Biology subjects

Zimin, A.

Publications and source records attributed to Zimin, A..

8 recordsLinked to original sources

bioRxiv2022

Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

The orb-web is a remarkable example of animal architecture that is observed in families of spiders that diverged over 200 million years ago. While several genomes exist for Araneid orb-weavers, none exist for other orb-weaving families, hampering efforts to investigate the genetic basis of this complex behavior. Here we present a chromosome-level genome assembly for the cribellate orb-weaving spider Uloborus diversus. The assembly reinforces evidence of an ancient arachnid genome duplication and identifies complete open reading frames for every class of spidroin gene, which encode the proteins that are the key structural components of spider silks. We identified the two X chromosomes for U. diversus and identify candidate sex-determining genes. This chromosome-level assembly will be a valuable resource for evolutionary research into the origins of orb-weaving, spidroin evolution, chromosomal rearrangement, and chromosomal sex-determination in spiders.

genomics↗

bioRxiv2020

A pseudomolecule assembly of the Rocky Mountain elk genome reveals putative immune system gene loss near chromosomal fissions

Rocky Mountain elk (Cervus canadensis) is a major reservoir for Brucella abortus in the Greater Yellowstone area, which has significant economic implications to the cattle industry. Vaccination attempts against intracellular bacterial diseases in elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination does not induce protective immunity. To overcome this limitation, PacBio, Illumina, and HiC sequencing with a total of 686-fold coverage was used to assemble the elk genome into 35 pseudomolecules. A robust gene annotation was generated resulting in 18,013 gene models and 33,422 mRNAs. The accuracy of the assembly was assessed using synteny to the red deer and cattle genomes identifying several chromosomal rearrangements, fusions and fissions. Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes. We conclude by comparing cattle immune system-related genes to the elk genome, revealing nine putative gene losses in elk. Author SummaryBrucellosis, also known as contagious abortion, is a bacterial disease that commonly affects livestock and remains prevalent in Rocky Mountain elk (Cervus canadensis). Since the 1920s the USDA has led a program to eradicate Brucellosis from cattle, yet wild Rocky Mountain elk continue to be a source of transmission. Attempts to vaccinate wild elk herds have been unsuccessful, due to a poor and short-lived immune response. To investigate the genetic basis for this inherent difference, we created the first genome and annotation for the Rocky Mountain elk. This genome assembly is of the highest quality and contains single linear sequences for all 35 chromosomes. In order to generate gene models, an array of RNA-Seq data and proteins from many different organ tissues and cells were used in gene prediction software. Specifically, we compare cattle immune system genes with the Rocky Mountain elk, revealing the putative loss of nine immune-system related genes in elk.

genomics↗

bioRxiv2020

Chromosome-scale assembly of the bread wheat genome, Triticum aestivum, reveals over 5700 new genes

Bread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all 3 wheat subgenomes at chromosome scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 gigabases of genomic sequence. We earlier published an independent wheat assembly (Triticum 3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC 1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum 4.0, contains 15.07 gigabases of non-gap sequence anchored to chromosomes, which is 1.2 gigabases more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered more than 5700 new genes, all of them duplications in the Chinese Spring genome that are missing from the IWGSC assembly and annotation. The Triticum 4.0 assembly and annotations are freely available at www.ncbi.nlm.nih.gov/bioproject/PRJNA392179.

genomics↗

bioRxiv2020

The giant sequoia genome and proliferation of disease resistance genes

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. As they grow primarily in isolated groves within a narrow range, conservation of existing trees has been a national goal for over 150 years. Genomic data are limited in giant sequoia, and the assembly and annotation of the first giant sequoia genome has been an important goal to allow marker development for restoration and management. Using Illumina and Oxford Nanopore sequencing combined with Dovetail chromosome conformation capture libraries, 8.125 Gbp of sequence was assembled into eleven chromosome-scale scaffolds. This giant sequoia assembly represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management. Beyond conservation and management applications, the giant sequoia assembly is a resource for answering questions about the life history of this enigmatic and robust species. Here we provide an example by taking an inventory of the large and complex family of NLR type disease resistance genes.

genomics↗

bioRxiv2019

High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome

The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) are full-length, which represents a significant improvement compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during catkin development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler v2.0 is a valuable resource to understand and explore walnut biology better.

genomics↗

bioRxiv2018

New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing.

High quality genomes are essential to resolve challenges in breeding, comparative biology, medicine and conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies for non-model organisms, moving them toward reference quality genomes. We report on the latest genome assembly of the Atlantic bottlenose dolphin leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs, long insert paired ends and standard paired ends. Data were assembled with the commercial DeNovoMAGICTM assembly software resulting in two assemblies, a traditional \"haploid\" assembly (Tur_tru_Illumina_hap_v1) that is a mosaic of the two parental haplotypes and a phased assembly (Tur_tru_Illumina_phased_v1) where each scaffold has sequence from a single homologous chromosome. We show that Tur_tru_Illumina_hap_v1 is more complete and accurate compared to the current best reference based on the amount and composition of sequence, the consistency of the mate pair alignments to the assembled scaffolds, and on the analysis of conserved single-copy mammalian orthologs. The phased de novo assembly Tur_tru_Illumina_phased_v1 is the first publicly available for this species and provides the community with novel and accurate ways to explore the heterozygous nature of the dolphin genome.

genomics↗

bioRxiv2018

A Russian validation study of the Coma Recovery Scale-Revised (CRS-R)

Introduction: The aim of the present study was to validate a Russian adaptation of the Coma Recovery Scale-Revised (CRS-R).\n\nSubjects and methods: We evaluated 58 patients diagnosed with chronic disorders of consciousness (>4 weeks post-injury, DOC) of various etiology and two patients in a locked-in state at different time points in their post-comatose recovery. We tested sensitivity for changes over 1 week, reliability, as well as criterion validity and diagnostic sensitivity of the Russian adaptation of the CRS-R in comparison with the Russian adaptations of Full Outline of UnResponsiveness Score (FOUR), and Glasgow Coma Scale (GCS).\n\nResults: We obtained good sensitivity for changes in neurological status over one week (p<0.0001) and good test-retest reliability (r=1, p<0.0001) of the CRS-R. Inter-rater reliability for the CRS-R total score ({kappa}=0.99, p<0.001) and subscale scores was good. We showed high internal consistency (=0.87 and 0.89 for the first and second visit respectively). We also showed good criterion validity between two other standardized behavioral scales (moderate correlation with GCS, r=0.597 and high correlation with FOUR Score, r=0.900). CRS-R also demonstrated a significantly higher sensitivity in differential diagnosis of DOC, as compared to GCS, and FOUR Score (p<0.001).\n\nConclusion: The results show that the Russian version of the CRS-R is a valid and sensitive tool for the evaluation of severely brain damaged patients with chronic DOC which can be used for differential diagnosis and for the assessment of dynamic recovery.

neuroscience↗

bioRxiv2017

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans)

Here we describe the sequencing and assembly of the pathogenic fungus Lomentospora prolificans using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,630,066 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8,656 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.

microbiology↗