Biology subjects

Massey, S. E.

Publications and source records attributed to Massey, S. E..

4 recordsLinked to original sources

bioRxiv2023

Accurate identification of Helicoverpa armigera / Helicoverpa zea hybrids using genome admixture analysis: implications for genomic surveillance

Helicoverpa armigera, the cotton bollworm moth, is one of the worlds most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive H.armigera has been reported to hybridize with local populations of Helicoverpa zea. The correct identification of H.armigera-H.zea hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate H.zea pesticide resistance and host plant range via introgression of H.armigera genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two H.armigera-H.zea F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8 % H.armigera for both F1 hybrids, confirming its accuracy. Genome sequences from five H.zea and one H.armigera that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four H.zea genomes generated from a previous study are predicted to possess a proportion of H.armigera genetic material. Using unsupervised clustering to identify non-hybridized H.armigera and H.zea genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor H.armigera component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of H.armigera-H.zea hybrids, and suggest measures that will improve such analyses.

genomics↗

bioRxiv2023

Identification of a novel HKU4-related coronavirus in single-cell datasets and clade viral host analysis

HKU4-related coronaviruses (CoVs) are merbecoviruses related to Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV). In 2022 and 2023, two HKU4-related CoV strains were discovered in Manis javanica (Malayan pangolin) metagenomic datasets derived from organ samples: HKU4-P251T and MjHKU4r-CoV-1. Together with the Tylonycteris robustula bat CoV 162275, which was discovered in 2022, pangolin CoVs HKU4-P251T and MjHKU4r-CoV-1 form a novel phylogenetic clade distinct from all previously documented HKU4-related CoVs. In this study, we identified a novel HKU4-related CoV in a pangolin single-cell sequencing dataset generated by BGI-Shenzhen in Shenzhen, Guangdong, China in 2020. The CoV phylogenetically belongs to the same newly identified clade. The single cell datasets were reported as generated from organ samples of a single pangolin that died of natural causes. 98% of the HKU4-related CoV reads were found in only one of the seven single cell datasets -- a large intestine cell dataset, cells of which exhibit low expression of DPP4. Bacterial contamination was found to be moderately correlated with HKU4-related CoV presence. We further identified with high confidence that the RNA-Seq dataset supporting one of four near identical variants of MjHKU4r-CoV-1 is a Sus scrofa (wild pig) metagenomic dataset, with only a trace level of Manis javanica genomic content. The presence of HKU4-related CoV reads in the dataset are almost certainly laboratory research-related and not from a premortal pangolin or pig infection. Our findings raise concerns about the provenance of the novel HKU4-related CoV we identify here, MjHKU4r-CoV-1 and its four near-identical variants.

genomics↗

bioRxiv2023

Discovery of a novel merbecovirus cDNA clone contaminating agricultural rice sequencing datasets from Wuhan, China

HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were generated by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence, Tylonycteris pachypus bat isolate BtTp-GX2012. Using in silico modeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the likely presence of a HKU4-related-MERS chimera in the datasets. Our findings contribute to the knowledge of HKU4-related coronaviruses and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related gain-of-function research. Our study also emphasizes the importance of improved biosafety protocols in sequencing centers and coronavirus research facilities.

genomics↗

bioRxiv2020

Protein coevolution and physicochemical adaptation in the APAF-1/apoptosome: structural and functional implications

The apoptosome is involved in the mitochondrial pathway of apoptosis, consisting of APAF-1, caspase 9 and cytochrome c, forming a heptamer that activates effector caspases, causing cell death. This protein complex has also been characterized in Drosophila melanogaster (DARK) and Caenorhabditis elegans (CED-4). Here we present an evolutionary guided in silico characterization of the APAF-1/apoptosome. The evolutionary history of the apoptosome was determined, taking the possible orthologs of the APAF-1 version, and executing a protein coevolution and a positive selection analysis, to make structural and functional inferences and identify residues under destabilizing changes, respectively. Results suggests that the APAF-1/apoptosome is not unique to vertebrates, but also some basal invertebrates could possess orthologous copies. New possible versions were also detected in other taxa. Not all insects and other arthropods have the DARK version, just as not all nematodes have the CED-4 version. In the APAF-1 version, amino acid clusters with coevolution signal located in the interior, gave more insights on new potential interactions, allowing us to infer a more detailed model that includes allosterism, of how cytochrome c associates with {beta} propellers during APAF-1 activation, as well as interactions essential for nucleotide exchange, activation of CASP9, the molecular timer and other pathways in mitochondria to induce apoptosis. Residues on the surface under destabilizing changes have guided the protein complex in adaptations necessary for conformational changes, interactions and folding.

biochemistry↗