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2. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Microbiology, Biological Sciences, Developmental Biology, Biological sciences
Abstract

Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.

Published
2021

3. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Chemoreceptor genes, Gene regulation, Insect adaptation, Insect immunity, Insect orthology, Metabolic detoxification genes, Muscid genomics, Opsin gene duplication, Stable fly genome, Biological Sciences, Developmental Biology
Abstract

BackgroundThe stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Published
2021

9. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Abstract

Background: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. Conclusions: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Published
2021

10. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control (BMC Biology, (2021), 19, 1, (41), 10.1186/s12915-021-00975-9)

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Abstract

Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.

Published
2021

11. Population genomics and phylogeography of the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), in the United States, northern Mexico, and Argentina

Author

Raszick, Tyler J., primary, Dickens, C. Michael, additional, Perkin, Lindsey C., additional, Tessnow, Ashley E., additional, Suh, Charles P.‐C., additional, Ruiz‐Arce, Raul, additional, Boratynski, Theodore N., additional, Falco, Marcelo R., additional, Johnston, J. Spencer, additional, and Sword, Gregory A., additional

Published
2021
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13. Functional genomics of the stable fly,Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., primary, Aksoy, Serap, additional, Attardo, Geoffrey M., additional, Buckmeier, Greta, additional, Chen, Xiaoting, additional, Coates, Craig J., additional, Davis, Megan, additional, Dykema, Justin, additional, Emrich, Scott J., additional, Friedrich, Markus, additional, Holmes, Christopher J., additional, Ioannidis, Panagiotis, additional, Jansen, Evan N., additional, Jennings, Emily C., additional, Lawson, Daniel, additional, Martinson, Ellen O., additional, Maslen, Gareth L., additional, Meisel, Richard P., additional, Murphy, Terence D., additional, Nayduch, Dana, additional, Nelson, David R., additional, Oyen, Kennan J., additional, Raszick, Tyler J., additional, Ribeiro, José M. C., additional, Robertson, Hugh M., additional, Rosendale, Andrew J., additional, Sackton, Timothy B., additional, Swiger, Sonja L., additional, Sze, Sing-Hoi, additional, Tarone, Aaron M., additional, Taylor, David B., additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Werren, John H., additional, Wilson, Richard K., additional, Zdobnov, Evgeny M., additional, and Benoit, Joshua B., additional

Published
2019
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14. Genome‐wide markers reveal temporal instability of local population genetic structure in the cotton fleahopper, Pseudatomoscelis seriatus (Hemiptera: Miridae).

Author

Raszick, Tyler J, Suh, Charles P‐C, Dickens, Charles Michael, and Sword, Gregory A

Subjects
COTTON quality, MIRIDAE, COTTON, GENE flow, HOST plants, GROWING season, HEMIPTERA
Abstract

BACKGROUND: The cotton fleahopper, Pseudatomoscelis seriatus (Reuter) (Hemiptera: Miridae), is a pest of upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), that attacks pre‐floral buds (squares), leading to abscission and yield losses. In the Brazos Valley cotton production area of Texas (USA), P. seriatus exhibits a seasonal pattern of host use. In spring, eggs hatch from stems of the overwintering host, woolly croton, Croton capitatus Michx. (Malpighiales: Euphorbiaceae). During the growing season, individuals feed on a variety of host plants, including cotton. Adults return to woolly croton at season end to oviposit. We investigated if genetic differentiation exists between populations infesting cotton and those infesting alternative hosts, and whether woolly croton serves as a year‐end site of admixture that could be suitable as a natural refuge for the purposes of insect resistance management. We combined high‐throughput DNA sequencing with fine‐scale spatio‐temporal sampling to test (i) whether a population genomic approach would recover patterns of genetic variation consistent with earlier studies and (ii) if local genetic population structure was robust to seasonal changes in local habitat over time. RESULTS: We found high gene flow among populations of P. seriatus collected from different host plants in the Brazos Valley. We also identified temporal instability of the local population genetic structure, including the near complete loss of a genotypic group that had been previously abundant. CONCLUSION: We support the status of woolly croton as a natural refuge that promotes year‐end gene flow between genotypes infesting cotton and those infesting alternative hosts. © 2019 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Published
2020
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16. Additional file 1 of The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Xiaoting Chen, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M. C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Perot Saelao, Swiger, Sonja L., Sing-Hoi Sze, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Subjects
2. Zero hunger
Abstract

Additional file 1: Main supplementary text file, including supplementary Tables S1-S12 and supplementary Figures S1-S21; Table S1. RNA-Sequencing and Whole Genome Sequencing Accession Numbers and Statistics. Table S2. Summary of Dfam repeat elements with > 1000 copies including number of unique elements for each family of elements and total number of genomic copies for each family. Table S3. Detailed list of repeat elements with total genomic copy number > 1000. Table S4. Autophagy genes identified from the Stomoxys genome. Table S5. Validation of Stomoxys transcript expression by RT-qPCR. Table S6. Bacterial contaminating scaffolds located in the Stomoxys genome assembly. Table S7. Predicted lateral gene transfer events identified from the Stomoxys genome. Table S8. Components of the immune deficiency, Toll, and JAK/STAT pathways identified from the Stomoxys genome. Table S9. Manually annotated Stomoxys immune system gene family members. Table S10. RNA-Seq normalized expression values for transcripts annotated as antimicrobial peptides. Table S11. Stomoxys opsin gene compilation. Table S12. Aquaporin gene names and corresponding symbols, model numbers, scaffolds, and arthropod homologues. Figure S1. Phylogenetic placement and genomic comparisons for Stomoxys calcitrans and other fly species. Figure S2. Pearson's correlation of RNA-Seq and RT-qPCR results. Figure S3. Average read depth across predicted lateral gene transfer candidates. Figure S4. Stomoxys calcitrans genomic scaffold housing 11 defensin gene models. Figure S5. Maximum likelihood phylogenetic tree of PGRP protein sequences from S. calcitrans (red), M. domestica (black), and D. melanogaster (blue). Figure S6. Alignment of Stomoxys PGRP-S sequences with characterized D. melanogaster PGRP-SC1 (C0HK98) and –SC2 (Q9VX2) and N-acetylmuramoyl-L-alanine amidase (P00806). Figure S7. Alignment of Stomoxys PGRP-L sequences with characterized D. melanogaster PGRP-L proteins and N-acetylmuramoyl-L-alanine amidase. Figure S8. Stomoxys calcitrans Odorant Binding Protein Gene Family. Figure S9. Duplicated OS-E-like and an OS-X ortholog in Stomoxys and Musca. Figure S10. Stomoxys calcitrans Odorant Receptor Gene Family. Figure S11. Stomoxys calcitrans Gustatory Receptor Gene Family. Figure S12. Stomoxys calcitrans Ionotropic Receptor Gene Family. Figure S13. Maximum likelihood tree of dipteran opsin gene relationships. Figure S14. Phylogenetic analysis of the Stomoxys Rh1 gene cluster and Genomic organization and evolution of the S. calcitrans Rh1 opsin subfamily. Figure S15. Analysis of tuning site 17 variation in Stomoxys and Musca Rh1 paralogs. Figure S16, S18, S19. Phylogenetic relationship of catalytic carboxyesterases (S16), glutathione-S-transferases (S18), and Cys-Loop Ligand Gated Ion Channels (S19) from Stomoxys relative to Musca and Drosophila. Figure S17. Phylogenetic analysis of carboxylesterases with a role in neuronal development. Figure S20. Cytochrome P450 (CYP450) genes clustered on Stomoxys scaffolds and evidence for expansions in muscids relative to Drosophila. Figure S21. Phylogenetic analysis of cytochrome P450 genes from Stomoxys calcitrans.

17. Additional file 1 of The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Xiaoting Chen, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M. C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Perot Saelao, Swiger, Sonja L., Sing-Hoi Sze, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Subjects
2. Zero hunger
Abstract

Additional file 1: Main supplementary text file, including supplementary Tables S1-S12 and supplementary Figures S1-S21; Table S1. RNA-Sequencing and Whole Genome Sequencing Accession Numbers and Statistics. Table S2. Summary of Dfam repeat elements with > 1000 copies including number of unique elements for each family of elements and total number of genomic copies for each family. Table S3. Detailed list of repeat elements with total genomic copy number > 1000. Table S4. Autophagy genes identified from the Stomoxys genome. Table S5. Validation of Stomoxys transcript expression by RT-qPCR. Table S6. Bacterial contaminating scaffolds located in the Stomoxys genome assembly. Table S7. Predicted lateral gene transfer events identified from the Stomoxys genome. Table S8. Components of the immune deficiency, Toll, and JAK/STAT pathways identified from the Stomoxys genome. Table S9. Manually annotated Stomoxys immune system gene family members. Table S10. RNA-Seq normalized expression values for transcripts annotated as antimicrobial peptides. Table S11. Stomoxys opsin gene compilation. Table S12. Aquaporin gene names and corresponding symbols, model numbers, scaffolds, and arthropod homologues. Figure S1. Phylogenetic placement and genomic comparisons for Stomoxys calcitrans and other fly species. Figure S2. Pearson's correlation of RNA-Seq and RT-qPCR results. Figure S3. Average read depth across predicted lateral gene transfer candidates. Figure S4. Stomoxys calcitrans genomic scaffold housing 11 defensin gene models. Figure S5. Maximum likelihood phylogenetic tree of PGRP protein sequences from S. calcitrans (red), M. domestica (black), and D. melanogaster (blue). Figure S6. Alignment of Stomoxys PGRP-S sequences with characterized D. melanogaster PGRP-SC1 (C0HK98) and –SC2 (Q9VX2) and N-acetylmuramoyl-L-alanine amidase (P00806). Figure S7. Alignment of Stomoxys PGRP-L sequences with characterized D. melanogaster PGRP-L proteins and N-acetylmuramoyl-L-alanine amidase. Figure S8. Stomoxys calcitrans Odorant Binding Protein Gene Family. Figure S9. Duplicated OS-E-like and an OS-X ortholog in Stomoxys and Musca. Figure S10. Stomoxys calcitrans Odorant Receptor Gene Family. Figure S11. Stomoxys calcitrans Gustatory Receptor Gene Family. Figure S12. Stomoxys calcitrans Ionotropic Receptor Gene Family. Figure S13. Maximum likelihood tree of dipteran opsin gene relationships. Figure S14. Phylogenetic analysis of the Stomoxys Rh1 gene cluster and Genomic organization and evolution of the S. calcitrans Rh1 opsin subfamily. Figure S15. Analysis of tuning site 17 variation in Stomoxys and Musca Rh1 paralogs. Figure S16, S18, S19. Phylogenetic relationship of catalytic carboxyesterases (S16), glutathione-S-transferases (S18), and Cys-Loop Ligand Gated Ion Channels (S19) from Stomoxys relative to Musca and Drosophila. Figure S17. Phylogenetic analysis of carboxylesterases with a role in neuronal development. Figure S20. Cytochrome P450 (CYP450) genes clustered on Stomoxys scaffolds and evidence for expansions in muscids relative to Drosophila. Figure S21. Phylogenetic analysis of cytochrome P450 genes from Stomoxys calcitrans.

18. Pangenomics Links Boll Weevil Divergence With Ancient Mesoamerican Cotton Cultivation.

Author

Cohen ZP, Perkin LC, Raszick TJ, Sim SB, Geib SM, Childers AK, Sword GA, and Suh CP

Abstract

The boll weevil, Anthonomus grandis grandis Boheman, and thurberia weevil, Anthonomus grandis thurberiae Pierce, together comprise a species complex that ranges throughout Mexico, the southwestern regions of the United States and parts of South America. The boll weevil is a historically damaging and contemporaneously threatening pest to commercial upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), whereas the thurberia weevil is regarded as an innocuous non-pest subspecies that is mostly found on non-cultivated Thurber's or Arizona cotton, Gossypium thurberi L., throughout its native range in western Mexico and the southwestern United States. Recent independent analyses, using mitochondrial and whole-genome markers, have suggested the independent evolution of these lineages is more attributable to geographic isolation than biotic factors. We suggest a combination of drivers after employing comparative genomic, population genetic and pangenome methodologies to identify large and small polymorphisms. By leveraging genetic differences, we determined 39,310 diagnostic loci between the subspecies, find genes under selection, and model the subspecies' shared and unique evolutionary history. Interestingly, structural variations capture a large proportion of genes at the population level and demographic reconstruction suggests a split between approximately 3,320-16,300 before present (YBP), which coincides with cotton cultivation in Mesoamerica, approximately 3,000-5,000 YBP. Observed polymorphisms are enriched for reproductive, regulatory, and metabolic genes, which may be attributed to the subspecies split and coevolution with cultivated cotton. Our results demonstrate the utility of a holistic, comparative framework utilising small and large polymorphisms to reconstruct demography and identify genetic novelty via pangenomics., (© 2025 John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Published
2025
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