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Revista mexicana de fitopatología

versión On-line ISSN 2007-8080versión impresa ISSN 0185-3309

Rev. mex. fitopatol vol.40 no.2 Texcoco may. 2022  Epub 03-Oct-2022

https://doi.org/10.18781/r.mex.fit.2202-7 

Phytopathological notes

Omics applications in plant-microorganism interactions: A view from plant genomics

June Simpson1  * 

Emmanuel Avila de Dios1 

Alan D. Gómez Vargas1 

Arely V. Pérez-López1 

Andrea Castro Mexicano1 

Yoselin Meléndez Barraza1 

Laura Hernández Soriano1 

Laura Gálvez Sandré1 

M. Erendira López Rosas1 

Rocío Medina Chávez1 

Katia D.C. Gil-Vega1 

1 Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados Unidad Irapuato, Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato, Guanajuato, CP 36821, México.


Abstract.

The advent of next generation sequencing has opened up the possibility to carry out detailed molecular genetic analysis on non-model species. Here we present strategies to carry out RNAseq analysis in Agave tequilana which for the first time have permitted the identification and characterization of genes involved in fructan metabolism and flowering time in Agave species. Based on in silico data, expression patterns for individual genes could be determined and later confirmed by qRT-PCR and cDNA´s of genes of interest were cloned and functionally characterized in heterologous systems such as Pichia pastoris and Arabidopsis thaliana. We also present data obtained by RNAseq analysis of the C. lindemuthianum-P. vulgaris pathosystem. Using strains of C. lindemuthianum expressing the green fluorescent protein, the infection process can easily be followed. RNAseq was carried out at different time points during the initial stages of infection by C. lindemuthianum on P. vulgaris cultivar BAT93 using virulent or non-virulent races of C. lindemuthianum (Race 1088 and Race 256 respectively). Differentially expressed genes specific to compatible and non-compatible reactions could therefore be identified.

Key words: Agave; RNA-seq; cDNA cloning; C. lindemuthianum/P.vulgaris; infection process; virulence/avirulence

Resumen.

El desarrollo de la secuenciación de nueva generación ha abierto la posibilidad de llevar a cabo análisis genéticos moleculares detallados en especies no-modelo. Aquí se presentan estrategias para llevar a cabo análisis de RNAseq en Agave tequilana que por primera vez han permitido la identificación y caracterización de genes involucrados en el metabolismo de fructanos y el tiempo de floración en especies de Agave. Basándose en datos in silico, los patrones de expresión de genes individuales fueron determinados y luego confirmados mediante qRT-PCR. Además, los cDNA´s correspondientes a genes de interés fueron clonados y caracterizados funcionalmente en sistemas heterólogos como Pichia pastoris y Arabidopsis thaliana. También se presentan datos obtenidos por análisis de RNAseq del patosistema C. lindemuthianum-P. vulgaris. Usando cepas de C. lindemuthianum que expresan la proteína fluorescente verde, es sencillo dar seguimiento al proceso de infección y se llevó a cabo RNAseq en diferentes etapas del proceso inicial de infección por C. lindemuthianum en P. vulgaris cultivar BAT93 usando razas virulentas o no virulentas de C. lindemuthianum (Raza 1088 y Raza 256 respectivamente). Por lo tanto, pudieron identificarse genes expresados diferencialmente y específicos para reacciones compatibles y no compatibles.

Palabras clave: Agave; ARN-seq; clonación cADN; C. lindemuthianum/P.vulgaris; proceso de infección; virulencia/avirulencia

The development of affordable “new generation” sequencing methods and the bioinformatic capacity to analyze the large amounts of data obtained, have unleashed the potential to carry out detailed genetic analysis in non-model organisms which were previously inaccessible. Our model of study is Agave tequilana, however the strategy we used can be applied to most organisms including plant, fungal, bacterial or insect species. Although A. tequilana is an important crop in Mexico predicted to generate around 6 billion dollars in profit annually by 2024 from tequila production, the perennial, monocarpic life cycle of this species, the practice of removing immature inflorescences in the field and the strict control by the Tequila Regulatory Council over the germplasm grown have led to a situation where a single cultivar (A. tequilana Weber var. azul) is reproduced asexually and grown over 95,000 hectares in the 5 Mexican states authorized under “Denomination of Origin” for tequila production. Very few breeding programs have been implemented in agave species and no improved cultivars have been developed either for yield in terms of sugar production, control of flowering or resistance to pests and pathogens. Disease and pest resistance are of particular importance given the practice of exploiting a single genotype over thousands of hectares making agave plantations extremely vulnerable to attack. Our initial omics analyses have focused on unraveling the genetics of sugar (fructan) metabolism and control of flowering in A. tequilana.

Strategy

For many crop plants such as corn, beans, tomato (Hirsch and Buell, 2013) among others, the determination of a whole genome sequence in order to carry out genetic analysis has been feasible, however, A. tequilana has a genome content of almost twice the size (4000Mb) (Palomino et al., 2007) of corn and development and construction of a whole genome sequence is still technically challenging. Therefore, our initial strategy was to develop methods for transcriptome (RNAseq) analysis in agave species. Transcriptome analysis offers the advantages that less data needs to be generated and processed lowering costs. Additionally, data can be related to tissue types or developmental stages providing information on expression levels of specific genes under specific conditions. We have generated transcriptome data for A. tequilana, A. deserti, A. striata and A. victoria-reginae (Ávila de Dios et al., 2015) and using this information have identified, cloned and characterized the cDNAs (coding sequences) responsible for the regulation of fructan metabolism and some members of a family of genes involved in the regulation of flowering time in A. tequilana.

A total of 15 genes involved in fructan/sucrose metabolism were identified and classified as encoding fructan synthesizing enzymes, fructan degrading enzymes or invertases. Genetic transformation of agave species is still laborious and inefficient and therefore we are using heterologous systems such as P. pastoris and A. thaliana in order to functionally characterize the identified genes/enzymes. In silico expression patterns based on transcriptome data indicate which genes are expressed in specific tissues or during specific developmental stages indicating their relative importance in different processes or metabolism. Based on these data we have determined and compared expression patterns for each of the fructan metabolism genes and most of these in silico expression patterns have now been confirmed by qRT-PCR (Ávila de Dios et al., 2019, Pérez-López et al., 2021).

By employing a similar strategy, genes from several families known to be involved in the regulation of flowering time in the model system A. thaliana (FT, gibberellin metabolism, MYB factors) were also identified in A. tequilana and based on in silico expression patterns a working model for regulation of flowering in A. tequilana was proposed (Ávila deDios et al., 2019). Currently we are functionally characterizing in detail the A. tequilana FT family.

An example of preliminary omics analysis in Colletotrichum lindemuthianum

The C. lindemuthianum - common bean pathosystem involves a gene-for-gene interaction between resistance (R) genes in the common bean host cultivars and avirulence (avr) genes in the fungal pathogen. Previous work in our group identified many distinct C. lindemuthianum races based on the differential series of common bean cultivars (González et al., 1998, Mendoza et al., 2001, Rodríguez-Guerra et al., 2003, González-Chavira et al., 2004). We initiated a transcriptome strategy to compare the differential gene expression patterns at the early stages of infection on the common bean cultivar BAT93 inoculated with either a virulent or a non-virulent race (Race 1088 and Race 256 respectively) of C. lindemuthianum (Figure 1 and Table 1). Details of the experimental strategy are shown in Table 2. RNAseq was carried out on samples from each time point (samples from 4-96 hours were pooled) (Table 3) and the data was analyzed and compared in order to eventually identify genes expressed differentially during compatible and incompatible interactions (Medina-Chavez and Simpson unpublished).

Figure 1 Microscopic analysis 7 days after inoculation of common bean seedlings with Colletotrichum lindemuthianum. In the upper left quadrant, the formation of reproductive structures (acervuli) by the pathogen is observed in the compatible interactions for both cultivars with strain 1088. On the right side for the same strain a large number of conidia and appresoria are shown. In the interactions with strain 256, a large number of hyphae are observed for the cultivar Victoria as well as the presence of young conidia on the necrotic tissue of the plant, whereas for the cultivar BAT 93, hypersensitive reactions caused by the defense response are observed with the localized death of cells in contact with the pathogen. 

Table 1 Reactions of BAT93 and Victoria to inoculation of C. lindemuthianum Races 256 and 1088. 

Cultivar Race Reaction Infection level
BAT93 1088 Compatible 4
Victoria Compatible 4
BAT93 256 Incompatible 0
Victoria Compatible 4

Genomic and transcriptomic analyses are currently essential and cost-effective tools for genetic analysis and can easily be applied to plants and/or their pathogens. The P. vulgaris-C. lindemuthianum pathosystem is particularly amenable given the well -documented series of differential cultivars and corresponding C. lindemuthianum races. The recent release and ongoing analysis of several P. vulgaris genomes (Rendón-Anaya et al., 2017) will greatly facilitate this research.

Table 2 Summary of samples taken for RNAseq analysis. 

Compatibility Sample time 15 min Compatibility Sample time 15 min Compatibility Sample time 15 min
Incompatible 30 min Compatible 30 min Un-inoculated 30 min
1 h 1 h 1 h
2 h 2 h 2 h
4 h 4 h 4 h
8 h 8 h 8 h
24 h 24 h 24 h
48 h 48 h 48 h
72 h 72 h 72 h
96 h 96 h 96 h

Table 3 Summary of RNAseq results. 

Compatibility No. of reads Total No. of Gb
Incompatible 33192887 230,040,125
17997712
23569435
31022980
68634904
Compatible 30262460
32000000
28907063
33087678
34510194
Un-inoculated 40019130 195,579,782
32603263
28756807
43056852
15635587

Acknowledgements

This work was supported in part by grants from the Basic Science program from CONACyT (Grant CB-2005-01 #49281 & CB-2013-01 # 220339) and by a Grant # 131 SEP CINVESTAV and all the students involved had a CONACyT Postgraduate Scholarship

Literature cited

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Avila de Dios, E Delaye AL and Simpson J. 2019. Transcriptome analysis of bolting in A. tequilana reveals roles for florigen, MADS, fructans and gibberellins. BioMed Central Genomics 20:473 https://doi.org/10.1186/s12864-019-5808-9 [ Links ]

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González M, Rodríguez R, Zavala ME, Jacobo JJ, Hernández F, Acosta J, Martínez O and Simpson J. 1998. Characterization of Mexican isolates of C. lindemuthianum using differential cultivars and molecular markers. Phytopathology 88: 292-299. https://doi.org/10.1094/PHYTO.1998.88.4.292 [ Links ]

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Mendoza A, Hernández F, Hernández S, Ruiz D, Martínez de la Vega O, De la Mora G, Acosta J and Simpson J. 2001. Identification of Co-1 Anthracnose Resistance and Linked Molecular Markers in Common Bean Line A193. Plant Disease 85: 252-255. https://doi.org/10.1094/PDIS.2001.85.3.252 [ Links ]

Palomino G, Martínez J and Méndez I. 2007. Variación inter e intraespecífica en especies de Agave por citometría de flujo y análisis de sus cromosomas. Pp:41-65. In: Colunga-GarcíaMarín P, Larqué SA, Eguiarte L y Zizumbo-Villarreal D (eds.). En lo Ancestral hay Futuro: Del Tequila, los Mezcales y otros Agaves. CONACyT, CONABIO, INE, ISBN: 978-968-6532-18-0 CICY, Mexico. 402p. https://twitter.com/conabio/status/1441461910898098177Links ]

Pérez-López AV, Simpson J, Clench MR, Gomez-Vargas AD and Ordaz-Ortiz JJ. 2021. Localization and Composition of Fructans in Stem and Rhizome of Agave tequilana Weber var. azul. Frontier Plant Science 11:608850 https://doi.org/10.3389/fpls.2020.608850 [ Links ]

Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S. Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldon T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A and Herrera-Estrella A. 2017. Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biology 18: 60. https://doi.org/10.1186/s13059-017-1190-6 [ Links ]

Rodríguez-Guerra R, Ramírez-Rueda MT, Martínez de la Vega O and Simpson J. 2003. Variation in genotype, pathotype and anastomosis groups of Colletotrichum lindemuthianum isolates from México. Plant Pathology 52:228-235. https://doi.org/10.1046/j.1365-3059.2003.00808.x [ Links ]

Received: March 23, 2021; Accepted: April 13, 2022

*Corresponding author: june.simpson@cinvestav.mx

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