Trujillo, D. | Search bioRxiv

bioRxiv2023

Accurate identification of Helicoverpa armigera / Helicoverpa zea hybrids using genome admixture analysis: implications for genomic surveillance

Helicoverpa armigera, the cotton bollworm moth, is one of the worlds most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive H.armigera has been reported to hybridize with local populations of Helicoverpa zea. The correct identification of H.armigera-H.zea hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate H.zea pesticide resistance and host plant range via introgression of H.armigera genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two H.armigera-H.zea F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8 % H.armigera for both F1 hybrids, confirming its accuracy. Genome sequences from five H.zea and one H.armigera that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four H.zea genomes generated from a previous study are predicted to possess a proportion of H.armigera genetic material. Using unsupervised clustering to identify non-hybridized H.armigera and H.zea genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor H.armigera component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of H.armigera-H.zea hybrids, and suggest measures that will improve such analyses.

genomics↗

bioRxiv2020

Environment dependence of rhizobial relative fitness in the legume-rhizobia symbiosis

The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and evolution of rhizobia and their symbiotic interactions with hosts. We examined how host genotype, nitrogen addition, rhizobial density, and community complexity affected selection on 68 rhizobia strains in the Ensifer meliloti - Medicago truncatula mutualism. As expected, the host genotype had the most substantial effect on the size, number, and strain composition of root nodules (the symbiotic organ). The understudied environmental variable of rhizobial density had a more significant effect on strain frequency in nodules than the addition of low nitrogen levels. Higher inoculum density resulted in a nodule community that was less diverse and more beneficial but only in the context of the more selective host genotype. Higher density resulted in more diverse and less beneficial nodule communities with the less selective host. Density effects on strain composition deserve additional scrutiny as they can create eco-evolutionary feedback. Lastly, we found that relative strain rankings were stable across increasing community complexity (community complexity (2, 3, 8, or 68 strains). This unexpected result suggests that higher-order interactions between strains are rare in the context of host nodule formation and development. Taken together, our empirical work highlights the importance of developing new theoretical predictions that incorporate density dependence. Further, it has translational relevance for overcoming establishment barriers in bio-inoculants and motivating host breeding programs that maintain beneficial plant-microbe interactions across diverse agro-ecological contexts. IMPORTANCELegume cash, forage, and cover crops establish beneficial associations with rhizobial bacteria who perform biological nitrogen fixation (BNF)--providing Nitrogen (N) fertilizer to plants without the economic and greenhouse gas emission costs of chemical N inputs. Here, for the first time, we examine the relative influence of three environmental factors that vary in agricultural fields on strain relative fitness in nodules when scores rhizobial strains compete. In addition to manipulating Nitrogen, we also use two biotic variables that have rarely been examined: the rhizobial communitys density and complexity. Taken together, our results suggest 1) breeding legume varieties that select beneficial strains despite environmental variation are possible, 2) changes in rhizobial population densities that occur routinely in agricultural fields could drive evolutionary changes in rhizobia populations, and 3) the lack of higher-order interactions between strains will allow the high-throughput assessments of rhizobia winners and losers during plant interactions.

ecology↗