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1. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

Author

Hogg, Carolyn J., Edwards, Richard J., Farquharson, Katherine A., Silver, Luke W., Brandies, Parice, Peel, Emma, Escalona, Merly, Jaya, Frederick R., Thavornkanlapachai, Rujiporn, Batley, Kimberley, Bradford, Tessa M., Chang, J. King, Chen, Zhiliang, Deshpande, Nandan, Dziminski, Martin, Ewart, Kyle M., Griffith, Oliver W., Marin Gual, Laia, Moon, Katherine L., Travouillon, Kenny J., Waters, Paul, Whittington, Camilla M., Wilkins, Marc R., Helgen, Kristofer M., Lo, Nathan, Ho, Simon Y. W., Ruiz Herrera, Aurora, Paltridge, Rachel, Marshall Graves, Jennifer A., Renfree, Marilyn, Shapiro, Beth, Ottewell, Kym, and Belov, Katherine

Published
2024
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2. Author Correction: Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

Author

Hogg, Carolyn J., Edwards, Richard J., Farquharson, Katherine A., Silver, Luke W., Brandies, Parice, Peel, Emma, Escalona, Merly, Jaya, Frederick R., Thavornkanlapachai, Rujiporn, Batley, Kimberley, Bradford, Tessa M., Chang, J. King, Chen, Zhiliang, Deshpande, Nandan, Dziminski, Martin, Ewart, Kyle M., Griffith, Oliver W., Marin Gual, Laia, Moon, Katherine L., Travouillon, Kenny J., Waters, Paul, Whittington, Camilla M., Wilkins, Marc R., Helgen, Kristofer M., Lo, Nathan, Ho, Simon Y. W., Ruiz Herrera, Aurora, Paltridge, Rachel, Marshall Graves, Jennifer A., Renfree, Marilyn, Shapiro, Beth, Ottewell, Kym, and Belov, Katherine

Published
2024
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8. Whole‐mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory

Author

Cheung, Kelton, Amos, Timothy G., Shine, Rick, Devore, Jayna L., Ducatez, Simon, Edwards, Richard J., Rollins, Lee Ann, Cheung, Kelton, Amos, Timothy G., Shine, Rick, Devore, Jayna L., Ducatez, Simon, Edwards, Richard J., and Rollins, Lee Ann

Abstract

Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long‐read sequence data. We combined whole‐genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.

Published
2024
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9. Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)?

Author

Yagound, Boris, Sarma, Roshmi R., Edwards, Richard J., Richardson, Mark F., Rodriguez lopez, Carlos M., Crossland, Michael R., Brown, Gregory P., Devore, Jayna L., Shine, Richard, Rollins, Lee A., Yagound, Boris, Sarma, Roshmi R., Edwards, Richard J., Richardson, Mark F., Rodriguez lopez, Carlos M., Crossland, Michael R., Brown, Gregory P., Devore, Jayna L., Shine, Richard, and Rollins, Lee A.

Abstract

Many organisms can adjust their development according to environmental conditions, including the presence of conspecifics. Although this developmental plasticity is common in amphibians, its underlying molecular mechanisms remain largely unknown. Exposure during development to either ‘cannibal cues’ from older conspecifics, or ‘alarm cues’ from injured conspecifics, causes reduced growth and survival in cane toad (Rhinella marina) tadpoles. Epigenetic modifications, such as changes in DNA methylation patterns, are a plausible mechanism underlying these developmental plastic responses. Here we tested this hypothesis, and asked whether cannibal cues and alarm cues trigger the same DNA methylation changes in developing cane toads. We found that exposure to both cannibal cues and alarm cues was associated with local changes in DNA methylation patterns. These DNA methylation changes affected genes putatively involved in developmental processes, but in different genomic regions for different conspecific‐derived cues. Genetic background explains most of the epigenetic variation among individuals. Overall, the molecular mechanisms triggered by exposure to cannibal cues seem to differ from those triggered by alarm cues. Studies linking epigenetic modifications to transcriptional activity are needed to clarify the proximate mechanisms that regulate developmental plasticity in cane toads.

Published
2024
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10. The Evolution of Ultraconserved Elements in Vertebrates.

Author

Cummins, Mitchell, Watson, Cadel, Edwards, Richard J, and Mattick, John S

Subjects
EMBRYOLOGY, NUMBERS of species, GENOMES, TETRAPODS, MAMMALS
Abstract

Ultraconserved elements were discovered two decades ago, arbitrarily defined as sequences that are identical over a length ≥ 200 bp in the human, mouse, and rat genomes. The definition was subsequently extended to sequences ≥ 100 bp identical in at least three of five mammalian genomes (including dog and cow), and shown to have undergone rapid expansion from ancestors in fish and strong negative selection in birds and mammals. Since then, many more genomes have become available, allowing better definition and more thorough examination of ultraconserved element distribution and evolutionary history. We developed a fast and flexible analytical pipeline for identifying ultraconserved elements in multiple genomes, dedUCE , which allows manipulation of minimum length, sequence identity, and number of species with a detectable ultraconserved element according to specified parameters. We suggest an updated definition of ultraconserved elements as sequences ≥ 100 bp and ≥97% sequence identity in ≥50% of placental mammal orders (12,813 ultraconserved elements). By mapping ultraconserved elements to ∼200 species, we find that placental ultraconserved elements appeared early in vertebrate evolution, well before land colonization, suggesting that the evolutionary pressures driving ultraconserved element selection were present in aquatic environments in the Cambrian–Devonian periods. Most (>90%) ultraconserved elements likely appeared after the divergence of gnathostomes from jawless predecessors, were largely established in sequence identity by early Sarcopterygii evolution—before the divergence of lobe-finned fishes from tetrapods—and became near fixed in the amniotes. Ultraconserved elements are mainly located in the introns of protein-coding and noncoding genes involved in neurological and skeletomuscular development, enriched in regulatory elements, and dynamically expressed throughout embryonic development. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

Author

Edwards, Richard J., Field, Matt A., Ferguson, James M., Dudchenko, Olga, Keilwagen, Jens, Rosen, Benjamin D., Johnson, Gary S., Rice, Edward S., Hillier, La Deanna, Hammond, Jillian M., Towarnicki, Samuel G., Omer, Arina, Khan, Ruqayya, Skvortsova, Ksenia, Bogdanovic, Ozren, Zammit, Robert A., Aiden, Erez Lieberman, Warren, Wesley C., and Ballard, J. William O.

Published
2021
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17. Feasibility of comparing medical management and surgery (with neurosurgery or stereotactic radiosurgery) with medical management alone in people with symptomatic brain cavernoma – protocol for the Cavernomas: A Randomised Effectiveness (CARE) pilot trial

Author

Loan, James J M, primary, Bacon, Andrew, additional, van Beijnum, Janneke, additional, Bhatt, Pragnesh, additional, Bjornson, Anna, additional, Broomes, Nicole, additional, Bullen, Alistair, additional, Bulters, Diederik, additional, Cahill, Julian, additional, Chavredakis, Emmanuel, additional, Colombo, Francesca, additional, Danciut, Mihai, additional, Digpal, Ronneil, additional, Edwards, Richard J, additional, Ferguson, Lucie, additional, Forsyth, Laura, additional, Fouyas, Ioannis, additional, Ganesan, Vijeya, additional, Grover, Patrick, additional, Gurusinghe, Nihal, additional, Hall, Peter S, additional, Harkness, Kirsty, additional, Harris, Lauren S, additional, Hayton, Tom, additional, Helmy, Adel, additional, Holsgrove, Daniel, additional, Hutchinson, Peter J, additional, Israni, Anil, additional, Kinsella, Elaine, additional, Lewis, Steff, additional, Majeed, Sohail, additional, Mallucci, Conor, additional, Mukerji, Nitin, additional, Nair, Ramesh, additional, Neilson, Aileen R, additional, Papadopoulos, Marios C, additional, Radatz, Matthias, additional, Rossdeutsch, Alex, additional, Raza-Knight, Saba, additional, Stephen, Jacqueline, additional, Stoddart, Andrew, additional, Teo, Mario, additional, Turner, Carole, additional, Wade, Julia, additional, Walsh, Daniel, additional, White, David, additional, White, Phil, additional, Wildman, Jack, additional, Wroe Wright, Oliver, additional, Uff, Christopher, additional, Ushewokunze, Shungu, additional, Vindlacheruvu, Raghu, additional, Kitchen, Neil, additional, and Al-Shahi Salman, Rustam, additional

Published
2023
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20. Cellular interactions with hydrogels

Author

Edwards, Richard J.

Subjects
660.294513, Chemical Engineering, Applied Chemistry, Chemical Engineering
Abstract

An efficient means of evaluating potential biomaterials is to use the in vitro fibroblast cell culture model. However, the chemistry which influences cell adhesion on polymer substrates is poorly understood. The work in this thesis aims to rationalise several theories of current opinion and introduce new chemical techniques that may predict cellular behaviour. The keratoprosthesis is a typical example of the need to be able to manipulate cell adhesion of materials since both adhesive and non adhesive sections are needed for proper integration and optical function. Calcein AM/ethidium homodimer-1 and DAPI assays were carried out using 3T3 and EKl.BR cells. Poly(HEMA) was found to be the most cell adhesive hydrogel tested. The reactivity of monomers and the resulting sequence distribution were found to affect surface properties and this may explain the poor levels of cell adhesion seen on NVP/MMA copolymers. Surface free energy is shown to be dependent on the polar and non polar groups present along the backbone chain of the polymers. Dehydrated and hydrated contact angle measurements show the effect of rotation of surface groups around the backbone chain. This effect is most apparent on hydrogels containing methacrylic acid. Dynamic contact angle measurements confirm sequence distribution irregularities and demonstrate the mobility of surface groups. Incorporation of NVI or DEAEMA into the hydrogels does not affect the mobility of the surface groups despite their bulkiness. Foetal calf serum was used for the first time as a test solution in an attempt to mimic a biological environment during surface experiments. A Vroman effect may be present, and may involve different surface proteins for each material tested. This interdisciplinary study combines surface characterisation and biological testing to further the knowledge of the biomaterial/host interface. Surface chemistry techniques appear to be insufficiently sensitive to predict cellular behaviour. The degree of ionisation of hydrogels containing ionic groups depends on the nature of the functional groups as well as the concentration and this is an important parameter to consider when comparing charged materials.

Published
2001
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24. The Australasian dingo archetype:De novochromosome-length genome assembly, DNA methylome, and cranial morphology

Author

Ballard, J. William O., primary, Field, Matt A., additional, Edwards, Richard J., additional, Wilson, Laura A.B., additional, Koungoulos, Loukas G., additional, Rosen, Benjamin D., additional, Chernoff, Barry, additional, Dudchenko, Olga, additional, Omer, Arina, additional, Keilwagen, Jens, additional, Skvortsova, Ksenia, additional, Bogdanovic, Ozren, additional, Chan, Eva, additional, Zammit, Robert, additional, Hayes, Vanessa, additional, and Aiden, Erez Lieberman, additional

Published
2023
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26. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Author

Ballard, J William O, primary, Field, Matt A, additional, Edwards, Richard J, additional, Wilson, Laura A B, additional, Koungoulos, Loukas G, additional, Rosen, Benjamin D, additional, Chernoff, Barry, additional, Dudchenko, Olga, additional, Omer, Arina, additional, Keilwagen, Jens, additional, Skvortsova, Ksenia, additional, Bogdanovic, Ozren, additional, Chan, Eva, additional, Zammit, Robert, additional, Hayes, Vanessa, additional, and Aiden, Erez Lieberman, additional

Published
2023
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29. Safety and effectiveness of the assessment and treatment of idiopathic normal pressure hydrocephalus in the Adult Hydrocephalus Clinical Research Network

Author

Williams, Michael A., primary, Nagel, Sean J., additional, Golomb, James, additional, Jensen, Hailey, additional, Dasher, Nickolas A., additional, Holubkov, Richard, additional, Edwards, Richard J., additional, Luciano, Mark G., additional, Zwimpfer, Thomas J., additional, Katzen, Heather, additional, Moghekar, Abhay, additional, Wisoff, Jeffrey H., additional, McKhann, Guy M., additional, and Hamilton, Mark G., additional

Published
2022
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30. Percutaneous Revascularization for Ischemic Left Ventricular Dysfunction

Author

Perera, Divaka, primary, Clayton, Tim, additional, O’Kane, Peter D., additional, Greenwood, John P., additional, Weerackody, Roshan, additional, Ryan, Matthew, additional, Morgan, Holly P., additional, Dodd, Matthew, additional, Evans, Richard, additional, Canter, Ruth, additional, Arnold, Sophie, additional, Dixon, Lana J., additional, Edwards, Richard J., additional, De Silva, Kalpa, additional, Spratt, James C., additional, Conway, Dwayne, additional, Cotton, James, additional, McEntegart, Margaret, additional, Chiribiri, Amedeo, additional, Saramago, Pedro, additional, Gershlick, Anthony, additional, Shah, Ajay M., additional, Clark, Andrew L., additional, and Petrie, Mark C., additional

Published
2022
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31. SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context

Author

Davey, Norman E., Haslam, Niall J., Shields, Denis C., Edwards, Richard J., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Dijkstra, Tjeerd M. H., editor, Tsivtsivadze, Evgeni, editor, Marchiori, Elena, editor, and Heskes, Tom, editor

Published
2010
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33. Transcript‐ and annotation‐guided genome assembly of the European starling

Author

Stuart, Katarina C., primary, Edwards, Richard J., additional, Cheng, Yuanyuan, additional, Warren, Wesley C., additional, Burt, David W., additional, Sherwin, William B., additional, Hofmeister, Natalie R., additional, Werner, Scott J., additional, Ball, Gregory F., additional, Bateson, Melissa, additional, Brandley, Matthew C., additional, Buchanan, Katherine L., additional, Cassey, Phillip, additional, Clayton, David F., additional, De Meyer, Tim, additional, Meddle, Simone L., additional, and Rollins, Lee A., additional

Published
2022
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35. The King's Outcome Scale for Childhood Head Injury and Injury Severity and Outcome Measures in Children with Traumatic Brain Injury

Author

Calvert, Sophie, Miller, Helen E., Curran, Andrew, Hameed, Biju, McCarter, Renee, Edwards, Richard J., Hunt, Linda, and Sharples, Peta Mary

Abstract

The aim of this study was to relate discharge King's Outcome Scale for Childhood Head Injury (KOSCHI) category to injury severity and detailed outcome measures obtained in the first year post-traumatic brain injury (TBI). We used a prospective cohort study. Eighty-one children with TBI were studied: 29 had severe, 15 moderate, and 37 mild TBI. The male:female ratio was 1.8:1. The mean age was 11 years 10 months (SD 3.6, range 5-16y). Discharge KOSCHI categories were good (n=34), moderate (n=39), severe (n=6), and unclassifiable (n=2). KOSCHI category correlated strongly with admission Glasgow Coma Score, length of hospital stay, and post-traumatic amnesia. It also correlated significantly with Verbal IQ and Performance IQ (Wechsler); measures of attention; health status (Health Utilities Index [HUI]); health-related quality of life (Pediatric Quality of Life Inventory [PedsQL]); depressive symptoms (Birleson Depression Scale) assessed within 3 months postTBI; and with Verbal IQ, selective attention (map mission), and HUI and PedsQL domains assessed at least 6 months post-TBI discharge. KOSCHI did not correlate with behaviour or executive function. We conclude that the KOSCHI scored at hospital discharge correlates with severity of injury and some cognitive, health status, and HRQL outcomes early after TBI. It is not helpful at predicting later difficulties, or behavioural and emotional problems.

Published
2008
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36. Effect of Transcatheter Aortic Valve Implantation vs Surgical Aortic Valve Replacement on All-Cause Mortality in Patients With Aortic Stenosis: A Randomized Clinical Trial

Author

Toff, William D., Hildick-Smith, David, Kovac, Jan, Mullen, Michael J., Wendler, Olaf, Mansouri, Anita, Rombach, Ines, Abrams, Keith R., Conroy, Simon P., Flather, Marcus D., Gray, Alastair M., MacCarthy, Philip, Monaghan, Mark J., Prendergast, Bernard, Ray, Simon, Young, Christopher P., Crossman, David C., Cleland, John G. F., de Belder, Mark A., Ludman, Peter F., Jones, Stephen, Densem, Cameron G., Tsui, Steven, Kuduvalli, Manoj, Mills, Joseph D., Banning, Adrian P., Sayeed, Rana, Hasan, Ragheb, Fraser, Douglas G. W., Trivedi, Uday, Davies, Simon W., Duncan, Alison, Curzen, Nick, Ohri, Sunil K., Malkin, Christopher J., Kaul, Pankaj, Muir, Douglas F., Owens, W. Andrew, Uren, Neal G., Pessotto, Renzo, Kennon, Simon, Awad, Wael I., Khogali, Saib S., Matuszewski, Maciej, Edwards, Richard J., Ramesh, Bandigowdanapalya C., Dalby, Miles, Raja, Shahzad G., Mariscalco, Giovanni, Lloyd, Clinton, Cox, Ian D., Redwood, Simon R., Gunning, Mark G., and Ridley, Paul D.

Subjects
Aged, 80 and over, Heart Valve Prosthesis Implantation, Male, Aortic Valve Insufficiency, General Medicine, Aortic Valve Stenosis, Transcatheter Aortic Valve Replacement, Treatment Outcome, Risk Factors, Aortic Valve, Heart Valve Prosthesis, Humans, Female, Aged, Original Investigation
Abstract

IMPORTANCE: Transcatheter aortic valve implantation (TAVI) is a less invasive alternative to surgical aortic valve replacement and is the treatment of choice for patients at high operative risk. The role of TAVI in patients at lower risk is unclear. OBJECTIVE: To determine whether TAVI is noninferior to surgery in patients at moderately increased operative risk. DESIGN, SETTING, AND PARTICIPANTS: In this randomized clinical trial conducted at 34 UK centers, 913 patients aged 70 years or older with severe, symptomatic aortic stenosis and moderately increased operative risk due to age or comorbidity were enrolled between April 2014 and April 2018 and followed up through April 2019. INTERVENTIONS: TAVI using any valve with a CE mark (indicating conformity of the valve with all legal and safety requirements for sale throughout the European Economic Area) and any access route (n = 458) or surgical aortic valve replacement (surgery; n = 455). MAIN OUTCOMES AND MEASURES: The primary outcome was all-cause mortality at 1 year. The primary hypothesis was that TAVI was noninferior to surgery, with a noninferiority margin of 5% for the upper limit of the 1-sided 97.5% CI for the absolute between-group difference in mortality. There were 36 secondary outcomes (30 reported herein), including duration of hospital stay, major bleeding events, vascular complications, conduction disturbance requiring pacemaker implantation, and aortic regurgitation. RESULTS: Among 913 patients randomized (median age, 81 years [IQR, 78 to 84 years]; 424 [46%] were female; median Society of Thoracic Surgeons mortality risk score, 2.6% [IQR, 2.0% to 3.4%]), 912 (99.9%) completed follow-up and were included in the noninferiority analysis. At 1 year, there were 21 deaths (4.6%) in the TAVI group and 30 deaths (6.6%) in the surgery group, with an adjusted absolute risk difference of −2.0% (1-sided 97.5% CI, −∞ to 1.2%; P

Published
2022

37. Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes

Author

Galbraith, James D., Ludington, Alastair J., Sanders, Kate L., Amos, Timothy G., Thomson, Vicki A., Tuipulotu, Daniel Enosi, Dunstan, Nathan, Edwards, Richard J., Suh, Alexander, Adelson, David L., Galbraith, James D., Ludington, Alastair J., Sanders, Kate L., Amos, Timothy G., Thomson, Vicki A., Tuipulotu, Daniel Enosi, Dunstan, Nathan, Edwards, Richard J., Suh, Alexander, and Adelson, David L.

Abstract

Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids similar to 30 Mya and have since rapidly diversified into six amphibious, similar to 60 marine and similar to 100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.

Published
2022
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38. The Australian dingo is an early offshoot of modern breed dogs

Author

Field, Matt A., Yadav, Sonu, Dudchenko, Olga, Esvaran, Meera, Rosen, Benjamin D., Skvortsova, Ksenia, Edwards, Richard J., Keilwagen, Jens, Cochran, Blake J., Manandhar, Bikash, Bustamante, Sonia, Rasmussen, Jacob Agerbo, Melvin, Richard G., Chernoff, Barry, Omer, Arina, Colaric, Zane, Chan, Eva K. F., Minoche, Andre E., Smith, Timothy P. L., Gilbert, M. Thomas P., Bogdanovic, Ozren, Zammit, Robert A., Thomas, Torsten, Aiden, Erez L., Ballard, J. William O., Field, Matt A., Yadav, Sonu, Dudchenko, Olga, Esvaran, Meera, Rosen, Benjamin D., Skvortsova, Ksenia, Edwards, Richard J., Keilwagen, Jens, Cochran, Blake J., Manandhar, Bikash, Bustamante, Sonia, Rasmussen, Jacob Agerbo, Melvin, Richard G., Chernoff, Barry, Omer, Arina, Colaric, Zane, Chan, Eva K. F., Minoche, Andre E., Smith, Timothy P. L., Gilbert, M. Thomas P., Bogdanovic, Ozren, Zammit, Robert A., Thomas, Torsten, Aiden, Erez L., and Ballard, J. William O.

Abstract

Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.

Published
2022

40. The Australian dingo is an early offshoot of modern breed dogs

Author

Field, Matt A., primary, Yadav, Sonu, additional, Dudchenko, Olga, additional, Esvaran, Meera, additional, Rosen, Benjamin D., additional, Skvortsova, Ksenia, additional, Edwards, Richard J., additional, Keilwagen, Jens, additional, Cochran, Blake J., additional, Manandhar, Bikash, additional, Bustamante, Sonia, additional, Rasmussen, Jacob Agerbo, additional, Melvin, Richard G., additional, Chernoff, Barry, additional, Omer, Arina, additional, Colaric, Zane, additional, Chan, Eva K. F., additional, Minoche, Andre E., additional, Smith, Timothy P. L., additional, Gilbert, M. Thomas P., additional, Bogdanovic, Ozren, additional, Zammit, Robert A., additional, Thomas, Torsten, additional, Aiden, Erez L., additional, and Ballard, J. William O., additional

Published
2022
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41. Cognitive and gait outcomes after primary endoscopic third ventriculostomy in adults with chronic obstructive hydrocephalus

Author

Zwimpfer, Thomas J., primary, Salterio, Nicholas, additional, Williams, Michael A., additional, Holubkov, Richard, additional, Katzen, Heather, additional, Luciano, Mark G., additional, Moghekar, Abhay, additional, Nagel, Sean J., additional, Wisoff, Jeffrey H., additional, Golomb, James, additional, McKhann, Guy M., additional, Edwards, Richard J., additional, Hamilton, Mark G., additional, and _, _, additional

Published
2022
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43. Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C

Author

Chen, Stephanie H., primary, Rossetto, Maurizio, additional, van der Merwe, Marlien, additional, Lu‐Irving, Patricia, additional, Yap, Jia‐Yee S., additional, Sauquet, Hervé, additional, Bourke, Greg, additional, Amos, Timothy G., additional, Bragg, Jason G., additional, and Edwards, Richard J., additional

Published
2022
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45. A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes.

Author

Chen, Stephanie H, Martino, Alyssa M, Luo, Zhenyan, Schwessinger, Benjamin, Jones, Ashley, Tolessa, Tamene, Bragg, Jason G, Tobias, Peri A, and Edwards, Richard J

Subjects
GENOMES, GENES, CHROMOSOMES, COASTAL wetlands, PLANT diversity, GENE families
Abstract

Background Melaleuca quinquenervia (broad-leaved paperbark) is a coastal wetland tree species that serves as a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. While extensively cultivated for its ornamental value, it has also become invasive in regions like Florida, USA. Long-lived trees face diverse pest and pathogen pressures, and plant stress responses rely on immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family. However, the comprehensive annotation of NLR encoding genes has been challenging due to their clustering arrangement on chromosomes and highly repetitive domain structure; expansion of the NLR gene family is driven largely by tandem duplication. Additionally, the allelic diversity of the NLR gene family remains largely unexplored in outcrossing tree species, as many genomes are presented in their haploid, collapsed state. Results We assembled a chromosome-level pseudo-phased genome for M. quinquenervia and described the allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, distinct clustering patterns, and differences in the types and numbers of novel integrated domains. Conclusions The high-quality M. quinquenervia genome assembly establishes a new framework for functional and evolutionary studies of this significant tree species. Our findings suggest that maintaining allelic diversity within the NLR gene family is crucial for enabling responses to environmental stress, particularly in long-lived plants. [ABSTRACT FROM AUTHOR]

Published
2023
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49. Supplemental methods and results from Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader

Author

Roshmi R. Sarma, Crossland, Michael R., Eyck, Harrison J. F., DeVore, Jayna L., Edwards, Richard J., Cocomazzo, Michael, Zhou, Jia, Brown, Gregory P., Shine, Richard, and Rollins, Lee A.

Abstract

In response to novel environments, invasive populations often evolve rapidly. Standing genetic variation is an important predictor of evolutionary response but epigenetic variation may also play a role. Here, we use an iconic invader, the cane toad (Rhinella marina), to investigate how manipulating epigenetic status affects phenotypic traits. We collected wild toads from across Australia, bred them, and experimentally manipulated DNA methylation of the subsequent two generations (G1, G2) through exposure to the DNA methylation inhibitor zebularine and/or conspecific tadpole alarm cues. Direct exposure to alarm cues (an indicator of predation risk) increased the potency of G2 tadpole chemical cues, but this was accompanied by reductions in survival. Exposure to alarm cues during G1 also increased the potency of G2 tadpole cues, indicating intergenerational plasticity in this inducible defence. In addition, the negative effects of alarm cues on tadpole viability (i.e. the costs of producing the inducible defence) were minimized in the second generation. Exposure to zebularine during G1 induced similar intergenerational effects, suggesting a role for alteration in DNA methylation. Accordingly, we identified intergenerational shifts in DNA methylation at some loci in response to alarm cue exposure. Substantial demethylation occurred within the sodium channel epithelial 1 subunit gamma gene (SCNN1G) in alarm cue exposed individuals and their offspring. This gene is a key to the regulation of sodium in epithelial cells and may help to maintain the protective epidermal barrier. These data suggest that early life experiences of tadpoles induce intergenerational effects through epigenetic mechanism, which enhance larval fitness.This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’.

Published
2021
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50. Additional file 1 of Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

Author

Edwards, Richard J., Field, Matt A., Ferguson, James M., Dudchenko, Olga, Keilwagen, Jens, Rosen, Benjamin D., Johnson, Gary S., Rice, Edward S., La Deanna Hillier, Hammond, Jillian M., Towarnicki, Samuel G., Omer, Arina, Ruqayya Khan, Skvortsova, Ksenia, Bogdanovic, Ozren, Zammit, Robert A., Aiden, Erez Lieberman, Warren, Wesley C., and Ballard, J. William O.

Abstract

Additional file 1: Supplementary Fig. 1. The workflow used to construct the de novo genomes. Supplementary Fig. 2. KAT kmer analysis of China assembly. Supplementary Fig. 3. Identification of putative regulatory elements in basenji’s genome using whole-genome bisulphite sequencing. Supplementary Fig. 4. Predicted copy number of BUSCO Complete genes for three dogs based on long-read read depth. Supplementary Fig. 5. CanFam_Bas nuclear mitochondrial DNA (NUMT) coverage. Supplementary Fig. 6. Comparative short read mapping and single nucleotide variant calling for 58 dog breeds versus three reference genomes: CanFam_Bas, CanFam_GSD (GSD) and CanFam3.1 (BOX).

Published
2021
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