Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization
The lichen symbiosis – consisting of fungal mycobionts and photoautotroph photobionts (green algae or cyanobacteria) – is globally successful. It covers an estimated 6% of the global surface with habitats ranging from deserts to the arctic. This success is reflected in the diversity of the mycobiont...
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ftunivfrankfurt:oai:publikationen.ub.uni-frankfurt.de:45701 2023-09-05T13:17:43+02:00 Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization Tzovaras, Bastian Greshake 2018-02-12 application/pdf http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/45701 https://nbn-resolving.org/urn:nbn:de:hebis:30:3-457013 http://publikationen.ub.uni-frankfurt.de/files/45701/BG_00-thesis-merged.v4.for_print.pdf eng eng http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/45701 urn:nbn:de:hebis:30:3-457013 https://nbn-resolving.org/urn:nbn:de:hebis:30:3-457013 http://publikationen.ub.uni-frankfurt.de/files/45701/BG_00-thesis-merged.v4.for_print.pdf http://publikationen.ub.uni-frankfurt.de/home/index/help#policies info:eu-repo/semantics/openAccess ddc:570 doctoralthesis doc-type:doctoralThesis 2018 ftunivfrankfurt 2023-08-13T22:40:30Z The lichen symbiosis – consisting of fungal mycobionts and photoautotroph photobionts (green algae or cyanobacteria) – is globally successful. It covers an estimated 6% of the global surface with habitats ranging from deserts to the arctic. This success is reflected in the diversity of the mycobionts, with around 21% of all fungal species participating in lichen symbioses that can be facultative or obligate. Lichenization is furthermore evolutionary old, with fossil evidence for lichens reaching back 415 million years. For an individual fungal lineage, the Lecanoromycetes, the lichenization happened around 300 million years ago. This longstanding symbiotic relationship and the diversity of observed symbiotic dependency make them promising models to study the genomic consequences that follow the establishment of symbioses. Despite this, only little is known about the genomic effects of lichenization and extreme symbiotic dependency. To fill this gap we sequenced the hologenome of the lichen Lasallia pustulata, where the mycobiont could so far not been cultivated, suggesting that it might be more dependent on its symbionts. As the poor culturability of lichen symbionts renders their genomes inaccessible to standard sequencing practices, we evaluated the extent to which different metagenome sequencing- and de novo assembly-strategies can be used to sequence and reconstruct the genomes of the individual symbionts. We find that the abundances of individual genomes present in the L. pustulata hologenome vary substantially, with the mycobiont being most abundant. Using in silico generated data sets and real Illumina sequencing data for L. pustulata we observe that the skewed abundances prevent a contiguous assembly of the underrepresented genomes when using only short-read sequencing. We conclude that short-read sequencing can offer first insights into lichen hologenomes. The fragmentation of the reconstructions hinders downstream analyses into the genomic consequences of lichenization though, as these are focused on ... Doctoral or Postdoctoral Thesis Arctic Publication Server of Goethe University Frankfurt am Main Arctic |
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Publication Server of Goethe University Frankfurt am Main |
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English |
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ddc:570 Tzovaras, Bastian Greshake Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization |
topic_facet |
ddc:570 |
description |
The lichen symbiosis – consisting of fungal mycobionts and photoautotroph photobionts (green algae or cyanobacteria) – is globally successful. It covers an estimated 6% of the global surface with habitats ranging from deserts to the arctic. This success is reflected in the diversity of the mycobionts, with around 21% of all fungal species participating in lichen symbioses that can be facultative or obligate. Lichenization is furthermore evolutionary old, with fossil evidence for lichens reaching back 415 million years. For an individual fungal lineage, the Lecanoromycetes, the lichenization happened around 300 million years ago. This longstanding symbiotic relationship and the diversity of observed symbiotic dependency make them promising models to study the genomic consequences that follow the establishment of symbioses. Despite this, only little is known about the genomic effects of lichenization and extreme symbiotic dependency. To fill this gap we sequenced the hologenome of the lichen Lasallia pustulata, where the mycobiont could so far not been cultivated, suggesting that it might be more dependent on its symbionts. As the poor culturability of lichen symbionts renders their genomes inaccessible to standard sequencing practices, we evaluated the extent to which different metagenome sequencing- and de novo assembly-strategies can be used to sequence and reconstruct the genomes of the individual symbionts. We find that the abundances of individual genomes present in the L. pustulata hologenome vary substantially, with the mycobiont being most abundant. Using in silico generated data sets and real Illumina sequencing data for L. pustulata we observe that the skewed abundances prevent a contiguous assembly of the underrepresented genomes when using only short-read sequencing. We conclude that short-read sequencing can offer first insights into lichen hologenomes. The fragmentation of the reconstructions hinders downstream analyses into the genomic consequences of lichenization though, as these are focused on ... |
format |
Doctoral or Postdoctoral Thesis |
author |
Tzovaras, Bastian Greshake |
author_facet |
Tzovaras, Bastian Greshake |
author_sort |
Tzovaras, Bastian Greshake |
title |
Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization |
title_short |
Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization |
title_full |
Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization |
title_fullStr |
Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization |
title_full_unstemmed |
Characterizing the hologenome of Lasallia pustulata and tracing genomic footprints of lichenization |
title_sort |
characterizing the hologenome of lasallia pustulata and tracing genomic footprints of lichenization |
publishDate |
2018 |
url |
http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/45701 https://nbn-resolving.org/urn:nbn:de:hebis:30:3-457013 http://publikationen.ub.uni-frankfurt.de/files/45701/BG_00-thesis-merged.v4.for_print.pdf |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/45701 urn:nbn:de:hebis:30:3-457013 https://nbn-resolving.org/urn:nbn:de:hebis:30:3-457013 http://publikationen.ub.uni-frankfurt.de/files/45701/BG_00-thesis-merged.v4.for_print.pdf |
op_rights |
http://publikationen.ub.uni-frankfurt.de/home/index/help#policies info:eu-repo/semantics/openAccess |
_version_ |
1776198778455326720 |