scholarly journals The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species

2019 ◽  
Vol 9 (12) ◽  
pp. 3933-3941 ◽  
Author(s):  
Remco Stam ◽  
Tetyana Nosenko ◽  
Anja C. Hörger ◽  
Wolfgang Stephan ◽  
Michael Seidel ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense

scholarly journals The de novo reference genome and transcriptome assemblies of the wild tomato species Solanum chilense

2019 ◽  
Author(s):  
Remco Stam ◽  
Tetyana Nosenko ◽  
Anja C. Hörger ◽  
Wolfgang Stephan ◽  
Michael Seidel ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Comparative Genomics ◽  
Reference Genome ◽  
Biotic And Abiotic Stress ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense ◽  
Tomato Breeding ◽  
Gene Models

ABSTRACTBackgroundWild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. In addition, S. chilense serves as a model system to study adaptation of plants to drought and to investigate the evolution of seed banks. However to date, the absence of a well annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.FindingsWe generated ∼134 Gb of DNA and 157 Gb of RNA sequence data of S chilense, which yielded a draft genome with an estimated length of 914 Mb in total encoding 25,885 high-confidence (hc) predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% (18,290) of the hc gene models are additionally supported by RNA-seq data derived from leaf tissue samples. A benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% BUSCO genes, which is in the current range of high-quality genomes for non-inbred plants. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We revealed the existence of unique gene families of NLRs to S. chilense. Comparative genomics analyses of S. chilense, cultivated tomato S. lycopersicum and its wild relative S. pennellii revealed similar levels of highly syntenic gene clusters between the three species.ConclusionsWe generated the first genome and transcriptome sequence assembly for the wild tomato species Solanum chilense and demonstrated its value in comparative genomics analyses. We make these genomes available for the scientific community as an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility, and for tomato breeding.

scholarly journals Comparative RNA-Seq Analysis Reveals Potentially Resistance-Related Genes in Response to Bacterial Canker of Tomato

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1745
Author(s):  
Leonardo I. Pereyra-Bistraín ◽  
Cesaré Ovando-Vázquez ◽  
Alejandra Rougon-Cardoso ◽  
Ángel G. Alpuche-Solís
Keyword(s):  
Defense Mechanism ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Natural Resistance ◽  
Human Consumption ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species

Tomato is one of the most important crops for human consumption. Its production is affected by the actinomycete Clavibacter michiganensis subsp. michiganensis (Cmm), one of the most devastating bacterial pathogens of this crop. Several wild tomato species represent a source of natural resistance to Cmm. Here, we contrasted the transcriptomes of the resistant wild tomato species Solanum arcanum LA2157 and the susceptible species Solanum lycopersicum cv. Ailsa Craig, during the first 24 h of challenge with Cmm. We used three analyses approaches which demonstrated to be complementary: mapping to S. lycopersicum reference genome SL3.0; semi de novo transcriptome assembly; and de novo transcriptome assembly. In a global context, transcriptional changes seem to be similar between both species, although there are some specific genes only upregulated in S. arcanum during Cmm interaction, suggesting that the resistance regulatory mechanism probably diverged during the domestication process. Although S. lycopersicum showed enriched functional groups related to defense, S. arcanum displayed a higher number of induced genes related to bacterial, oomycete, and fungal defense at the first few hours of interaction. This study revealed genes that may contribute to the resistance phenotype in the wild tomato species, such as those that encode for a polyphenol oxidase E, diacyl glycerol kinase, TOM1-like protein 6, and an ankyrin repeat-containing protein, among others. This work will contribute to a better understanding of the defense mechanism against Cmm, and the development of new control methods.

scholarly journals Quantitative resistance differences between and within natural populations of Solanum chilense against the oomycete pathogen Phytophthora infestans

2021 ◽  
Author(s):  
Parvinderdeep Kahlon ◽  
Melissa Verin ◽  
Ralph Hückelhoven ◽  
Remco Stam
Keyword(s):  
Phytophthora Infestans ◽  
Phenotypic Diversity ◽  
Quantitative Resistance ◽  
Natural Populations ◽  
Infection Frequency ◽  
Plant Genotype ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense

The wild tomato species Solanum chilense is divided in geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype vs. pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance properties can be observed between but also within populations at the level of individual plants. Data also did not reveal clear indications for complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggest that quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is likely not the result of specific adaptations of hosts to the pathogen but of basal defence responses that depend on the host genotype and are pathogen isolate-unspecific.

scholarly journals Intraspecific diversity observed in the wild tomato species Solanum chilense in initial immune responses towards a glucan elicitor.

2021 ◽  
Author(s):  
Parvinderdeep S. Kahlon ◽  
Andrea Förner ◽  
Michael Muser ◽  
Mhaned Oubounyt ◽  
Michael Gigl ◽  
...  
Keyword(s):  
Immune Responses ◽  
Resistance Phenotype ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Multiple Components ◽  
In The Wild ◽  
Defence Responses ◽  
Solanum Chilense ◽  
High Diversity

Natural plant populations are highly polymorphic and often show intraspecific quantitative, variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on the perception of conserved pathogen-associated molecular patterns (PAMPs). To dissect and understand such variation, we evaluated the diversity of responses induced by laminarin (representing a general glucan elicitor of plant immune responses) in the wild tomato species Solanum chilense. We confirm considerable overlap of the plant's global transcriptional responses to laminarin and to the oomycete pathogen Phytophthora infestans. We further measured key components of basal defence responses such as reactive oxygen species (ROS) production and levels of diverse phytohormones and their derivatives upon elicitation with laminarin in 83 plants originating from nine natural populations of S. chilense from distinct geographic origin. We found high diversity in these components at basal and elicitor-induced levels. We generated generalised linear mixed models (GLMMs) with these components to explain the observed resistance phenotype against P. infestans in the plants and found that additive effects of multiple components best explain resistance at the species level. For individual components, we observed the strongest positive correlation between the resistance phenotype and ethylene (ET) production upon laminarin elicitation. The strength of this correlation differed between individual populations. Chemical inhibition of ET production in individuals from a population, in which ET production was associated with resistance, provoked more severe disease symptoms. Our findings reveal high diversity in the strength of induced defence responses within a species and in the basal levels of other stress-related phytohormones. We show the involvement of multiple components with a quantitatively different contribution of individual components to resistance in geographically separated populations of S. chilense against P. infestans.

Sign in / Sign up

Export Citation Format

Share Document