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Items: 1 to 50 of 82

1.

Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions.

Sforça DA, Vautrin S, Cardoso-Silva CB, Mancini MC, Romero-da Cruz MV, Pereira GDS, Conte M, Bellec A, Dahmer N, Fourment J, Rodde N, Van Sluys MA, Vicentini R, Garcia AAF, Forni-Martins ER, Carneiro MS, Hoffmann HP, Pinto LR, Landell MGA, Vincentz M, Berges H, de Souza AP.

Front Plant Sci. 2019 May 7;10:553. doi: 10.3389/fpls.2019.00553. eCollection 2019.

2.

Brazilian-adapted soybean Bradyrhizobium strains uncover IS elements with potential impact on biological nitrogen fixation.

Barros-Carvalho GA, Hungria M, Lopes FM, Van Sluys MA.

FEMS Microbiol Lett. 2019 Mar 12. pii: fnz046. doi: 10.1093/femsle/fnz046. [Epub ahead of print]

PMID:
30860585
3.

The control of endopolygalacturonase expression by the sugarcane RAV transcription factor during aerenchyma formation.

Tavares EQP, De Souza AP, Romim GH, Grandis A, Plasencia A, Gaiarsa JW, Grima-Pettenati J, de Setta N, Van Sluys MA, Buckeridge MS.

J Exp Bot. 2019 Jan 7;70(2):497-506. doi: 10.1093/jxb/ery362.

4.

Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, Yue J, Nelson DR, Huang L, Li Z, Xu H, Zhou D, Wang Y, Hu W, Lin J, Deng Y, Pandey N, Mancini M, Zerpa D, Nguyen JK, Wang L, Yu L, Xin Y, Ge L, Arro J, Han JO, Chakrabarty S, Pushko M, Zhang W, Ma Y, Ma P, Lv M, Chen F, Zheng G, Xu J, Yang Z, Deng F, Chen X, Liao Z, Zhang X, Lin Z, Lin H, Yan H, Kuang Z, Zhong W, Liang P, Wang G, Yuan Y, Shi J, Hou J, Lin J, Jin J, Cao P, Shen Q, Jiang Q, Zhou P, Ma Y, Zhang X, Xu R, Liu J, Zhou Y, Jia H, Ma Q, Qi R, Zhang Z, Fang J, Fang H, Song J, Wang M, Dong G, Wang G, Chen Z, Ma T, Liu H, Dhungana SR, Huss SE, Yang X, Sharma A, Trujillo JH, Martinez MC, Hudson M, Riascos JJ, Schuler M, Chen LQ, Braun DM, Li L, Yu Q, Wang J, Wang K, Schatz MC, Heckerman D, Van Sluys MA, Souza GM, Moore PH, Sankoff D, VanBuren R, Paterson AH, Nagai C, Ming R.

Nat Genet. 2018 Dec;50(12):1754. doi: 10.1038/s41588-018-0293-7.

PMID:
30425353
5.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, Yue J, Nelson DR, Huang L, Li Z, Xu H, Zhou D, Wang Y, Hu W, Lin J, Deng Y, Pandey N, Mancini M, Zerpa D, Nguyen JK, Wang L, Yu L, Xin Y, Ge L, Arro J, Han JO, Chakrabarty S, Pushko M, Zhang W, Ma Y, Ma P, Lv M, Chen F, Zheng G, Xu J, Yang Z, Deng F, Chen X, Liao Z, Zhang X, Lin Z, Lin H, Yan H, Kuang Z, Zhong W, Liang P, Wang G, Yuan Y, Shi J, Hou J, Lin J, Jin J, Cao P, Shen Q, Jiang Q, Zhou P, Ma Y, Zhang X, Xu R, Liu J, Zhou Y, Jia H, Ma Q, Qi R, Zhang Z, Fang J, Fang H, Song J, Wang M, Dong G, Wang G, Chen Z, Ma T, Liu H, Dhungana SR, Huss SE, Yang X, Sharma A, Trujillo JH, Martinez MC, Hudson M, Riascos JJ, Schuler M, Chen LQ, Braun DM, Li L, Yu Q, Wang J, Wang K, Schatz MC, Heckerman D, Van Sluys MA, Souza GM, Moore PH, Sankoff D, VanBuren R, Paterson AH, Nagai C, Ming R.

Nat Genet. 2018 Nov;50(11):1565-1573. doi: 10.1038/s41588-018-0237-2. Epub 2018 Oct 8. Erratum in: Nat Genet. 2018 Dec;50(12):1754.

PMID:
30297971
6.

A mosaic monoploid reference sequence for the highly complex genome of sugarcane.

Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan A, Van Sluys MA, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, van der Vossen E, Henry R, Schmutz J, D'Hont A.

Nat Commun. 2018 Jul 6;9(1):2638. doi: 10.1038/s41467-018-05051-5.

7.

Complete chloroplast genome sequences contribute to plant species delimitation: A case study of the Anemopaegma species complex.

Firetti F, Zuntini AR, Gaiarsa JW, Oliveira RS, Lohmann LG, Van Sluys MA.

Am J Bot. 2017 Oct;104(10):1493-1509. doi: 10.3732/ajb.1700302.

8.

Earth BioGenome Project: Sequencing life for the future of life.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, Yang H, Zhang G.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115.

9.

An Efficient Approach to Explore and Discriminate Anomalous Regions in Bacterial Genomes Based on Maximum Entropy.

Barros-Carvalho GA, Van Sluys MA, Lopes FM.

J Comput Biol. 2017 Nov;24(11):1125-1133. doi: 10.1089/cmb.2017.0042. Epub 2017 Jun 1.

PMID:
28570142
10.

Plant immunity: unravelling the complexity of plant responses to biotic stresses.

Miller RN, Costa Alves GS, Van Sluys MA.

Ann Bot. 2017 Mar 1;119(5):681-687. doi: 10.1093/aob/mcw284.

11.

An operon for production of bioactive gibberellin A4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola.

Nagel R, Turrini PC, Nett RS, Leach JE, Verdier V, Van Sluys MA, Peters RJ.

New Phytol. 2017 May;214(3):1260-1266. doi: 10.1111/nph.14441. Epub 2017 Jan 30.

12.

Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum.

Vilela MM, Del Bem LE, Van Sluys MA, de Setta N, Kitajima JP, Cruz GM, Sforça DA, de Souza AP, Ferreira PC, Grativol C, Cardoso-Silva CB, Vicentini R, Vincentz M.

Genome Biol Evol. 2017 Feb 1;9(2):266-278. doi: 10.1093/gbe/evw293.

13.

RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease.

Schaker PD, Palhares AC, Taniguti LM, Peters LP, Creste S, Aitken KS, Van Sluys MA, Kitajima JP, Vieira ML, Monteiro-Vitorello CB.

PLoS One. 2016 Sep 1;11(9):e0162237. doi: 10.1371/journal.pone.0162237. eCollection 2016.

14.

Virus-like attachment sites as structural landmarks of plants retrotransposons.

Ochoa Cruz EA, Cruz GM, Vieira AP, Van Sluys MA.

Mob DNA. 2016 Jul 28;7:14. doi: 10.1186/s13100-016-0069-5. eCollection 2016.

15.

Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.

Metcalfe CJ, Oliveira SG, Gaiarsa JW, Aitken KS, Carneiro MS, Zatti F, Van Sluys MA.

J Exp Bot. 2015 Jul;66(14):4239-50. doi: 10.1093/jxb/erv283. Epub 2015 Jun 19.

16.

Building the sugarcane genome for biotechnology and identifying evolutionary trends.

de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GM, Del Bem LE, Vicentini R, Nogueira FT, Campos RA, Nunes SL, Turrini PC, Vieira AP, Ochoa Cruz EA, Corrêa TC, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY Jr, Cardoso-Silva CB, Scortecci KC, Garcia AA, Carneiro MS, Kim C, Paterson AH, Bergès H, D'Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA.

BMC Genomics. 2014 Jun 30;15:540. doi: 10.1186/1471-2164-15-540.

17.

Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons.

Cruz GM, Metcalfe CJ, de Setta N, Cruz EA, Vieira AP, Medina R, Van Sluys MA.

PLoS One. 2014 May 21;9(5):e97099. doi: 10.1371/journal.pone.0097099. eCollection 2014.

18.

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids.

Garcia AA, Mollinari M, Marconi TG, Serang OR, Silva RR, Vieira ML, Vicentini R, Costa EA, Mancini MC, Garcia MO, Pastina MM, Gazaffi R, Martins ER, Dahmer N, Sforça DA, Silva CB, Bundock P, Henry RJ, Souza GM, van Sluys MA, Landell MG, Carneiro MS, Vincentz MA, Pinto LR, Vencovsky R, Souza AP.

Sci Rep. 2013 Dec 2;3:3399. doi: 10.1038/srep03399.

19.

Complete Genome Sequence of Leifsonia xyli subsp. cynodontis Strain DSM46306, a Gram-Positive Bacterial Pathogen of Grasses.

Monteiro-Vitorello CB, Zerillo MM, Van Sluys MA, Camargo LE, Kitajima JP.

Genome Announc. 2013 Nov 7;1(6). pii: e00915-13. doi: 10.1128/genomeA.00915-13.

20.

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads.

Darrasse A, Carrère S, Barbe V, Boureau T, Arrieta-Ortiz ML, Bonneau S, Briand M, Brin C, Cociancich S, Durand K, Fouteau S, Gagnevin L, Guérin F, Guy E, Indiana A, Koebnik R, Lauber E, Munoz A, Noël LD, Pieretti I, Poussier S, Pruvost O, Robène-Soustrade I, Rott P, Royer M, Serres-Giardi L, Szurek B, van Sluys MA, Verdier V, Vernière C, Arlat M, Manceau C, Jacques MA.

BMC Genomics. 2013 Nov 6;14:761. doi: 10.1186/1471-2164-14-761.

21.

The role of prophage in plant-pathogenic bacteria.

Varani AM, Monteiro-Vitorello CB, Nakaya HI, Van Sluys MA.

Annu Rev Phytopathol. 2013;51:429-51. doi: 10.1146/annurev-phyto-081211-173010. Epub 2013 May 24. Review.

PMID:
23725471
22.

Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum.

Kajihara D, de Godoy F, Hamaji TA, Blanco SR, Van Sluys MA, Rossi M.

Genet Mol Biol. 2012 Jul;35(3):632-9. doi: 10.1590/S1415-47572012005000038. Epub 2012 Jul 5.

23.

Mutator System Derivatives Isolated from Sugarcane Genome Sequence.

Manetti ME, Rossi M, Cruz GM, Saccaro NL Jr, Nakabashi M, Altebarmakian V, Rodier-Goud M, Domingues D, D'Hont A, Van Sluys MA.

Trop Plant Biol. 2012 Sep;5(3):233-243. Epub 2012 Jul 6.

24.

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers.

Palhares AC, Rodrigues-Morais TB, Van Sluys MA, Domingues DS, Maccheroni W Jr, Jordão H Jr, Souza AP, Marconi TG, Mollinari M, Gazaffi R, Garcia AA, Vieira ML.

BMC Genet. 2012 Jun 28;13:51. doi: 10.1186/1471-2156-13-51.

25.

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns.

Domingues DS, Cruz GM, Metcalfe CJ, Nogueira FT, Vicentini R, Alves Cde S, Van Sluys MA.

BMC Genomics. 2012 Apr 16;13:137. doi: 10.1186/1471-2164-13-137.

26.

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains.

Varani AM, Monteiro-Vitorello CB, de Almeida LG, Souza RC, Cunha OL, Lima WC, Civerolo E, Van Sluys MA, Vasconcelos AT.

Genet Mol Biol. 2012 Jan;35(1):149-52. Epub 2012 Feb 16.

27.

Diversification of hAT transposase paralogues in the sugarcane genome.

de Jesus EM, Cruz EA, Cruz GM, Van Sluys MA.

Mol Genet Genomics. 2012 Mar;287(3):205-19. doi: 10.1007/s00438-011-0670-8. Epub 2012 Jan 7.

28.

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL.

J Bacteriol. 2011 Oct;193(19):5450-64. doi: 10.1128/JB.05262-11. Epub 2011 Jul 22.

29.

Pathogenomics of Xanthomonas: understanding bacterium-plant interactions.

Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM.

Nat Rev Microbiol. 2011 May;9(5):344-55. doi: 10.1038/nrmicro2558. Epub 2011 Apr 11. Review.

PMID:
21478901
30.

Copia retrotransposon in the Zaprionus genus: another case of transposable element sharing with the Drosophila melanogaster subgroup.

de Setta N, Van Sluys MA, Capy P, Carareto CM.

J Mol Evol. 2011 Mar;72(3):326-38. doi: 10.1007/s00239-011-9435-6. Epub 2011 Feb 24.

PMID:
21347850
31.

High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane.

Garsmeur O, Charron C, Bocs S, Jouffe V, Samain S, Couloux A, Droc G, Zini C, Glaszmann JC, Van Sluys MA, D'Hont A.

New Phytol. 2011 Jan;189(2):629-42. doi: 10.1111/j.1469-8137.2010.03497.x. Epub 2010 Oct 29.

32.

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes.

Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys MA, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ming R.

BMC Genomics. 2010 Apr 23;11:261. doi: 10.1186/1471-2164-11-261.

33.

Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola.

Lang JM, Hamilton JP, Diaz MGQ, Van Sluys MA, Burgos MRG, Vera Cruz CM, Buell CR, Tisserat NA, Leach JE.

Plant Dis. 2010 Mar;94(3):311-319. doi: 10.1094/PDIS-94-3-0311.

PMID:
30754246
34.

Nitric oxide mediates the hormonal control of Crassulacean acid metabolism expression in young pineapple plants.

Freschi L, Rodrigues MA, Domingues DS, Purgatto E, Van Sluys MA, Magalhaes JR, Kaiser WM, Mercier H.

Plant Physiol. 2010 Apr;152(4):1971-85. doi: 10.1104/pp.109.151613. Epub 2010 Feb 10.

35.

Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits.

Kamenetzky L, Asís R, Bassi S, de Godoy F, Bermúdez L, Fernie AR, Van Sluys MA, Vrebalov J, Giovannoni JJ, Rossi M, Carrari F.

Plant Physiol. 2010 Apr;152(4):1772-86. doi: 10.1104/pp.109.150532. Epub 2010 Jan 29.

36.

ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds.

Gomes KA, Almeida TC, Gesteira AS, Lôbo IP, Guimarães AC, de Miranda AB, Van Sluys MA, da Cruz RS, Cascardo JC, Carels N.

Genomics Insights. 2010 Oct 28;3:29-56. doi: 10.4137/GEI.S4340. eCollection 2010.

37.

Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila.

de Setta N, Van Sluys MA, Capy P, Carareto CM.

BMC Evol Biol. 2009 Dec 2;9:279. doi: 10.1186/1471-2148-9-279.

38.

Thermoperiod affects the diurnal cycle of nitrate reductase expression and activity in pineapple plants by modulating the endogenous levels of cytokinins.

Freschi L, Nievola CC, Rodrigues MA, Domingues DS, Van Sluys MA, Mercier H.

Physiol Plant. 2009 Nov;137(3):201-12. doi: 10.1111/j.1399-3054.2009.01283.x.

PMID:
19832938
39.

Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation.

de Mello Varani A, Souza RC, Nakaya HI, de Lima WC, Paula de Almeida LG, Kitajima EW, Chen J, Civerolo E, Vasconcelos AT, Van Sluys MA.

PLoS One. 2008;3(12):e4059. doi: 10.1371/journal.pone.0004059. Epub 2008 Dec 31.

40.

The Tnt1 family member Retrosol copy number and structure disclose retrotransposon diversification in different Solanum species.

Manetti ME, Rossi M, Nakabashi M, Grandbastien MA, Van Sluys MA.

Mol Genet Genomics. 2009 Mar;281(3):261-71. doi: 10.1007/s00438-008-0408-4. Epub 2008 Dec 18.

PMID:
19093134
41.

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, Brendel V, Bogdanove AJ.

PLoS One. 2008;3(11):e3828. doi: 10.1371/journal.pone.0003828. Epub 2008 Nov 27.

42.

Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli.

Zerillo MM, Van Sluys MA, Camargo LE, Monteiro-Vitorello CB.

BMC Microbiol. 2008 Jul 25;8:127. doi: 10.1186/1471-2180-8-127.

43.

A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit.

Bermúdez L, Urias U, Milstein D, Kamenetzky L, Asis R, Fernie AR, Van Sluys MA, Carrari F, Rossi M.

J Exp Bot. 2008;59(10):2875-90. doi: 10.1093/jxb/ern146. Epub 2008 Jun 13.

44.

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Won Lee S, Seo YS, Sriariyanum M, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ.

BMC Genomics. 2008 May 1;9:204. doi: 10.1186/1471-2164-9-204. Erratum in: BMC Genomics. 2008;9:534.. Seo, Young-Su [added]; Sriariyanum, Malinee [added].

45.

Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism.

Lima WC, Paquola AC, Varani AM, Van Sluys MA, Menck CF.

FEMS Microbiol Lett. 2008 Apr;281(1):87-97. doi: 10.1111/j.1574-6968.2008.01083.x.

46.

Sugarcane functional genomics: gene discovery for agronomic trait development.

Menossi M, Silva-Filho MC, Vincentz M, Van-Sluys MA, Souza GM.

Int J Plant Genomics. 2008;2008:458732. doi: 10.1155/2008/458732.

47.

Transposon display supports transpositional activity of P elements in species of the saltans group of Drosophila.

de Setta N, Costa AP, Lopes FR, Van Sluys MA, Carareto CM.

J Genet. 2007 Apr;86(1):37-43.

48.

Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera.

Manetti ME, Rossi M, Costa AP, Clausen AM, Van Sluys MA.

BMC Evol Biol. 2007 Mar 7;7:34.

49.

MudrA-like sequences from rice and sugarcane cluster as two bona fide transposon clades and two domesticated transposases.

Saccaro NL Jr, Van Sluys MA, de Mello Varani A, Rossi M.

Gene. 2007 May 1;392(1-2):117-25. Epub 2006 Dec 6.

PMID:
17289300
50.

GMOs: building the future on the basis of past experience.

Reis LF, Van Sluys MA, Garratt RC, Pereira HM, Teixeira MM.

An Acad Bras Cienc. 2006 Dec;78(4):667-86. Review.

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