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4. A117 VALIDITY EVIDENCE FOR ENDOSCOPIC RETROGRADE CHOLANGIOPANCREATOGRAPHY COMPETENCY ASSESSMENT TOOLS: A SYSTEMATIC REVIEW

Author

Khan, R, primary, Homsi, H, additional, Gimpaya, N, additional, Sabrie, N, additional, Gholami, R, additional, Bansal, R, additional, Scaffidi, M, additional, Lightfoot, D, additional, James, P, additional, Siau, K, additional, Forbes, N, additional, Wani, S, additional, Keswani, R, additional, Walsh, C, additional, and Grover, S, additional

Published
2023
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8. List of Contributors

Author

Allen, M., primary, Bellard, E., additional, Berg, E., additional, Canevari de Paredes, D., additional, Chester-Fangman, C., additional, Courtney, M., additional, DeJonghe, J., additional, Desilets, M.R., additional, Detterbeck, K., additional, Doi, C., additional, Dumond, J., additional, Eichenholtz, S., additional, Filkins, M.M., additional, Flaccavento, M., additional, Francis, D., additional, Garber, G., additional, Getts, E., additional, Glisson, L., additional, Hagedon, M., additional, Hall, R., additional, Hess, A.N., additional, Iverson, S., additional, Judd, C., additional, Kelt, M., additional, Kline, E., additional, Kumaran, M., additional, Larson, C.M., additional, Lightfoot, D., additional, Logan, J., additional, Long, J., additional, Lucky, S., additional, Maddison, T., additional, Marcum, B., additional, Morant, B., additional, Ridlen, P., additional, Roth, A., additional, Sciangula, M., additional, Secovnie, K.O., additional, Sult, L., additional, Theissen, J.M., additional, Turnbow, D., additional, Wallace, N., additional, Webb, J., additional, and Ziegler, C., additional

Published
2017
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15. Potential Impact of the 2016 Consensus Definitions of Sepsis and Septic Shock on Future Sepsis Research

Author

Peake, Sandra L., Delaney, Anthony, Bailey, Michael, Bellomo, Rinaldo, Bennett, V., Board, J., McCracken, P., McGloughlin, S., Nanjayya, V., Teo, A., Hill, E., Jones, P., O’Brien, E., Sawtell, F., Schimanski, K., Wilson, D., Bellomo, R., Bolch, S., Eastwood, G., Kerr, F., Peak, L., Young, H., Edington, J., Fletcher, J., Smith, J., Ghelani, D., Nand, K., Sara, T., Cross, A., Flemming, D., Grummisch, M., Purdue, A., Fulton, E., Grove, K., Harney, A., Milburn, K., Millar, R., Mitchell, I., Rodgers, H., Scanlon, S., Coles, T., Connor, H., Dennett, J., Van Berkel, A., Barrington-Onslow, S., Henderson, S., Mehrtens, J., Dryburgh, J., Tankel, A., Braitberg, G., O’Bree, B., Shepherd, K., Vij, S., Allsop, S., Haji, D., Haji, K., Vuat, J., Bone, A., Elderkin, T., Orford, N., Ragg, M., Kelly, S., Stewart, D., Woodward, N., Harjola, V.-P., Okkonen, M., Pettilä, V., Sutinen, S., Wilkman, E., Fratzia, J., Halkhoree, J., Treloar, S., Ryan, K., Sandford, T., Walsham, J., Jenkins, C., Williamson, D., Burrows, J., Hawkins, D., Tang, C., Dimakis, A., Holdgate, A., Micallef, S., Parr, M., White, H., Morrison, L., Sosnowski, K., Ramadoss, R., Soar, N., Wood, J., Franks, M., Williams, A., Hogan, C., Song, R., Tilsley, A., Rainsford, D., Wells, R., Dowling, J., Galt, P., Lamac, T., Lightfoot, D., Walker, C., Braid, K., DeVillecourt, T., Tan, H. S., Seppelt, I., Chang, L. F., Cheung, W. S., Fok, S. K., Lam, P. K., Lam, S. M., So, H. M., Yan, W. W., Altea, A., Lancashire, B., Gomersall, C. D., Graham, C. A., Leung, P., Arora, S., Bass, F., Shehabi, Y., Isoardi, J., Isoardi, K., Powrie, D., Lawrence, S., Ankor, A., Chester, L., Davies, M., O’Connor, S., Poole, A., Soulsby, T., Sundararajan, K., Williams, J., Greenslade, J. H., MacIsaac, C., Gorman, K., Jordan, A., Moore, L., Ankers, S., Bird, S., Delaney, A., Fogg, T., Hickson, E., Jewell, T., Kyneur, K., O’Connor, A., Townsend, J., Yarad, E., Brown, S., Chamberlain, J., Cooper, J., Jenkinson, E., McDonald, E., Webb, S., Buhr, H., Coakley, J., Cowell, J., Hutch, D., Gattas, D., Keir, M., Rajbhandari, D., Rees, C., Baker, S., Roberts, B., Farone, E., Holmes, J., Santamaria, J., Winter, C., Finckh, A., Knowles, S., McCabe, J., Nair, P., Reynolds, C., Ahmed, B., Barton, D., Meaney, E., Nichol, A., Harris, R., Shields, L., Thomas, K., Karlsson, S., Kuitunen, A., Kukkurainen, A., Tenhunen, J., Varila, S., Ryan, N., Trethewy, C., Crosdale, J., Smith, J. C., Vellaichamy, M., Furyk, J., Gordon, G., Jones, L., Senthuran, S., Bates, S., Butler, J., French, C., Tippett, A., Kelly, J., Kwans, J., Murphy, M., O’Flynn, D., Kurenda, C., Otto, T., Peake, S., Raniga, V., Williams, P., Ho, H. F., Leung, A., and Wu, H.

Published
2017
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24. Gender differences in mortality and quality of life after septic shock: A post-hoc analysis of the ARISE study

Author

Luethi, N, Bailey, M, Higgins, A, Howe, B, Peake, S, Delaney, A, Bellomo, R, Bennett, V, Board, J, McCracken, P, McGloughlin, S, Nanjayya, V, Teo, A, Hill, E, O'Brien, PJE, Sawtell, F, Schimanski, K, Wilson, D, Bolch, S, Eastwood, G, Kerr, F, Peak, L, Young, H, Edington, J, Fletcher, J, Smith, J, Ghelani, D, Nand, K, Sara, T, Cross, A, Flemming, D, Grummisch, M, Purdue, A, Fulton, E, Grove, K, Harney, A, Milburn, K, Millar, R, Mitchell, I, Rodgers, H, Scanlon, S, Coles, T, Connor, H, Dennett, J, Van Berkel, A, Barrington-Onslow, S, Henderson, S, Mehrtens, J, Dryburgh, J, Tankel, A, Braitberg, G, O'Bree, B, Shepherd, K, Vij, S, Allsop, S, Haji, D, Haji, K, Vuat, J, Bone, A, Elderkin, T, Orford, N, Ragg, M, Kelly, S, Stewart, D, Woodward, N, Harjola, V-P, Pettila, MO, Sutinen, S, Wilkman, E, Fratzia, J, Halkhoree, J, Treloar, S, Ryan, K, Sandford, T, Walsham, J, Jenkins, C, Williamson, D, Burrows, J, Hawkins, D, Tang, C, Dimakis, A, Holdgate, A, Micallef, S, Parr, M, White, H, Morrison, L, Sosnowski, K, Ramadoss, R, Soar, N, Wood, J, Franks, M, Williams, A, Hogan, C, Song, R, Tilsley, A, Rainsford, D, Wells, R, Dowling, J, Galt, P, Lamac, T, Lightfoot, D, Walker, C, Braid, K, DeVillecourt, T, Tan, HS, Seppelt, I, Chang, LF, Cheung, WS, Fok, SK, Lam, PK, Lam, SM, So, HM, Yan, W, Altea, A, Lancashire, B, Gomersall, CD, Graham, CA, Leung, P, Arora, S, Bass, F, Shehabi, Y, Isoardi, J, Isoardi, K, Powrie, D, Lawrence, S, Ankor, A, Chester, L, Davies, M, O'Connor, S, Poole, A, Soulsby, T, Sundararajan, K, Williams, J, Greenslade, JH, MacIsaac, C, Gorman, K, Jordan, A, Moore, L, Ankers, S, Bird, S, Fogg, T, Hickson, E, Jewell, T, Kyneur, K, O'Connor, A, Townsend, J, Yarad, E, Brown, S, Chamberlain, J, Cooper, J, Jenkinson, E, McDonald, E, Webb, S, Buhr, H, Coakley, J, Cowell, J, Hutch, D, Gattas, D, Keir, M, Rajbhandari, D, Rees, C, Baker, S, Roberts, B, Farone, E, Holmes, J, Santamaria, J, Winter, C, Finckh, A, Knowles, S, McCabe, J, Nair, P, Reynolds, C, Ahmed, B, Barton, D, Meaney, E, Nichol, A, Harris, R, Shields, L, Thomas, K, Karlsson, S, Kuitunen, A, Kukkurainen, A, Tenhunen, J, Varila, S, Ryan, N, Trethewy, C, Crosdale, J, Smith, JC, Vellaichamy, M, Furyk, J, Gordon, G, Jones, L, Senthuran, S, Bates, S, Butler, J, French, C, Tippett, A, Kelly, J, Kwans, J, Murphy, M, O'Flynn, D, Kurenda, C, Otto, T, Raniga, V, Williams, P, Ho, HF, Leung, A, Wu, H, Luethi, N, Bailey, M, Higgins, A, Howe, B, Peake, S, Delaney, A, Bellomo, R, Bennett, V, Board, J, McCracken, P, McGloughlin, S, Nanjayya, V, Teo, A, Hill, E, O'Brien, PJE, Sawtell, F, Schimanski, K, Wilson, D, Bolch, S, Eastwood, G, Kerr, F, Peak, L, Young, H, Edington, J, Fletcher, J, Smith, J, Ghelani, D, Nand, K, Sara, T, Cross, A, Flemming, D, Grummisch, M, Purdue, A, Fulton, E, Grove, K, Harney, A, Milburn, K, Millar, R, Mitchell, I, Rodgers, H, Scanlon, S, Coles, T, Connor, H, Dennett, J, Van Berkel, A, Barrington-Onslow, S, Henderson, S, Mehrtens, J, Dryburgh, J, Tankel, A, Braitberg, G, O'Bree, B, Shepherd, K, Vij, S, Allsop, S, Haji, D, Haji, K, Vuat, J, Bone, A, Elderkin, T, Orford, N, Ragg, M, Kelly, S, Stewart, D, Woodward, N, Harjola, V-P, Pettila, MO, Sutinen, S, Wilkman, E, Fratzia, J, Halkhoree, J, Treloar, S, Ryan, K, Sandford, T, Walsham, J, Jenkins, C, Williamson, D, Burrows, J, Hawkins, D, Tang, C, Dimakis, A, Holdgate, A, Micallef, S, Parr, M, White, H, Morrison, L, Sosnowski, K, Ramadoss, R, Soar, N, Wood, J, Franks, M, Williams, A, Hogan, C, Song, R, Tilsley, A, Rainsford, D, Wells, R, Dowling, J, Galt, P, Lamac, T, Lightfoot, D, Walker, C, Braid, K, DeVillecourt, T, Tan, HS, Seppelt, I, Chang, LF, Cheung, WS, Fok, SK, Lam, PK, Lam, SM, So, HM, Yan, W, Altea, A, Lancashire, B, Gomersall, CD, Graham, CA, Leung, P, Arora, S, Bass, F, Shehabi, Y, Isoardi, J, Isoardi, K, Powrie, D, Lawrence, S, Ankor, A, Chester, L, Davies, M, O'Connor, S, Poole, A, Soulsby, T, Sundararajan, K, Williams, J, Greenslade, JH, MacIsaac, C, Gorman, K, Jordan, A, Moore, L, Ankers, S, Bird, S, Fogg, T, Hickson, E, Jewell, T, Kyneur, K, O'Connor, A, Townsend, J, Yarad, E, Brown, S, Chamberlain, J, Cooper, J, Jenkinson, E, McDonald, E, Webb, S, Buhr, H, Coakley, J, Cowell, J, Hutch, D, Gattas, D, Keir, M, Rajbhandari, D, Rees, C, Baker, S, Roberts, B, Farone, E, Holmes, J, Santamaria, J, Winter, C, Finckh, A, Knowles, S, McCabe, J, Nair, P, Reynolds, C, Ahmed, B, Barton, D, Meaney, E, Nichol, A, Harris, R, Shields, L, Thomas, K, Karlsson, S, Kuitunen, A, Kukkurainen, A, Tenhunen, J, Varila, S, Ryan, N, Trethewy, C, Crosdale, J, Smith, JC, Vellaichamy, M, Furyk, J, Gordon, G, Jones, L, Senthuran, S, Bates, S, Butler, J, French, C, Tippett, A, Kelly, J, Kwans, J, Murphy, M, O'Flynn, D, Kurenda, C, Otto, T, Raniga, V, Williams, P, Ho, HF, Leung, A, and Wu, H

Abstract

PURPOSE: To assess the impact of gender and pre-menopausal state on short- and long-term outcomes in patients with septic shock. MATERIAL AND METHODS: Cohort study of the Australasian Resuscitation in Sepsis Evaluation (ARISE) trial, an international randomized controlled trial comparing early goal-directed therapy (EGDT) to usual care in patients with early septic shock, conducted between October 2008 and April 2014. The primary exposure in this analysis was legal gender and the secondary exposure was pre-menopausal state defined by chronological age (≤ 50 years). RESULTS: 641 (40.3%) of all 1591 ARISE trial participants in the intention-to-treat population were females and overall, 337 (21.2%) (146 females) patients were 50 years of age or younger. After risk-adjustment, we could not identify any survival benefit for female patients at day 90 in the younger (≤50 years) (adjusted Odds Ratio (aOR): 0.91 (0.46-1.89), p = .85) nor in the older (>50 years) age-group (aOR: 1.10 (0.81-1.49), p = .56). Similarly, there was no gender-difference in ICU, hospital, 1-year mortality nor quality of life measures. CONCLUSIONS: This post-hoc analysis of a large multi-center trial in early septic shock has shown no short- or long-term survival effect for women overall as well as in the pre-menopausal age-group.

Published
2020

29. Variation between pathogenic serovars within Salmonella pathogenicity islands

Author

Amavisit, P., Lightfoot, D., Browning, G.F., and Markham, P.F.

Subjects
Variation (Biology) -- Genetic aspects, Genetic transformation -- Analysis, Salmonella -- Identification and classification, Bacteria, Pathogenic -- Genetic aspects, Biological sciences
Abstract

Although four of the five Salmonella pathogenicity islands (SPIs) have been characterized in detail for Salmonella enterica serovar Typhimurium, and the fifth has been characterized for Salmonella enterica serovar Dublin, there have been limited studies to examine them in detail in a range of pathogenic serovars of S. enterica. The aim of this study was to examine these regions, shown to be crucial in virulence, in pathogenic serovars to identify any major deletions or insertions that may explain variation in virulence and provide further understanding of the elements involved in the evolution of these regions. Multiple strains of each of the 13 serovars were compared by Southern blot hybridization using a series of probes that together encompassed the full length of all five SPIs. With the exception of serovar Typhimurium, all strains of the same serovar were identical in all five SPIs. Those serovars that differed from serovar Typhimurium in SPI-1 to SPI-4 and from serovar Dublin in SPI-5 were examined in more detail in the variant regions by PCR, and restriction endonuclease digestion and/or DNA sequencing. While most variation in hybridization patterns was attributable to loss or gain of single restriction endonuclease cleavage sites, three regions, in SPI-1, SPI-3, and SPI-5, had differences due to major insertions or deletions. In SPI-1 the avrA gene was replaced by a 200-base fragment in three serovars, as reported previously. In SPI-5, two serovars had acquired an insertion with similarity to the pagJ and pagK genes between pipC and pipD. In SPI-3 the genes sugR and rhuM were deleted in most serovars and in some were replaced by sequences that were very similar to either the Escherichia coli fimbrial operon, flanked by two distinct insertion sequence elements, or to the E. coli retron phage [PHI]R73. The distribution of these differences suggests that there have been a number of relatively recent horizontal transfers of genes into S. enterica and that in some cases the same event has occurred in multiple lineages of S. enterica. Thus, it seems that insertion sequences and retron phages are likely to be involved in continuing evolution of the pathogenicity islands of pathogenic Salmonella serovars.

Published
2003

41. Can pre-hospital administration reduce time to initial antibiotic therapy in septic patients?.

Author

Lightfoot D., Santamaria J., Winter C., Bates S., Butler J., French C., Tippett A., Shepherd K., Vij S., Cudini D., Smith K., Bernard S., Stephenson M., Andrew E., Cameron P., Lum M., Udy A., Bennett V., Board J., McCracken P., McGloughlin S., Nanjayya V., Teo A., Bellomo R., Bolch S., Eastwood G., Kerr F., Peak L., Young H., Edington J., Fletcher J., Smith J., Cross A., Flemming D., Grummisch M., Purdue A., Coles T., Connor H., Dennett J., Van Berkel A., Braitberg G., O'Bree B., Allsop S., Haji D., Haji K., Vuat J., Bone A., Elderkin T., Orford N., Ragg M., Dowling J., Galt P., Lamac T., Walker C., MacIsaac C., Gorman K., Jordan A., Moore L., Farone E., Holmes J., Lightfoot D., Santamaria J., Winter C., Bates S., Butler J., French C., Tippett A., Shepherd K., Vij S., Cudini D., Smith K., Bernard S., Stephenson M., Andrew E., Cameron P., Lum M., Udy A., Bennett V., Board J., McCracken P., McGloughlin S., Nanjayya V., Teo A., Bellomo R., Bolch S., Eastwood G., Kerr F., Peak L., Young H., Edington J., Fletcher J., Smith J., Cross A., Flemming D., Grummisch M., Purdue A., Coles T., Connor H., Dennett J., Van Berkel A., Braitberg G., O'Bree B., Allsop S., Haji D., Haji K., Vuat J., Bone A., Elderkin T., Orford N., Ragg M., Dowling J., Galt P., Lamac T., Walker C., MacIsaac C., Gorman K., Jordan A., Moore L., Farone E., and Holmes J.

Abstract

Objective: To quantify the potential time saved with pre-hospital antibiotic therapy in sepsis. Method(s): Study data for adult patients transported by Ambulance Victoria (AV), and enrolled into the Australasian Resuscitation In Sepsis Evaluation (ARISE), were linked with pre-hospital electronic records. Result(s): An AV record was identified for 240 of 341 ARISE patients. The pre-hospital case notes referred to potential infection in 165 patients. The median time to first antibiotic administration from loading the patient into the ambulance was 107 (74-160) min. Conclusion(s): ARISE patients in Victoria were frequently identified pre-hospital. An opportunity exists to study the feasibility of pre-hospital antibiotic therapy.Copyright © 2019 Australasian College for Emergency Medicine

Published
2019

48. BioTIME : a database of biodiversity time series for the Anthropocene [data paper]

Author

Dornelas, M., Antao, L. H., Moyes, F., Bates, A. E., Magurran, A. E., Adam, D., Akhmetzhanova, A. A., Appeltans, W., Arcos, J. M., Arnold, H., Ayyappan, N., Badihi, G., Baird, A. H., Barbosa, M., Barreto, T. E., Baessler, C., Bellgrove, A., Belmaker, J., Benedetti-Cecchi, L., Bett, B. J., Bjorkman, A. D., Blazewicz, M., Blowes, S. A., Bloch, C. P., Bonebrake, T. C., Boyd, S., Bradford, M., Brooks, A. J., Brown, J. H., Bruelheide, H., Budy, P., Carvalho, F., Castaneda-Moya, E., Chen, C. A., Chamblee, J. F., Chase, T. J., Collier, L., Collinge, S. K., Condit, R., Cooper, E. J., Cornelissen, J. H. C., Cotano, U., Crow, S. K., Damasceno, G., Davies, C. H., Davis, R. A., Day, F. P., Degraer, S., Doherty, T. S., Dunn, T. E., Durigan, G., Duffy, J. E., Edelist, D., Edgar, G. J., Elahi, R., Elmendorf, S. C., Enemar, A., Ernest, S. K. M., Escribano, R., Estiarte, M., Evans, B. S., Fan, T. Y., Farah, F. T., Fernandes, L. L., Farneda, F. Z., Fidelis, A., Fitt, R., Fosaa, A. M., Franco, G. A. C., Frank, G. E., Fraser, W. R., Garcia, H., Gatti, R. C., Givan, O., Gorgone-Barbosa, E., Gould, W. A., Gries, C., Grossman, G. D., Gutierrez, J. R., Hale, S., Harmon, M. E., Harte, J., Haskins, G., Henshaw, D. L., Hermanutz, L., Hidalgo, P., Higuchi, P., Hoey, A., Hoey, G., Hofgaard, A., Holeck, K., Hollister, R. D., Holmes, R., Hoogenboom, M., Hsieh, C. H., Hubbell, S. P., Huettmann, F., Huffard, C. L., Hurlbert, A. H., Ivanauskas, N. M., Janik, D., Jandt, U., Jazdzewska, A., Johannessen, T., Johnstone, J., Jones, J., Jones, F. A. M., Kang, J., Kartawijaya, T., Keeley, C., Kelt, D. A., Kinnear, R., Klanderud, K., Knutsen, H., Koenig, C. C., Kortz, A. R., Kral, K., Kuhnz, L. A., Kuo, C. Y., Kushner, D. J., Laguionie-Marchais, C., Lancaster, L. T., Lee, C., Lefcheck, J. S., Levesque, E., Lightfoot, D., Lloret, F., Lloyd, J. D., Lopez-Baucells, A., Louzao, M., Madin, J. S., Magnusson, B., Malamud, S., Matthews, I., McFarland, K. P., McGill, B., McKnight, D., McLarney, W. O., Meador, J., Meserve, P. L., Metcalfe, D. J., Meyer, C. F. J., Michelsen, A., Milchakova, N., Moens, T., Moland, E., Moore, J., Moreira, C. M., Mueller, J., Murphy, G., Myers-Smith, I. H., Myster, R. W., Naumov, A., Neat, F., Nelson, J. A., Nelson, M., Newton, S. F., Norden, N., Oliver, J. C., Olsen, E. M., Onipchenko, V. G., Pabis, K., Pabst, R. J., Paquette, A., Pardede, S., Paterson, D. M., and Pélissier, Raphaël

Subjects
spatial, temporal, turnover, species richness, global, biodiversity
Abstract

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km(2) (158 cm(2)) to 100 km(2) (1,000,000,000,000 cm(2)). Time period and grainBio: TIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Published
2018

49. First draft genome assembly of the Argane tree (Argania spinosa) [version 1; peer review: 1 approved, 1 approved with reservations]

Author

Khayi, S., Elhouda Azza, N., Gaboun, F., Pirro, S., Badad, O., Gonzalo Claros, M., Lightfoot, D. A., Unver, T., Chaouni, B., Merrouch, R., Rahim, B., Essayeh, S., Ganoudi, M., Abdelwahd, R., Diria, G., Alaoui Mdarhi, M., Labhilili, M., Iraqi, D., Mouhaddab, J., Sedrati, H., Memari, M., Hamamouch, N., Alché Ramírez, Juan de Dios, Boukhatem, N., Mrabet, R., Dahan, R., Legssyer, A., Khalfaoui, M., Badraoui, M., Vande Peer, Y., Tatusova, T., El Mousadik, A., Mentag, R., Ghazal, Hassan, Fulbright Commission, and Iridian Genome Foundation

Subjects
Endemic, Morocco, Argane, Argania spinosa, Genome, Assembly, International Argane Genome Consortium
Abstract

Background: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.2 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3% of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological purposes., This work was supported by the Iridian Genome Foundation (MD, USA). H.G. is supported by a Grant from the NIH (MD, USA) for H3ABioNet/H3Africa (grant numbers U41HG006941 and U24 HG006941). O.B. and B.C. are Fulbright JSD (USA) grant recipients. This work also benefited from support of Midterm Research Program of INRA-Morocco through the use of its bioinformatics platform.

Published
2018

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