). Only pgp-13 showed significant downregulation in response to IVM (0.77 fold change at 6 h, 0.96 fold change at 12 h) and MOX (0.84 fold change at 12 h). In contrast, mrp-5 was significantly, albeit minimally, upregulated in the presence of IVM, but not MOX, after 12 h (1.02 fold change).ConclusionsDespite little observable ML-inducible gene expression in the isolate examined here, some of the changes in the baseline expression levels might well contribute to ML resistance in the context of additional changes in a multigenic resistance model. However, neither cyp genes nor the ABC transporters appear to be the main drivers that can explain the high levels of resistance observed in the resistant isolate examined here.Graphical

Genome Assembly and Winged fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses.

The genomic basis and biology of winged fruit are interesting issues in ecological and evolutionary biology. Chinese wingnut (Pterocarya stenoptera) is an important garden and economic tree species in China. The genomic resources of this hardwood tree could provide advanced genomic studies of Juglandaceae and their evolutionary relationships. Here, we reported a high-quality reference genome of P. stenoptera (N50 = 35.15 Mb) and provided a comparative analysis of Juglandaceae genomes. Paralogous relationships among the 16 chromosomes of the Chinese wingnut genome revealed eight main duplications representing the subgenome. Molecular dating suggested that the most recent common ancestor of P. stenopetera and Cyclocarya paliurus diverged from Juglans around 56.7 million years ago (Mya). The expanded and contracted gene families were associated with cutin, suberine, and wax biosynthesis, cytochrome P450, and anthocyanin biosynthesis. We identified large inversion blocks between the P. stenoptera genome and its relatives, which are enriched in genes related lipid biosynthesis and metabolism, and starch and sucrose metabolism. The twenty-eight individuals were clearly clustered into three groups responding to three species, namely Pterocarya macroptera, Pterocarya hupehensis, and P. stenoptera, based on whole genome resequencing data. Morphological and gene expression analysis showed that CAD, COMT, LOX, and MADS-box play important roles during the five developmental stages of wingnuts. Our study highlights the evolutionary history of the P. stenoptera genome and supports P. stenoptera as an appropriate Juglandaceae model for studying winged fruits. These results provide a theoretical basis for the evolution, development, and diversity of woody plant winged fruits.

Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.

Metaproteomics offers a profound understanding of the functional dynamics of the gut microbiome, which is crucial for personalized healthcare strategies. The selection of an appropriate database is a critical step for the identification of peptides and proteins, as well as for the provision of accurate taxonomic and functional annotations. The matched metagenomic-derived database is considered to be the best, but its limitations include the identification of low-abundance organisms and taxonomic resolution. Herein, we constructed a protein database (DBCGR2) based on Cultivated Genome Reference 2 (CGR2) and developed a complete peptide-centric analysis workflow for database searching and for the annotation of taxonomy and function. This workflow was subsequently appraised in comparison with metagenomics-derived databases for the analysis of metaproteomic data. Our findings suggested that the performance of DBCGR2 in identification was comparable with metagenomics-derived databases with improvement in identification rates of peptides from low-abundance species. The database searching results could be fully annotated using the pepTaxa taxonomic annotation approach developed in this study, and the taxonomic resolution was enhanced to strain level. Additionally, the results demonstrated that the sensitivity of functional annotation could be enhanced by employing DBCGR2. Overall, the DBCGR2 combined with pepTaxa can be considered an alternative for metaproteomic data analysis with superior analysis performances.IMPORTANCEMass spectrometry-based metaproteomics offers a profound understanding of the gut microbial taxonomy and functionality. The databases utilized in the analysis of metaproteomic data are crucial, as they determine the identification of proteins that can be recognized and linked to overall human health, in addition to the quality of taxonomic and functional annotation. Among the most effective approaches for constructing protein databases is the utilization of metagenomic sequencing to create matched databases. However, the database, derived from isolated genomes, has yet to undergo rigorous testing for their efficacy and accuracy in protein identification and taxonomic and functional annotation. Here, we constructed a protein database DBCGR2 derived from Cultivated Genome Reference 2 (CGR2) and a complete workflow for data analysis. We compared the performances of DBCGR2 and metagenomics-derived databases. Our results indicated that DBCGR2 can be regarded as an alternative to metagenomics-derived databases, which contribute to metaproteomic data analysis.

A Decade of Non-Invasive Prenatal Testing (NIPT) for Chromosomal Abnormalities in Croatia: First National Monocentric Study to Inform Country's Future Prenatal Care Strategy.

Chromosomal numerical and structural alterations are significant causes of various developmental disorders in foetuses. Non-invasive prenatal testing (NIPT) has emerged as an effective screening tool for detecting common aneuploidies, aiding in the identification of individuals who may require further diagnostic work-up. This retrospective, monocentric observational study evaluates the usage patterns, test choices, turnaround times (TAT), and outcomes of NIPT between 2013 and 2023 on a sample of 2431 pregnant women at a special hospital offering outpatient services and comprehensive gynaecological/obstetric inpatient care. We analysed the trends in NIPT usage, high-risk results, prior screening procedures, as well as factors such as age, gestational age and in vitro fertilisation (IVF) status. NIPT was performed using cell-free foetal DNA (cffDNA) extracted from maternal plasma, followed by library construction, sequencing and result analysis. The sequencing results were aligned with reference genomes, and z-scores were calculated to assess the likelihood of aneuploidy. Statistical significance was set at p < 0.05. The average age of women undergoing NIPT decreased from 36.1 years in 2013 to 33.01 years in 2023 (p = 0.0287), and mean TAT dropped from 12.44 days in 2013 to 7.08 days in 2023 (p = 0.0121), with the most substantial reduction occurring between 2013 and 2019. The study identified a stable rate of women who underwent IVF seeking prenatal testing, with no statistically significant difference between the first half and the second half of the analysed period (p = 0.2659). Among high-risk results, there were 39 chromosomal abnormalities detected, most of them belonging to trisomy 21 (59%). Our findings demonstrate the increasing efficiency and accessibility of NIPT in prenatal care in Croatia, while the significant reduction in TAT and the decreasing age of women undergoing NIPT reflect enhanced operational practices and broader acceptance. Introducing NIPT into the public healthcare system in the Republic of Croatia could improve equitable access to advanced prenatal care and enhance pregnancy outcomes. Future advancements in technology and genetic counselling will further enhance its role, requiring careful attention to ethical and regulatory considerations.

Evaluation of photosynthetic Taxa in the Venice Lagoon from the nineteenth century to present day

The Venice Lagoon is the largest transitional environment within the Mediterranean Sea (almost 550 km2). Being a transitional environment, it contains many different ecological niches, hence the biodiversity in this environment is very high. However, at the same time, this lagoon system is under constant pressure from human activities, and it has been greatly modified by humans during the centuries. Examples are the construction of the city of Venice, the digging of the canals for commercial ships, and the modifications of the three inlets to the lagoon. All these activities altered the circulation inside the lagoon, modifying the equilibrium between river and sea inputs, also influencing the sediment intake, fundamental for saltmarshes stability. During the centuries, many authors monitored the photosynthetic taxa (seaweeds, halophytes, and seagrasses) inhabiting the Venice Lagoon. In this study, we reviewed works from the nineteenth century to the present time to obtain a complete and updated view of the photosynthetic species that inhabit this environment, observing a decrease in the presence of charophytes and heterokontophytes and an increase in rhodophytes in the analyzed period. Moreover, we also considered the ecological valence of the species reported in this environment through two different ecological indexes (Macroalgae Quality Index – MaQI, Ecological Evaluation Index – EEI), observing a decrease in the relative contribution of the species with high ecological valence along the centuries. We also reviewed the presence of threatened and non-indigenous species, observing some differences in the considered works. Finally, we also considered the molecular resources available on online databases, finding only half macroalgal species with a reference sequence, compared to almost 90% for higher plants.

Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species.

Genomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a reference genome. Here we describe a methodology for identifying and genotyping thousands of SNP loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of freshwater stream quality classified as near-threatened, with locally declining populations. We used a hybrid approach combining reduced representation sequencing and target enrichment. First, we identified putative SNP loci using ddRADseq and de novo assembly. Then, single primer enrichment technology targeted 6,000 of these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, and aberrant FIS values. We provide recommendations to address such issues. After multiple filtering steps, 2,092 SNPs were retained and used to analyse the genetic structure of 131 individuals belonging to 11 populations in France, comparing central and marginal populations. Genetic differentiation was lower among central populations, with no sign of inbreeding. As compared to microsatellite loci, SNPs exhibited greater resolution in detecting fine-scaled genetic structure, identifying putative hybrids in adjacent populations. In this study, we emphasise the difficulties of large-scale SNP genotyping in non-model species via a hybrid method that ultimately did not offer the expected cost and time saving compared to classical ddRAD approaches. However, SNPs showed greater power than previously available markers in identifying conservation units or admixture events, and the panel of reusable probes we describe here offers the potential to improve conservation efforts through future diachronic studies or finer estimations of key parameters like effective population size.

MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data.

Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.

Enhanced resolution of optical genome mapping utilizing telomere-to-telomere reference in genetic disorders.

Reference genomes serve as a baseline criterion for comparison of personal genomes to deduce clinical variants. The widely used reference genome, GRCh38, contains stretches of gaps and unresolved bases particularly in complex regions which could obscure variant discovery. In contrast, the gapless telomere-to-telomere CHM13 (T2T-CHM13) reference genome can be used to assess difficult regions of the genome. Optical genome mapping (OGM), an imaging technique for structural variation identification has improved resolution compared to traditional cytogenetic methods. Our study showcases the utility of the T2T-CHM13 reference genome for enhanced structural variant (SV) detection in complex regions. We illustrate this through two clinical cases, where improved alignment with T2T-CHM13 led to significantly higher confidence scores for critical SVs. We demonstrate improved clinical diagnostic outcomes with the updated T2T-CHM13 reference and advocate its adoption.

SpudDB: A database for accessing potato genomic data.

Potato is a key food crop with a complex, polyploid genome. Advancements in sequencing technologies coupled with improvements in genome assembly algorithms have enabled generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato. The SpudDB database houses potato genome sequence and annotation, with the doubled monoploid DM 1-3 516 R44 (hereafter DM) genome serving as the reference genome and haplotype. Diverse annotation data types for DM genes are provided through a suite of Gene Report Pages including gene expression profiles across 438 potato samples. To further annotate potato genes based on expression, 65 gene co-expression modules were constructed that permit identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress. Genome browser views of DM and 28 other potato genomes are provided along with a download page for genome sequence and annotation. To link syntenic genes within and between haplotypes, syntelogs were identified across 25 cultivated potato genomes. Through access to potato genome sequences and associated annotations, SpudDB can enable potato biologists, geneticists and breeders to continue to improve this key food crop.

Four new genome sequences of the Pallas’s cat (Otocolobus manul): an insight into the patterns of within-species variability

Manul (Otocolobus manul) is the only representative of the genus Otocolobus, which makes up the Leopard Cat lineage along with the genus Prionailurus. Their habitat is characterized by harsh environmental conditions. Although their populations are probably more stable than previously thought, it is still the case that their population size is declining. Conservation programs exist to protect manuls, but those based on captive breeding are often unsuccessful due to their increased susceptibility to diseases. The manul is therefore a suitable model species for evolutionary and diversity studies as well as for studying mechanisms of adaptation to harsh environment and mechanisms of susceptibility to diseases. Recently, the genome of the O. manul based on nanopore long-range sequencing has been published. Aiming to better understand inter- and intraspecific variation of the species, we obtained information on genome sequences of four other manuls, based on whole genome resequencing via the Illumina platform. On average, we detected a total of 3,636,571 polymorphic variants. Information on different types of structural variants and on the extent of SNP homozygosity, not available from the reference genome, was retrieved. The average whole-genome heterozygosity was almost identical to that found in the O. manul reference genome. In this context, we performed a more detailed analysis of the candidate gene EPAS1 potentially related to adaptation to the hypoxic environment. This analysis revealed both inter- and intraspecific variation, confirmed the presence of a previously described non-synonymous substitution in exon 15 unique to manuls and identified three additional unique non-synonymous substitutions located in so far not analyzed EPAS1 exonic sequences. The analysis of lncRNA located in the intron 7 of EPAS1 revealed interspecific variability and monomorphic nature of the sequence among analyzed manuls. The data obtained will allow more detailed analyses of the manul genome, focusing on genes and pathways involved in their adaptation to the environment and in susceptibility to diseases. This information can be helpful for optimizing conservation programs for this understudied species.

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems.

The availability of large databases of biological sequences presents an opportunity for in-depth exploration of gene diversity and function. Bacterial defense systems are a rich source of diverse but difficult to annotate genes with biotechnological applications. In this work, we present Domainator, a flexible and modular software suite for domain-based gene neighborhood and protein search, extraction and clustering. We demonstrate the utility of Domainator through three examples related to bacterial defense systems. First, we cluster CRISPR-associated Rossman fold (CARF) containing proteins with difficult to annotate effector domains, classifying most of them as likely transcriptional regulators and a subset as likely RNases. Second, we extract and cluster P4-like phage satellite defense hotspots, identify an abundant variant of Lamassu defense systems and demonstrate its in vivo activity against several T-even phages. Third, we integrate a protein language model into Domainator and use it to identify restriction endonucleases with low similarity to known reference sequences, validating the activity of one example in vitro. Domainator is made available as an open-source package with detailed documentation and usage examples.

Differential quantification of alternative splicing events on spliced pangenome graphs.

Pangenomes are becoming a powerful framework to perform many bioinformatics analyses taking into account the genetic variability of a population, thus reducing the bias introduced by a single reference genome. With the wider diffusion of pangenomes, integrating genetic variability with transcriptome diversity is becoming a natural extension that demands specific methods for its exploration. In this work, we extend the notion of spliced pangenomes to that of annotated spliced pangenomes; this allows us to introduce a formal definition of Alternative Splicing (AS) events on a graph structure. To investigate the usage of graph pangenomes for the quantification of AS events across conditions, we developed pantas, the first pangenomic method for the detection and differential analysis of AS events from short RNA-Seq reads. A comparison with state-of-the-art linear reference-based approaches proves that pantas achieves competitive accuracy, making spliced pangenomes effective for conducting AS events quantification and opening future directions for the analysis of population-based transcriptomes.

Identification and Precise Mapping of PmHSM, a Novel Recessive Powdery Mildew Resistance Allele from Wheat Landrace Heshangmai.

Common wheat (Triticum aestivum L.) is the world's primary food crop, and ensuring its safe production is of utmost importance for global peace and human development. However, the continuous threat of fungal diseases, including Fusarium head scab, rusts, sharp eyespot, and powdery mildew (PM), poses a significant challenge to production. PM caused by Blumeria graminis f. sp. tritici causes substantial yield losses. Heshangmai (HSM), a wheat landrace originating from Sichuan Province, possesses high levels of resistance to PM. A comprehensive study using a large segregating population of a cross between HSM and Ningmaizi119 (NMZ119) revealed a single recessive allele conferring resistance. The gene, provisionally designated PmHSM, was located on the long arm of chromosome 4A (4AL). Molecular marker analysis, a PM response array, and an allelism test indicated that PmHSM is a novel recessive resistance gene that shares an allelic relationship with PmHHXM. Thirteen simple sequence repeat markers were developed using the sequence information of the 4AL region in the Chinese spring reference sequence version 2.1. PmHSM was flanked by the markers Xmp1567 and Xmp1444 at genetic distances of 0.11 and 0.18 cM, respectively, and cosegregated with the markers Xmp1439/Xmp1440/Xmp1442.

CGC1, a new reference genome for Caenorhabditis elegans.

The original 100.3 Mb reference genome for Caenorhabditis elegans, generated from the wild-type laboratory strain N2, has been crucial for analysis of C. elegans since 1998 and has been considered complete since 2005. Unexpectedly, this long-standing reference was shown to be incomplete in 2019 by a genome assembly from the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere genome assembly of C. elegans, generated from CGC1, an isogenic derivative of the N2 strain. We used improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies, and to assemble tandem repeat loci including a 772-kb sequence for the 45S rRNA genes. While many differences from earlier assemblies came from repeat regions, unique additions to the genome were also found. Of 19,972 protein-coding genes in the N2 assembly, 19,790 (99.1%) encode products that are unchanged in the CGC1 assembly. The CGC1 assembly also may encode 183 new protein-coding and 163 new ncRNA genes. CGC1 thus provides both a completely defined reference genome and corresponding isogenic wild-type strain for C. elegans, allowing unique opportunities for model and systems biology.

A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae)

Here, we present novel high quality genome assemblies for five invasive tephritid species of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (read depths between 65 and 78x). Three assemblies (C. capitata, C. quilicii and Z. cucurbitae) were scaffolded with chromosome conformation data and annotated using RNAseq reads. For some species this is the first reference genome available (B. zonata, C. quilicii and C. rosa), for others we have published improved annotated genomes (C. capitata and Z. cucurbitae). Together, the new references provide an important resource to advance research on genetic techniques for population control, develop rapid species identification methods, and explore eco-evolutionary studies.

The complete telomere-to-telomere sequence of a mouse genome.

The current reference genome of Mus musculus, GRCm39, has major gaps in both euchromatic and heterochromatic regions associated with repetitive sequences. In this work, we have sequenced and assembled the telomere-to-telomere genome of mouse haploid embryonic stem cells. The results reveal more than 7.7% of previously uncovered sequences of the mouse genome, including ribosomal DNA arrays and pericentromeric and subtelomeric regions, as well as an additional 140 genes predicted to be protein-coding. This study helps to address knowledge gaps in the mouse genome.

Molecular identification of a Pm4 allele conferring powdery mildew resistance in durum wheat DR88

BackgroundPowdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive wheat diseases worldwide. Durum wheat (Triticum turgidum L. var. durum Desf.) is a crucial gene donor for improving common wheat.ResultsIn this study, we investigated a durum wheat accession, DR88, which exhibits broad and high levels of resistance to powdery mildew. Using bulked segregant RNA-Seq (BSR-Seq), we identified a dominant gene, tentatively designated PmDR88, and localized it to 743–776 Mb interval on chromosome arm 2AL according to the reference genome of durum wheat cv. Svevo. Subsequently, PmDR88 was mapped in a genetic region of 3.9 cM flanked by the markers WGRE77410 and WGRC872 at genetic distances of 1.6 and 2.3 cM, respectively; it also co-segregated with JS717×JS718, the diagnostic marker for the Pm4 locus. Genotyping of a large population comprising 5,174 F2:3 families using JS717×JS718 confirmed that PmDR88 is located at the Pm4 locus on 2AL. Sequence alignment revealed that PmDR88 shares identical amino acid sequences with Pm4d, while qRT-PCR analysis suggested distinct expression patterns for PmDR88 compared with previously reported Pm4 alleles. Two complementary DNA markers, including the dominant co-segregating marker JS717×JS718 and a newly developed closely-linked co-dominant marker WGRE77410, were confirmed to be available for efficiently transferring PmDR88 into the tested wheat backgrounds by marker-assisted selection (MAS) strategy.ConclusionsPmDR88 was mapped in the Pm4 locus. Despite sharing identical amino acid sequences with Pm4d, PmDR88 exhibits distinct expression patterns. Moreover, DR88 shows broad and high levels of resistance to powdery mildew. Two complementary DNA markers were identified for MAS breeding. The molecular identification of PmDR88 will facilitate transfer of this Pm4 allele into susceptible cultivars for resistance improvement or into resistant cultivars for resistance-enhanced pyramiding breeding.