Chloroplast and nuclear phylogenomics reveals concordant phylogenetic structure in wild tomatoes (Solanum sect. Lycopersicon, Solanaceae)

Research output: Conference materialsPosterResearchpeer-review

Abstract

Tomato (Solanum lycopersicon) is one of the most important crops worldwide with 177 million tonnes produced over 4.7 million ha. Compared to many other crops plant used in commercial production show very little genetic variation due to selection for a limited set of traits during its domestication. This group consisting of 13 inter-crossable diploid (2n = 2x = 24) species under extensive taxonomic studies, is an important source of traits and genes for tomato improvement. Tomato is the most intensively studied solanaceous species both in terms of its genetics and genomics. In addition to marker, sequence, and bioinformatic resources, various molecular genetic tools for functional analyses have been developed extensively. It is surprizing that these large-scale genome-sequencing initiatives generated quasi-complete plastid sequences, which were later discarded as non-target contamination without further analysis. They provide an untapped treasure trove of plastid genomic in raw read archives and other repositories for tomatoes. Chloroplast DNA is organized in compact gene-rich genomes, which are present in high copy number within plant cells. In Solanaceae plastid gene content and synteny are highly conserved, which is also preserved to some level in the intergenic spacer regions (IGS & ITS). In the present study, we utilized high-throughput sequencing data to gather a transcriptome based nuclear matrix and to assemble complete plastid genome sequences for all species of the core tomato clade (Solanum sect. Lycopersicon). We compare the genome organization, structure and phylogenetic relationships based on these data and investigate incongruences found between nuclear and plastid genomic trees. Our study allowed us to construct the first interspecific analysis including all species of wild tomatoes based on entire plastid sequences and compare genomic rearrangements with congeneric taxa. We found that plastome based trees provide strong support for two major groups in the tomato clade with S. pennellii and S. habrochaites in two distinct groups with the rest of the species. On the other hand, these two species form a clade in a basal position as compared with other tomato species in the phylogenetic analyses based on nuclear genes. This topological incongruence observed might be caused by the chloroplast capture event. In this process, a new combination of nuclear and chloroplast genomes were formed through inter-species hybridization and subsequent backcrosses with S. pennellii and S. habrochaites. Cross-species transfer of the chloroplast from one species to another has been reported among hybridizing plant groups, but it has not been hypothesised previously in Solanaceae.
Original languageEnglish
Pages78
Number of pages1
Publication statusPublished - 2018
MoE publication typeNot Eligible
EventThe 15th Solanaceae Conference: Applied Genomics, Accelerated Breeding, Gene Targeting - Le Meridien, Chiang Mai, Thailand
Duration: 30 Sep 20184 Oct 2018
Conference number: 15
https://www.solanaceae2018.com/

Conference

ConferenceThe 15th Solanaceae Conference
CountryThailand
CityChiang Mai
Period30/09/201804/10/2018
Internet address

Fields of Science

  • 414 Agricultural biotechnology
  • 1183 Plant biology, microbiology, virology
  • 1181 Ecology, evolutionary biology

Cite this

@conference{e429c7841a4442b09981b6b22be1ad98,
title = "Chloroplast and nuclear phylogenomics reveals concordant phylogenetic structure in wild tomatoes (Solanum sect. Lycopersicon, Solanaceae)",
abstract = "Tomato (Solanum lycopersicon) is one of the most important crops worldwide with 177 million tonnes produced over 4.7 million ha. Compared to many other crops plant used in commercial production show very little genetic variation due to selection for a limited set of traits during its domestication. This group consisting of 13 inter-crossable diploid (2n = 2x = 24) species under extensive taxonomic studies, is an important source of traits and genes for tomato improvement. Tomato is the most intensively studied solanaceous species both in terms of its genetics and genomics. In addition to marker, sequence, and bioinformatic resources, various molecular genetic tools for functional analyses have been developed extensively. It is surprizing that these large-scale genome-sequencing initiatives generated quasi-complete plastid sequences, which were later discarded as non-target contamination without further analysis. They provide an untapped treasure trove of plastid genomic in raw read archives and other repositories for tomatoes. Chloroplast DNA is organized in compact gene-rich genomes, which are present in high copy number within plant cells. In Solanaceae plastid gene content and synteny are highly conserved, which is also preserved to some level in the intergenic spacer regions (IGS & ITS). In the present study, we utilized high-throughput sequencing data to gather a transcriptome based nuclear matrix and to assemble complete plastid genome sequences for all species of the core tomato clade (Solanum sect. Lycopersicon). We compare the genome organization, structure and phylogenetic relationships based on these data and investigate incongruences found between nuclear and plastid genomic trees. Our study allowed us to construct the first interspecific analysis including all species of wild tomatoes based on entire plastid sequences and compare genomic rearrangements with congeneric taxa. We found that plastome based trees provide strong support for two major groups in the tomato clade with S. pennellii and S. habrochaites in two distinct groups with the rest of the species. On the other hand, these two species form a clade in a basal position as compared with other tomato species in the phylogenetic analyses based on nuclear genes. This topological incongruence observed might be caused by the chloroplast capture event. In this process, a new combination of nuclear and chloroplast genomes were formed through inter-species hybridization and subsequent backcrosses with S. pennellii and S. habrochaites. Cross-species transfer of the chloroplast from one species to another has been reported among hybridizing plant groups, but it has not been hypothesised previously in Solanaceae.",
keywords = "414 Agricultural biotechnology, 1183 Plant biology, microbiology, virology, 1181 Ecology, evolutionary biology",
author = "P{\'e}ter Poczai and Ali Amiryousefi and Hyv{\"o}nen, {Jaakko Tapani} and Gaurav Sablok",
year = "2018",
language = "English",
pages = "78",
note = "The 15th Solanaceae Conference : Applied Genomics, Accelerated Breeding, Gene Targeting ; Conference date: 30-09-2018 Through 04-10-2018",
url = "https://www.solanaceae2018.com/",

}

Chloroplast and nuclear phylogenomics reveals concordant phylogenetic structure in wild tomatoes (Solanum sect. Lycopersicon, Solanaceae). / Poczai, Péter; Amiryousefi, Ali; Hyvönen, Jaakko Tapani; Sablok, Gaurav.

2018. 78 Poster session presented at The 15th Solanaceae Conference, Chiang Mai, Thailand.

Research output: Conference materialsPosterResearchpeer-review

TY - CONF

T1 - Chloroplast and nuclear phylogenomics reveals concordant phylogenetic structure in wild tomatoes (Solanum sect. Lycopersicon, Solanaceae)

AU - Poczai, Péter

AU - Amiryousefi, Ali

AU - Hyvönen, Jaakko Tapani

AU - Sablok, Gaurav

PY - 2018

Y1 - 2018

N2 - Tomato (Solanum lycopersicon) is one of the most important crops worldwide with 177 million tonnes produced over 4.7 million ha. Compared to many other crops plant used in commercial production show very little genetic variation due to selection for a limited set of traits during its domestication. This group consisting of 13 inter-crossable diploid (2n = 2x = 24) species under extensive taxonomic studies, is an important source of traits and genes for tomato improvement. Tomato is the most intensively studied solanaceous species both in terms of its genetics and genomics. In addition to marker, sequence, and bioinformatic resources, various molecular genetic tools for functional analyses have been developed extensively. It is surprizing that these large-scale genome-sequencing initiatives generated quasi-complete plastid sequences, which were later discarded as non-target contamination without further analysis. They provide an untapped treasure trove of plastid genomic in raw read archives and other repositories for tomatoes. Chloroplast DNA is organized in compact gene-rich genomes, which are present in high copy number within plant cells. In Solanaceae plastid gene content and synteny are highly conserved, which is also preserved to some level in the intergenic spacer regions (IGS & ITS). In the present study, we utilized high-throughput sequencing data to gather a transcriptome based nuclear matrix and to assemble complete plastid genome sequences for all species of the core tomato clade (Solanum sect. Lycopersicon). We compare the genome organization, structure and phylogenetic relationships based on these data and investigate incongruences found between nuclear and plastid genomic trees. Our study allowed us to construct the first interspecific analysis including all species of wild tomatoes based on entire plastid sequences and compare genomic rearrangements with congeneric taxa. We found that plastome based trees provide strong support for two major groups in the tomato clade with S. pennellii and S. habrochaites in two distinct groups with the rest of the species. On the other hand, these two species form a clade in a basal position as compared with other tomato species in the phylogenetic analyses based on nuclear genes. This topological incongruence observed might be caused by the chloroplast capture event. In this process, a new combination of nuclear and chloroplast genomes were formed through inter-species hybridization and subsequent backcrosses with S. pennellii and S. habrochaites. Cross-species transfer of the chloroplast from one species to another has been reported among hybridizing plant groups, but it has not been hypothesised previously in Solanaceae.

AB - Tomato (Solanum lycopersicon) is one of the most important crops worldwide with 177 million tonnes produced over 4.7 million ha. Compared to many other crops plant used in commercial production show very little genetic variation due to selection for a limited set of traits during its domestication. This group consisting of 13 inter-crossable diploid (2n = 2x = 24) species under extensive taxonomic studies, is an important source of traits and genes for tomato improvement. Tomato is the most intensively studied solanaceous species both in terms of its genetics and genomics. In addition to marker, sequence, and bioinformatic resources, various molecular genetic tools for functional analyses have been developed extensively. It is surprizing that these large-scale genome-sequencing initiatives generated quasi-complete plastid sequences, which were later discarded as non-target contamination without further analysis. They provide an untapped treasure trove of plastid genomic in raw read archives and other repositories for tomatoes. Chloroplast DNA is organized in compact gene-rich genomes, which are present in high copy number within plant cells. In Solanaceae plastid gene content and synteny are highly conserved, which is also preserved to some level in the intergenic spacer regions (IGS & ITS). In the present study, we utilized high-throughput sequencing data to gather a transcriptome based nuclear matrix and to assemble complete plastid genome sequences for all species of the core tomato clade (Solanum sect. Lycopersicon). We compare the genome organization, structure and phylogenetic relationships based on these data and investigate incongruences found between nuclear and plastid genomic trees. Our study allowed us to construct the first interspecific analysis including all species of wild tomatoes based on entire plastid sequences and compare genomic rearrangements with congeneric taxa. We found that plastome based trees provide strong support for two major groups in the tomato clade with S. pennellii and S. habrochaites in two distinct groups with the rest of the species. On the other hand, these two species form a clade in a basal position as compared with other tomato species in the phylogenetic analyses based on nuclear genes. This topological incongruence observed might be caused by the chloroplast capture event. In this process, a new combination of nuclear and chloroplast genomes were formed through inter-species hybridization and subsequent backcrosses with S. pennellii and S. habrochaites. Cross-species transfer of the chloroplast from one species to another has been reported among hybridizing plant groups, but it has not been hypothesised previously in Solanaceae.

KW - 414 Agricultural biotechnology

KW - 1183 Plant biology, microbiology, virology

KW - 1181 Ecology, evolutionary biology

M3 - Poster

SP - 78

ER -