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Molecular determinism of ecological adaptation and speciation in two strains of the Lepidoptera Spodoptera frugiperda – ADA-SPODO

What makes an insect a pest of crops and how do new pest species may appear?

While a global food crisis threatens, 20 % of crops are eaten by insects. Providing knowledge on insect pest genomes, and on the ability of insects to adapt to different host-plants and to diversify may help deciphering new crop plant protection strategies.

Speciation, adaptation and genomes, transcriptome, epigenome

Speciation is a gradual process through which two populations of the same species will accumulate genetic differences and lose the ability to cross. Adaptation to the environment, including the host-plant for herbivores, can lead to the formation of new species. <br />Our insect model, the moth Spodoptera frugiperda, the “fall armyworm” is a pest of crops. It exist as two variants, one found on corn, the other found on rice or pasture grass. Both variants coexist in the same geographical areas and are morphologically indistinguishable. The primary goal of the project is to know whether they correspond to one or two species.<br />We want to know if they cross each other in the laboratory, but also in nature. On the other hand we want to know if they have accumulated genetic differences (mutations, rearrangements, differences in transposable elements).<br />Our second goal is to identify genes involved in adaptation to the host plant and and to know how their expression is regulated on the two plants. In other words, we want to know if the two variants use the same genes when making their life cycle on one or the other of the two host plants or whether certain genes are turned on (expressed) on plants and off (not expressed) on the other. The ability of a living to turn on or off certain genes depending on its environment is what is called «the regulation of gene expression.« It involves modifications of proteins and DNA or proteins associated with DNA. We want to identify some of these changes.<br />Finally we want to determine if the host plant had a role in the formation of two variants, or if they diverged before the arrival of rice and corn crops.<br />This project brings together the complementary skills of four laboratories, DGIMI for genomics of adaptation to the plant and its regulation, CBGP for phylogenetics and study of natural populations structure, INRIA Rennes for comparative genomes analysis, URGI, for comparative analysis of transposable elements.<br />

Physiology / genetics
In order to determineif the 2 variants are species or populations of the same species, we perform crosses of lab individuals. We measure the number of fertile couples. If an offspring is obtained, we check whether the larvae carry the genetic material of their parents in expected proportion. To see which genes are necessary for the insect to develop on one or the other host plants, we follow the development of the two variants on plants under controlled temperature, humidity, lighting conditions: We measure the weight of insect and their development time on the two plants.
Transcriptomics
The genetic material is stored in the cell nuclei, as genes carried by the chromosomes. Copies of genes called mRNA contain a message that can be translated into proteins in the cytoplasm of cells. To know which genes are necessary for the insect to grow on one plant, mRNA will be extracted from larvae. By sequencing, the messages coded by these mRNA will be analyzed. We will then compare the messages expressed on different plants.
Genomics
We will compare the whole genome sequence of the two insects, not only the genes, but the genomic region located between genes containing transposable elements.
Epigenomics
We will look at the factors that regulate gene expression by chromatin immunoprecipitation experiments, which permit identification of marks that are transmitted from one cell generation to the next in addition to the genetic code of bases.
Phylogenetic
It is from the comparison of gene sequences of individuals from natural populations to trace their genealogy and estimate their divergence times.
phylogeographic / population genetics
It is to study the distribution of the two variants over a wide geographical area. At a more local level we try to see if variants cross each other in nature, looking if they exchange genes and they have alleles (forms of genes) in common by sequence analysis of some markers in individuals collected in the field.

When we cross the two strains, in one direction of the cross ((corn female with rice male), the number of viable eggs obtained is reduced compared to the result obtained in the reciprocal cross. When we follow segregation of genetic markers at the second generation, we find that half of them show unexpected genetic ratio: These results are indicative of some genetic incompatibility between the strains and show that they are closer to two sister species than to two strains. Through phylogenetic analysis of individuals taken in the wild, we could show also that the two strains are as divergent as well characterized pairs of species taken in the genus. Experiments carried out on plants showed that the two strains survive better on their host-plant than on the alternative host. Nevertheless, both strains weight better on corn than on rice. Concerning gene expression depending on the host plant, we found more differences when we compare the same strain on two host-plants than when we compare the two variants on the same plant. Among these genes, some were expected to participate in adaptation to the plant, while some others have an unknown function. Concerning the genome comparison of the two strains, a database has been built in order to allow visualization of genes and transposable elements of the corn strain by the international community. For the rice strain, genome sequence and recently been assemblesd, and comparison with the corn strain genome is currently starting.

Development of new insecticides
Knowledge about the two pest genomes organization will help deciphering mechanisms responsible for resistance to currently used pesticides and may allow identification of new target genes for insecticides in an environment friendly, biological plant protection purpose.
Control of pest populations:
Il we see that pairs resulting from the crossing of the two variants are infertile, a possibility to limit expansion of one of them, would be to release an excess of males from the other. If we see that the variants have better performance on one plant compared to the other, a possibility to reduce populations would be to alternate cultures or to create entrapment aereas.
Analysis of the structure of natural populations is a milestone to model the evolution of populations in response to invasions consecutive of climate change or human exchange.

Peered review journals:
1. P. Dumas, F. Legeai, E. Scaon, C. Lemaitre, K. Labadie, S. Gimenez, A.-L. Clamens, P. Fournier, G.J. Kergoat, and E. d’Alençon. 2014. Spodoptera frugiperda host plant variants: two strains or two distinct species? Submitted to BMC Genetics.
2. P. Dumas, J. Barbut, B.P. Le Ru, J.F. Sylvain, A.L. Clamens, E. d’Alençon, GJ. Kergoat. 2014. Molecular species delimitations unravel potential new species in the pest genus Spodoptera (Lepidoptera, Noctuidae). To be submitted to Mol. Phyl. Evol.
Communications to international conferences:
1. P. Dumas, G. J. Kergoat, F. Legeai, C. Lemaitre, A. Breteaudau, E. Scaon, A.L. Clamens, S. Gimenez, M. Orsucci, N. Nègre, E. d’Alençon. Questioning the status of the two FAW (Spodoptera frugiperda, Noctuidae) host races using integrative approaches.The Seventh International Symposium on Molecular Insect Science. Amsterdam. July 2014.
2. E. d’Alençon et al. Invited speaker at the workshop « the International Meeting on Spodoptera litura genome project » in Chongqing, China, January 6-7 2014.
3. P. Dumas, G. J. Kergoat, A.L. Clamens, S. Gimenez, E. d’Alençon. Questioning the status of the two FAW (Spodoptera frugiperda, Noctuidae) host races using integrative approaches.
Congress of the European Society for Evolutionary Biology, Lisbon, 19-August 24th, 2013.
1. P. Dumas, G. J. Kergoat, A.L. Clamens, S. Gimenez, E. d’Alençon. Questioning the status of the two FAW (Spodoptera frugiperda, Noctuidae) host races using integrative approaches. Congrès de Biologie de l’Insecte. Montpellier. October 2013.
2. P. Dumas, G. J. Kergoat, A.L. Clamens, S. Gimenez, E. d’Alençon. Questioning the status of the two FAW (Spodoptera frugiperda, Noctuidae) host races using integrative approaches. ADALEP network workshop. Paris. February 2014.
3. N. Nègre Genetic and epigenetic variations associated to host plant specialization of Spodoptera frugiperda (Fall Army Worm) - Congrès de Biologie de l’Insecte, Montpellier, October 2013.

While a global food crisis threatens, 20 % of crops are eaten by insects. Providing knowledge on insect pest genomes, and on the ability of insects to adapt to different host-plants and to diversify may help deciphering new crop plant protection strategies. One such pest is the Lepidoptera Spodoptera frugiperda, the fall armyworm (FAW). It exists as two different host-plant strains, one mostly associated to corn (C strain) whereas the other is mostly associated to rice (R strain). The two strains are morphologically indistinguishable but they exhibit pheromone and behavioral differences, and some degree of genetic incompatibility.
The first aim of the project is to record all sources of genetic variation between the two strains by comparing the whole genomes of both lab strains, but also by measuring levels of host-based genetic divergence and of genes flow between field individuals on different host-plants. The second aim of the project is to identify genes involved in adaptation to the host-plant and their regulation, and to determine if adaptation to the host-plant has a role in speciation.
We will start the project from the already available full genome assembly and genes annotation of the C strain genome(from Genoscope), and the whole genome assembly of the R strain (from one/two laboratory individuals in each case) as well as from transcriptomic data of both strains and of a 300 microsatellites markers based genetic map.
The project will include:
- A complete structural annotation of both laboratory strains recording all orthologs, and mutations (SNP, rearrangements, TE insertions) that make heterogeneity between the two genomes. Candidate genes under divergent selection or under the direct influence of positive selection will be listed.
- A functional annotation of the two genomes. It will be performed by comparing transcriptomes (mRNAs and small ncRNAs) of the two strains on two host-plants at larval and adult stages. Genes with modulated expression will be identified and their epigenetic regulators (histones modifications and small ncRNAs) will be analyzed on the same samples.
Analysis of these data will rely on bioinformatic data integration effort.
- A set of 50 genes chosen among divergent and differentially expressed genes will be further analyzed. We will focus on gene families possibly involved in host-plant adaptation. We will check on field individuals if the modulated expression variation is found also associated to the host-plant, or if divergent alleles are enriched in natural populations on the cognate host-plants. We will also follow the expression level and sequence of these genes in laboratory individuals upon 12 successive host-plant choice trials in order to check whether they are subject to microevolution.
- A measurement of host-based genetic divergence and genes flow between individuals on different host-plants at a local scale. We will perform a phylogeographic analysis in order to describe population structure and measure strain divergence at a regional scale.
The consortium includes four partners. The DGIMI’s coordinator lab is expert in genomics, transcriptomics and epigenomics of insects. The URGI lab is expert in de novo detection of Transposable Elements (TE) in genomes and their classification, Symbiose lab is expert in bioinformatic treatment and analysis of genomic and post-genomic data, whereas CBGP lab is expert in population genetics and phylogeography of insects. . None of the partner would have been able to conduct such a project alone, and the complementary expertises in genomics, genetics, evolution and bio-informatics will constitute a major strength for this joint scientific innovative

Project coordinator

Madame Emmanuelle d'Alençon (Diversité, Génomes et Interactions micro-organismes insectes) – alencon@supagro.inra.fr

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

DGIMI Diversité, Génomes et Interactions micro-organismes insectes
UMR1062 Centre de Biologie et Génétique des Populations
URGI Unité de Recherche Génomique Info
INRIA Rennes - Bretagne Atlantique INRIA, centre de recherche de Rennes - Bretagne Atlantique

Help of the ANR 409,007 euros
Beginning and duration of the scientific project: October 2012 - 36 Months

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