Metatranscriptomics and multi-omics exploration of the phyllosphere and rhizosphere of potato and cassava
(2022) BINP52 20212Degree Projects in Bioinformatics
- Abstract
- As important components of the ecological system on earth, microorganisms and plants collectively constitute an assemblage of species called the holobionts. Microorganisms play an important role in the growth, development, and immunity of plants. Microorganisms may act as pathogens of plants, but they may also contribute to plant growth and development as well as help plants to tolerate both biotic and abiotic stresses. Genetic features of plant hosts can influence the structure and diversity of microbiota inhabiting them. Through the study of microbes living in the phyllosphere and rhizosphere of plants, it is possible to regulate all aspects of plant growth and development, and to significantly improve crop yields and quality in the... (More)
- As important components of the ecological system on earth, microorganisms and plants collectively constitute an assemblage of species called the holobionts. Microorganisms play an important role in the growth, development, and immunity of plants. Microorganisms may act as pathogens of plants, but they may also contribute to plant growth and development as well as help plants to tolerate both biotic and abiotic stresses. Genetic features of plant hosts can influence the structure and diversity of microbiota inhabiting them. Through the study of microbes living in the phyllosphere and rhizosphere of plants, it is possible to regulate all aspects of plant growth and development, and to significantly improve crop yields and quality in the agricultural industry. In this study, metatranscriptomics has been applied to study the microbiome of the world's most important crops, Potato (Solanum tuberosum L.) and cassava (Manihot esculenta Crantz). Metatranscriptomics analysis was performed using a combination of two strategies based on two different microbial classifiers, each of which was applied separately to short reads and long contigs. Additionally, a multi-omics analysis tool was introduced as a means of providing a comprehensive analysis of the integration of different omics data. In conclusion, the site-specificity of fungi living on potato leaves has been determined using short reads and long contigs. Additionally, it was discovered that both the cassava genotype and root color had an influence on microbial community composition. In the multi-omics analysis, a significant factor explaining the source of variation in all modalities was identified. (Less)
- Popular Abstract
- The microscopic world in plant leaf and root
There is a mysterious microscopic world existing in the leaves and roots of plants. It is invisible but constantly at work. ——The microorganisms, which inhabit every corner of the planet, including plants. Potatoes and cassava, two of the world's most important food crops, naturally host a variety of microorganisms. Microbes play a significant role in the growth and development of these two crops up to the point when they are consumed by people. Microorganisms influence indirectly the amount of nutrition that people can get from crops, as well as the taste of the crops.
We collected RNA from the field, which is comprised of both microbes and plants. The mixed RNA data of various species is... (More) - The microscopic world in plant leaf and root
There is a mysterious microscopic world existing in the leaves and roots of plants. It is invisible but constantly at work. ——The microorganisms, which inhabit every corner of the planet, including plants. Potatoes and cassava, two of the world's most important food crops, naturally host a variety of microorganisms. Microbes play a significant role in the growth and development of these two crops up to the point when they are consumed by people. Microorganisms influence indirectly the amount of nutrition that people can get from crops, as well as the taste of the crops.
We collected RNA from the field, which is comprised of both microbes and plants. The mixed RNA data of various species is called the metatranscriptome. We hoped to distinguish microbial RNA from plant RNA with the help of a huge RNA database and learn how plant hosts affect microbes in different ways. We first separated plant RNA from the metatranscriptome and then used a classification software to identify specific microorganisms. In addition to this, we also used multi-omics tools to explore the association between RNA data and metabolite data also collected from the field.
We were finally able to identify a variety of microorganisms, which reside in potato and cassava. It was also found that the genetics composition of the host plants (species and cultivars of potato and cassava, including the colour of the cassava root) contribute to the differences between microbiomes. Furthermore, the location in which potatoes were grown impacted the composition of microbial communities. If we know what microorganisms are living on crops, we can uncover a previous hidden aspect of agricultural production and regulate the growth and development of crops, thus improving both quality and yield of crops.
Master’s Degree Project in Biology/Molecular Biology/Bioinformatics 60 credits 2022
Department of Biology, Lund University
Advisor: Erik Alexandersson
Department of Plant Protection Biology, Swedish University of Agricultural Sciences
Co-advisor: Andreas Gisel
International Institute of Tropical Agriculture (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9102731
@misc{9102731,
abstract = {{As important components of the ecological system on earth, microorganisms and plants collectively constitute an assemblage of species called the holobionts. Microorganisms play an important role in the growth, development, and immunity of plants. Microorganisms may act as pathogens of plants, but they may also contribute to plant growth and development as well as help plants to tolerate both biotic and abiotic stresses. Genetic features of plant hosts can influence the structure and diversity of microbiota inhabiting them. Through the study of microbes living in the phyllosphere and rhizosphere of plants, it is possible to regulate all aspects of plant growth and development, and to significantly improve crop yields and quality in the agricultural industry. In this study, metatranscriptomics has been applied to study the microbiome of the world's most important crops, Potato (Solanum tuberosum L.) and cassava (Manihot esculenta Crantz). Metatranscriptomics analysis was performed using a combination of two strategies based on two different microbial classifiers, each of which was applied separately to short reads and long contigs. Additionally, a multi-omics analysis tool was introduced as a means of providing a comprehensive analysis of the integration of different omics data. In conclusion, the site-specificity of fungi living on potato leaves has been determined using short reads and long contigs. Additionally, it was discovered that both the cassava genotype and root color had an influence on microbial community composition. In the multi-omics analysis, a significant factor explaining the source of variation in all modalities was identified.}},
author = {{Li, Leli}},
language = {{eng}},
note = {{Student Paper}},
title = {{Metatranscriptomics and multi-omics exploration of the phyllosphere and rhizosphere of potato and cassava}},
year = {{2022}},
}