The genomic basis and gene expression of adaptation to a novel host plant in the peacock fly Tephritis conura
(2023) BINP51 20222Degree Projects in Bioinformatics
- Abstract
- The genetic underpinnings of ecological adaptations, such as host-plant use in herbivorous insects, is a vital area of research in evolutionary biology because they reveal how phenotypic variation arises and the extent to which this can happen through parallel mechanisms. This study provides unique insights into the genomic basis and gene expression changes in Tephritis conura's adaptation to new host plants. Utilizing genome-wide analysis from 31 T. conura specimens, along with an examination of host-associated transcriptional differences, we investigated the impact of these adaptations on the fly's genome and phenotypic plasticity. Genomic differentiation and population structure analyses did not indicate genetic clustering according to... (More)
- The genetic underpinnings of ecological adaptations, such as host-plant use in herbivorous insects, is a vital area of research in evolutionary biology because they reveal how phenotypic variation arises and the extent to which this can happen through parallel mechanisms. This study provides unique insights into the genomic basis and gene expression changes in Tephritis conura's adaptation to new host plants. Utilizing genome-wide analysis from 31 T. conura specimens, along with an examination of host-associated transcriptional differences, we investigated the impact of these adaptations on the fly's genome and phenotypic plasticity. Genomic differentiation and population structure analyses did not indicate genetic clustering according to host plant use, suggesting phenotypic plasticity as the primary adaptation mechanism. Yet, specific genomic regions exhibited differentiation based on the fly's host plant, indicating potential local adaptations. A Gene Ontology (GO) enrichment analysis illuminated significant representation of metabolic processes and organelle assembly regulation in differentiating genomic regions, potentially suggesting differential metabolic adaptations. Host plant-related genomic variations were found mostly outside of genes showing differential expression, supporting phenotypic plasticity as a crucial adaptive response. The genetic differentiation of host plant adaptation revealed potential mechanisms for interacting with and adapting to different host plants. Nevertheless, our results suggested limited parallelism between early host use divergence and late stages of host-associated differentiation. Overall, this study advances our understanding of the interplay between genomics and phenotypic plasticity in ecological adaptations, underscoring the complex mechanisms of host plant adaptation in T. conura, and providing a foundation for future research into the genomic features underlying ecological speciation. (Less)
- Popular Abstract
- The Secret Lives of Flies: Unravelling the Mysteries of Plant-Host Adaptation
Have you ever wondered about the tiny creatures flitting about our gardens and fields? Believe it or not, they might be engaged in a complex evolutionary dance that is every bit as fascinating as the great migrations of birds or the deep-sea travels of whales. This article unveils a recent exploration into the world of Tephritis conura, commonly known as the true fruit flies, shedding light on their intriguing journey of adaptation and survival.
The primary stars of this narrative are two fruit fly ecotypes, or ecologically different varieties, in Scotland, known for their ability to thrive on two different types of thistle plants: Cirsium heterophyllum and... (More) - The Secret Lives of Flies: Unravelling the Mysteries of Plant-Host Adaptation
Have you ever wondered about the tiny creatures flitting about our gardens and fields? Believe it or not, they might be engaged in a complex evolutionary dance that is every bit as fascinating as the great migrations of birds or the deep-sea travels of whales. This article unveils a recent exploration into the world of Tephritis conura, commonly known as the true fruit flies, shedding light on their intriguing journey of adaptation and survival.
The primary stars of this narrative are two fruit fly ecotypes, or ecologically different varieties, in Scotland, known for their ability to thrive on two different types of thistle plants: Cirsium heterophyllum and C. palustre. Their European counterparts, on the other hand, prefer to stick to one plant type, showcasing a ‘pickier’ dietary preference. It is a bit like some people being content with a particular cuisine, while others embrace a smorgasbord of culinary delights.
In this project, we aimed to understand genomic (changes in the DNA sequences) and transcriptomic (changes in the genes expressed) differences that underly the different ecotypes. We compared the genetic background of the two Scottish ecotypes, first to determine whether they represent two different groups or one interbreeding population, then to identify regions of the genome that differ between the Scottish and continental flies. In this process, we determined that the Scottish flies are not likely to be two isolated groups, but a single population with individuals that can use either host plant. The flies have evolved genetic differences from the continental populations that likely underly this wider range in diet. Notably, it appears they express different genes that allow them to switch between different types of host plants. Fascinatingly, their evolution has equipped them with a broad range of strategies, from regulating their metabolism to adapting their cellular machinery, all in the service of their survival.
Meanwhile, the ‘choosier’ European flies, like specialists, have refined their genes to exploit their preferred plant hosts most efficiently, resulting in much larger genomic differences between continental specialist populations than we found between the Scottish ecotypes. They are somewhat like connoisseurs who know every detail about their chosen interest and use this knowledge to their advantage. In this case, however, it has resulted in these populations becoming more isolated from one another and more divergent at the genomic level.
Understanding precisely how these genomic and transcriptomic differences contribute to the ability to eat the different thistle host plants will require further investigation. For example, this research also opened new questions around the large number of highly repetitive genetic elements in Tephritis conura, which could play a significant role in its evolutionary story. In conclusion, this exploration into the world of fruit flies is a testament to the vast and intricate interplay of evolution, adaptation, and survival. It underscores how much there is still to discover and appreciate in the world around us - even in the tiniest of inhabitants.
Master’s Degree Project in Bioinformatics 45 credits 2023
Department of Biology, Lund University
Advisor: Rachel Steward
Advisors Lund University/Department of Biology (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9135472
- author
- Huang, Yajuan
- supervisor
- organization
- course
- BINP51 20222
- year
- 2023
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 9135472
- date added to LUP
- 2023-08-29 10:34:54
- date last changed
- 2023-08-29 10:34:54
@misc{9135472,
abstract = {{The genetic underpinnings of ecological adaptations, such as host-plant use in herbivorous insects, is a vital area of research in evolutionary biology because they reveal how phenotypic variation arises and the extent to which this can happen through parallel mechanisms. This study provides unique insights into the genomic basis and gene expression changes in Tephritis conura's adaptation to new host plants. Utilizing genome-wide analysis from 31 T. conura specimens, along with an examination of host-associated transcriptional differences, we investigated the impact of these adaptations on the fly's genome and phenotypic plasticity. Genomic differentiation and population structure analyses did not indicate genetic clustering according to host plant use, suggesting phenotypic plasticity as the primary adaptation mechanism. Yet, specific genomic regions exhibited differentiation based on the fly's host plant, indicating potential local adaptations. A Gene Ontology (GO) enrichment analysis illuminated significant representation of metabolic processes and organelle assembly regulation in differentiating genomic regions, potentially suggesting differential metabolic adaptations. Host plant-related genomic variations were found mostly outside of genes showing differential expression, supporting phenotypic plasticity as a crucial adaptive response. The genetic differentiation of host plant adaptation revealed potential mechanisms for interacting with and adapting to different host plants. Nevertheless, our results suggested limited parallelism between early host use divergence and late stages of host-associated differentiation. Overall, this study advances our understanding of the interplay between genomics and phenotypic plasticity in ecological adaptations, underscoring the complex mechanisms of host plant adaptation in T. conura, and providing a foundation for future research into the genomic features underlying ecological speciation.}},
author = {{Huang, Yajuan}},
language = {{eng}},
note = {{Student Paper}},
title = {{The genomic basis and gene expression of adaptation to a novel host plant in the peacock fly Tephritis conura}},
year = {{2023}},
}