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1. Flat-precover completing domains

Author

Amzil, Houda, Bennis, Driss, Rozas, J. R. Garcia, and Oyonarte, Luis

Subjects
Mathematics - Commutative Algebra, Mathematics - Rings and Algebras, 16D40, 16D50, 16D80
Abstract

Recently, many authors have embraced the study of certain properties of modules such as projectivity, injectivity and flatness from an alternative point of view. Rather than saying a module has a certain property or not, each module is assigned a relative domain which, somehow, measures to which extent it has this particular property. In this work, we introduce a new and fresh perspective on flatness of modules. However, we will first investigate a more general context by introducing domains relative to a precovering class $\x$. We call these domains $\x$-precover completing domains. In particular, when $\x$ is the class of flat modules, we call them flat-precover completing domains. This approach allows us to provide a common frame for a number of classical notions. Moreover, some known results are generalized and some classical rings are characterized in terms of these domains., Comment: 21 pages

Published
2021

2. A new approach to projectivity in the categories of complexes

Author

Bennis, Driss, Rozas, J. R. Garcia, Ouberka, Hanane, and Oyonarte, Luis

Subjects
Mathematics - Rings and Algebras, Mathematics - Category Theory, 16E05
Abstract

Recently, several authors have adopted new alternative approaches in the study of some classical notions of modules. Among them, we find the notion of subprojectivity which was introduced to measure in a way the degree of projectivity of modules. The study of subprojectivity has recently been extended to the context of abelian categories, which has brought to light some interesting new aspects. For instance, in the category of complexes, it gives a new way to measure, among other things, the exactness of complexes. In this paper, we prove that the subprojectivity notion provides a new sight of null-homotopic morphisms in the category of complexes. This will be proven through two main results. Moreover, various results which emphasize the importance of subprojectivity in the category of complexes are also given. Namely, we give some applications by characterizing some classical rings and establish various examples that allow us to reflect the scope and limits of our results., Comment: 19 pages

Published
2021

3. Subprojectivity in abelian categories

Author

Amzil, Houda, Bennis, Driss, Rozas, J. R. Garcia, Ouberka, Hanane, and Oyonarte, Luis

Subjects
Mathematics - Category Theory, Mathematics - Rings and Algebras
Abstract

In the last few years, Lopez-Permouth and several collaborators have introduced a new approach in the study of the classical projectivity, injectivity and flatness of modules. This way, they introduced subprojectivity domains of modules as a tool to measure, somehow, the projectivity level of such a module (so not just to determine whether or not the module is projective). In this paper we develop a new treatment of the subprojectivity in any abelian category which shed more light on some of its various important aspects. Namely, in terms of subprojectivity, some classical results are unified and some classical rings are characterized. It is also shown that, in some categories, the subprojectivity measures notions other than the projectivity. Furthermore, this new approach allows, in addition to establishing nice generalizations of known results, to construct various new examples such as the subprojectivity domain of the class of Gorenstein projective objects, the class of semi-projective complexes and particular types of representations of a finite linear quiver. The paper ends with a study showing that the fact that a subprojectivity domain of a class coincides with its first right Ext-orthogonal class can be characterized in terms of the existence of preenvelopes and precovers.

Published
2021

5. The category of modules on an n-trivial extension: the basic properties

Author

Benkhadra, Dirar, Bennis, Driss, and Rozas, J. R. Garcia

Subjects
Mathematics - Category Theory, Mathematics - Commutative Algebra, Mathematics - Rings and Algebras, 18A05, 18E99, 18G05, 18G20
Abstract

In this paper we investigate a categorical aspect of $n$-trivial extension of a ring by a family of modules. Namely, we introduce the right (resp., left) $n$-trivial extension of a category by a family of endofunctors. Among other results, projective, injective and flat objects of this category are characterized. We end the paper with two applications. We characterize when an $n$-trivial extension ring is $k$-perfect and we establish a result on the selfinjective dimension of an $n$-trivial extension ring., Comment: To appear Algebra Colloquium: Volume 27 (2020), Number 3. (Special Issue; proceedings of The International Conference on Algebra and Related Topics; ICART 2018)

Published
2019

6. On proper and exact relative homological dimensions

Author

Bennis, Driss, Rozas, J. R. Garcia, Mao, Lixin, and Oyonarte, Luis

Subjects
Mathematics - Category Theory, Mathematics - Commutative Algebra, Mathematics - Rings and Algebras, Primary 18G25. Secondary 16E30
Abstract

In Enochs' relative homological dimension theory occur the so called (co)resolvent and (co)proper dimensions which are defined using proper and coproper resolutions constructed by precovers and preenvelopes, respectively. Recently, some authors have been interested in relative homological dimensions defined by just exact sequences. In this paper, we contribute to the investigation of these relative homological dimensions. We first study the relation between these two kinds of relative homological dimensions and establish some "transfer results" under adjoint pairs. Then, relative global dimensions are studied which lead to nice characterizations of some properties of particular cases of self-orthogonal subcategories. At the end of the paper, relative derived functors are studied and generalizations of some known results of balance for relative homology are established., Comment: To appear in a Special Issue of Algebra Colloquium; proceedings of The International Conference on Algebra and Related Topics (ICART 2018)

Published
2019

14. Filtered products of injective objects in Grothendieck categories.

Author

Bennis, Driss, García Rozas, J. R., Mbarki, Maroua, and Oyonarte, Luis

Subjects
*TRANSFER (Law)
Abstract

AbstractThe transfer of properties from a family of modules to their direct product or to their direct sum has always been a topical subject of great interest. In this paper we address this type of questions in the general framework of (locally finitely generated) Grothendieck categories and for more general constructions that leave as particular cases direct sums or products: F -products, F being a filter on the chosen index set. Thus, we study the conditions on the categories for the F -products of any family of (M-)injective objects, or else of any family of copies of a single injective object, to be injective. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Gorenstein categories and Tate cohomology on projective schemes

Author

Enochs, Edgar, Estrada, Sergio, and Garcia-Rozas, J. R.

Subjects
Mathematics - Category Theory, Mathematics - Algebraic Geometry
Abstract

We study Gorenstein categories. We show that such a category has Tate cohomological functors and Avramov-Martsinkovsky exact sequences connecting the Gorenstein relative, the absolute and the Tate cohomological functors. We show that such a category has what Hovey calls an injective model structure and also a projective model structure in case the category has enough projectives. As examples we show that if X is a locally Gorenstein projective scheme then the category Qco(X) of quasi-coherent sheaves on $X$ is such a category and so has these features., Comment: to appear in Mathematische Nachrichten (accepted in June'06)

Published
2007

16. Injective representations of infinite quivers. Applications

Author

Enochs, E., Estrada, S., and Garcia-Rozas, J. R.

Subjects
Mathematics - Rings and Algebras
Abstract

In this article we study injective representations of infinite quivers. We classify the indecomposable injective representations of trees and then describe Gorenstein injective and projective representations of barren trees.

Published
2007

17. Group convolutional codes

Author

Estrada, S., Rozas, J. R. Garcia, Peralta, J., and Garcia, E. Sanchez

Subjects
Mathematics - Rings and Algebras, 16S36, 94B10
Abstract

In this note we introduce the concept of group convolutional code. We make a complete classification of the minimal $S_3$-convolutional codes over the field of five elements by means of Jategaonkar's theorems.

Published
2007

18. Locally projective monoidal model structure for complexes of quasi-coherent sheaves on P^1(k)

Author

Enochs, Edgar, Estrada, Sergio, and Garcia-Rozas, J. R.

Subjects
Mathematics - Algebraic Geometry
Abstract

We will generalize the projective model structure in the category of unbounded complexes of modules over a commutative ring to the category of unbounded complexes of quasi-coherent sheaves over the projective line. Concretely we will define a locally projective model structure in the category of complexes of quasi-coherent sheaves on the projective line. In this model structure the cofibrant objects are the dg-locally projective complexes. We also describe the fibrations of this model structure and show that the model structure is monoidal. We point out that this model structure is necessarily different from other known model structures such as the injective model structure and the locally free model structure.

Published
2007
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23. Coherent quivers

Author

Bennis, Driss, primary, Rozas, J. R. García, additional, Oyonarte, Luis, additional, and Roudi, Adnane, additional

Published
2022
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27. Precover completing domains and approximations.

Author

Amzil, Houda, Bennis, Driss, Rozas, J. R. García, and Oyonarte, Luis

Abstract

In this paper, we introduce an X -precover completing domain X − 1 (L) , with L being a class of modules and not necessarily a single module, and then investigate when every module in L has an X − 1 (L) -preenvelope. Epic and monic X − 1 (L) -preenvelopes are also investigated. This study plays a key role in setting a general framework for several classical results. Then, for a class of finitely generated modules M , we introduce the notion of M -R-Mittag-Leffler modules as a natural extension of R-Mittag-Leffler modules. This enabled us to find easier proofs of some known results and also establish new ones. [ABSTRACT FROM AUTHOR]

Published
2023
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31. On relative counterpart of Auslander's conditions.

Author

Bennis, Driss, El Maaouy, Rachid, Rozas, J. R. García, and Oyonarte, Luis

Abstract

It is now well known that the conditions used by Auslander to define the Gorenstein projective modules on Noetherian rings are independent. Recently, Ringel and Zhang adopted a new approach in investigating Auslander's conditions. Instead of looking for examples, they investigated rings on which certain implications between Auslander's conditions hold. In this paper, we investigate the relative counterpart of Auslander's conditions. So, we extend Ringel and Zhang's work and introduce other concepts. Namely, for a semidualizing module C , we introduce weakly C -Gorenstein and partially C -Gorenstein rings as rings representing relations between the relative counterpart of Auslander's conditions. Moreover, we introduce a relative notion of the well-known Frobenius category. We show how useful are C -Frobenius categories in characterizing weakly C -Gorenstein and partially C -Gorenstein rings. [ABSTRACT FROM AUTHOR]

Published
2023
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35. Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

Author

Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G

Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.

Published
2021

45. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G

Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

46. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author

Rispe, C, Legeai, F, Nabity, PD, Fernandez, R, Arora, AK, Baa-Puyoulet, P, Banfill, CR, Bao, L, Barbera, M, Bouallegue, M, Bretaudeau, A, Brisson, JA, Calevro, F, Capy, P, Catrice, O, Chertemps, T, Couture, C, Deliere, L, Douglas, AE, Dufault-Thompson, K, Escuer, P, Feng, H, Forneck, A, Gabaldon, T, Guigo, R, Hilliou, F, Hinojosa-Alvarez, S, Hsiao, Y-M, Hudaverdian, S, Jacquin-Joly, E, James, EB, Johnston, S, Joubard, B, Le Goff, G, Le Trionnaire, G, Librado, P, Liu, S, Lombaert, E, Lu, H-L, Maibeche, M, Makni, M, Marcet-Houben, M, Martinez-Torres, D, Meslin, C, Montagne, N, Moran, NA, Papura, D, Parisot, N, Rahbe, Y, Lopes, MR, Ripoll-Cladellas, A, Robin, S, Roques, C, Roux, P, Rozas, J, Sanchez-Gracia, A, Sanchez-Herrero, JF, Santesmasses, D, Scatoni, I, Serre, R-F, Tang, M, Tian, W, Umina, PA, van Munster, M, Vincent-Monegat, C, Wemmer, J, Wilson, ACC, Zhang, Y, Zhao, C, Zhao, J, Zhao, S, Zhou, X, Delmotte, F, Tagu, D, Rispe, C, Legeai, F, Nabity, PD, Fernandez, R, Arora, AK, Baa-Puyoulet, P, Banfill, CR, Bao, L, Barbera, M, Bouallegue, M, Bretaudeau, A, Brisson, JA, Calevro, F, Capy, P, Catrice, O, Chertemps, T, Couture, C, Deliere, L, Douglas, AE, Dufault-Thompson, K, Escuer, P, Feng, H, Forneck, A, Gabaldon, T, Guigo, R, Hilliou, F, Hinojosa-Alvarez, S, Hsiao, Y-M, Hudaverdian, S, Jacquin-Joly, E, James, EB, Johnston, S, Joubard, B, Le Goff, G, Le Trionnaire, G, Librado, P, Liu, S, Lombaert, E, Lu, H-L, Maibeche, M, Makni, M, Marcet-Houben, M, Martinez-Torres, D, Meslin, C, Montagne, N, Moran, NA, Papura, D, Parisot, N, Rahbe, Y, Lopes, MR, Ripoll-Cladellas, A, Robin, S, Roques, C, Roux, P, Rozas, J, Sanchez-Gracia, A, Sanchez-Herrero, JF, Santesmasses, D, Scatoni, I, Serre, R-F, Tang, M, Tian, W, Umina, PA, van Munster, M, Vincent-Monegat, C, Wemmer, J, Wilson, ACC, Zhang, Y, Zhao, C, Zhao, J, Zhao, S, Zhou, X, Delmotte, F, and Tagu, D

Abstract

Background Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. Results Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. Conclusions The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.

Published
2020

47. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest (vol 18, 90, 2020)

Author

Rispe, C, Legeai, F, Nabity, PD, Fernandez, R, Arora, AK, Baa-Puyoulet, P, Banfill, CR, Bao, L, Barbera, M, Bouallegue, M, Bretaudeau, A, Brisson, JA, Calevro, F, Capy, P, Catrice, O, Chertemps, T, Couture, C, Deliere, L, Douglas, AE, Dufault-Thompson, K, Escuer, P, Feng, H, Forneck, A, Gabaldon, T, Guigo, R, Hilliou, F, Hinojosa-Alvarez, S, Hsiao, Y-M, Hudaverdian, S, Jacquin-Joly, E, James, EB, Johnston, S, Joubard, B, Le Goff, G, Le Trionnaire, G, Librado, P, Liu, S, Lombaert, E, Lu, H-L, Maibeche, M, Makni, M, Marcet-Houben, M, Martinez-Torres, D, Meslin, C, Montagne, N, Moran, NA, Papura, D, Parisot, N, Rahbe, Y, Lopes, MR, Ripoll-Cladellas, A, Robin, S, Roques, C, Roux, P, Rozas, J, Sanchez-Gracia, A, Sanchez-Herrero, JF, Santesmasses, D, Scatoni, I, Serre, R-F, Tang, M, Tian, W, Umina, PA, van Munster, M, Vincent-Monegat, C, Wemmer, J, Wilson, ACC, Zhang, Y, Zhao, C, Zhao, J, Zhao, S, Zhou, X, Delmotte, F, Tagu, D, Rispe, C, Legeai, F, Nabity, PD, Fernandez, R, Arora, AK, Baa-Puyoulet, P, Banfill, CR, Bao, L, Barbera, M, Bouallegue, M, Bretaudeau, A, Brisson, JA, Calevro, F, Capy, P, Catrice, O, Chertemps, T, Couture, C, Deliere, L, Douglas, AE, Dufault-Thompson, K, Escuer, P, Feng, H, Forneck, A, Gabaldon, T, Guigo, R, Hilliou, F, Hinojosa-Alvarez, S, Hsiao, Y-M, Hudaverdian, S, Jacquin-Joly, E, James, EB, Johnston, S, Joubard, B, Le Goff, G, Le Trionnaire, G, Librado, P, Liu, S, Lombaert, E, Lu, H-L, Maibeche, M, Makni, M, Marcet-Houben, M, Martinez-Torres, D, Meslin, C, Montagne, N, Moran, NA, Papura, D, Parisot, N, Rahbe, Y, Lopes, MR, Ripoll-Cladellas, A, Robin, S, Roques, C, Roux, P, Rozas, J, Sanchez-Gracia, A, Sanchez-Herrero, JF, Santesmasses, D, Scatoni, I, Serre, R-F, Tang, M, Tian, W, Umina, PA, van Munster, M, Vincent-Monegat, C, Wemmer, J, Wilson, ACC, Zhang, Y, Zhao, C, Zhao, J, Zhao, S, Zhou, X, Delmotte, F, and Tagu, D

Abstract

An amendment to this paper has been published and can be accessed via the original article.

Published
2020

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