Biology subjects

Conte, M. A.

Publications and source records attributed to Conte, M. A..

6 recordsLinked to original sources

bioRxiv2022

Clustered Cases of Human Adenovirus types 4, 7 and 14 Infections during the 2018 - 2019 Season revealed by US Department of Defense Respiratory Pathogen Surveillance and Whole Genome Sequencing

Human adenoviruses (HAdV) are genetically diverse and can infect a number of tissues with severities varied from mild to fatal. HAdV types 3, 4, 7, 11, 14, 21 and 55 were associated with acute respiratory illnesses (ARI) outbreaks in the US and in other countries. The risk of outbreaks can be effectively controlled by HAdV vaccination or mitigated by screening and preventive measures. During the influenza season 2018 - 2019, the DoD Global Respiratory Pathogen Surveillance Program (DoDGRS) received 24,300 specimens. HAdV samples that produced positive cytopathic effects in viral cultivation were subjected to next-generation sequencing for genome sequence assembly, genome typing, whole genome phylogeny, and sequence comparative analyses. Variety of HAdV types were identified in this study, including HAdV types 1 - 7, 14, 55 and 56. HAdV types 4, 7 and 14 were found in clustered cases in Colorado, Florida, New York, and South Carolina. Comparative sequence analyses of these isolates revealed the emergence of novel genetic mutations despite the stability of adenovirus genomes. Genomic surveillance of HAdV related to possible outbreaks, shed light on prevalence, genetic divergence, and viral evolution of human adenoviruses. Continued surveillance will inform risk assessment and countermeasures.

genomics↗

bioRxiv2022

Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns

Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.

genomics↗

bioRxiv2021

A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.

genomics↗

bioRxiv2020

Evolution of a sex megachromosome

Chromosome size and morphology vary within and among species, but little is known about either the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual megachromosome that is ~3 times longer than any of the other chromosomes. This megachromosome functions as a sex chromosome in some of these species. We explore two hypotheses of how this sex megachromosome may have evolved. The first hypothesis proposes that it developed by the accumulation of repetitive elements as recombination was reduced around a dominant sex-determination locus, as suggested by traditional models of sex chromosome evolution. An alternative hypothesis is that the megachromosome originated via the fusion of an autosome with a highly-repetitive B chromosome, one of which had carried a sex-determination locus. Here we test these hypotheses using comparative analysis of several chromosome-scale cichlid and teleost genomes. We find the megachromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. A WZ sex-determination locus encompasses the last ~105Mbp of the 134Mbp megachromosome and the last 47Mbp of the megachromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal the megachromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long non-coding RNAs. Although the origin of this megachromosome remains ambiguous, it has clearly been a focal point of extensive evolutionary genomic conflicts. This megachromosome represents an interesting system for studying sex chromosome evolution and genomic conflicts.

evolutionary biology↗

bioRxiv2018

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

BackgroundAfrican cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to understand the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.\n\nResultsWe re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes.\n\nLarge intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (< 10Mbp total). Placement of the centromeres within chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11 and LG20 are associated with reductions in recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element (TE) insertions compared to O. niloticus, suggesting that several TE families have a higher rate of insertion in the haplochromine cichlid lineage.\n\nConclusionThis study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.

genomics↗

bioRxiv2017

A High Quality Assembly of the Nile Tilapia (Oreochromis niloticus) Genome Reveals the Structure of Two Sex Determination Regions

We report a high-quality assembly of the tilapia genome, a perciform fish important in aquaculture around the world. A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recent vasa gene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both an ~9Mbp XY sex-determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex-determination region on LG3 in the related species O. aureus. This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome.

genomics↗