Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth
Annual bluegrass ( L.) is one of the most widespread weed species in this world. As a young allotetraploid, has occupied diverse environments from Antarctic area to subtropical regions. To unveil the evolutionary mystery behind ’s wide distribution, extensive adaptability and phenotypic plasticity n...
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ftdoajarticles:oai:doaj.org/article:4f4e9194c66c40a9b07929e142a93d4f 2023-05-15T13:32:40+02:00 Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth Shu Chen J. Scott McElroy Fenny Dane Leslie R. Goertzen 2016-03-01T00:00:00Z https://doi.org/10.3835/plantgenome2015.06.0050 https://doaj.org/article/4f4e9194c66c40a9b07929e142a93d4f EN eng Wiley https://dl.sciencesocieties.org/publications/tpg/articles/9/1/plantgenome2015.06.0050 https://doaj.org/toc/1940-3372 1940-3372 doi:10.3835/plantgenome2015.06.0050 https://doaj.org/article/4f4e9194c66c40a9b07929e142a93d4f The Plant Genome, Vol 9, Iss 1 (2016) Plant culture SB1-1110 Genetics QH426-470 article 2016 ftdoajarticles https://doi.org/10.3835/plantgenome2015.06.0050 2022-12-31T03:38:53Z Annual bluegrass ( L.) is one of the most widespread weed species in this world. As a young allotetraploid, has occupied diverse environments from Antarctic area to subtropical regions. To unveil the evolutionary mystery behind ’s wide distribution, extensive adaptability and phenotypic plasticity needs collaboration from multiple research scopes from ecology and plant physiology to population genetics and molecular biology. However, the lack of omic data and reference has greatly hampered the study. This is the first comprehensive transcriptome study on species. Total RNA was extracted from and its two proposed diploid parents, Schrad and Kunth, and sequenced in Illumina Hiseq2000. Optimized, nonredundant transcriptome references were generated for each species using four de novo assemblers (Trinity, Velvet, SOAPdenovo, and CLC Genomics Workbench) and a redundancy-reducing pipeline (CD-HIT-EST and EvidentialGene tr2aacds). Using the constructed transcriptomes together with sequencing reads, we found high similarity in nucleotide sequences and homeologous polymorphisms between and the two proposed parents. Comparison of chloroplast and mitochondrion genes further confirmed as the maternal parent. Less nucleotide percentage differences were observed between and homeologs than between and homeologs, indicating a higher nucleotide substitution rates in homeologs than in homeologs. Gene ontology (GO) enrichment analysis suggested the more compatible cytoplasmic environment and cellular apparatus for homeologs as the major cause for this phenomenon. Article in Journal/Newspaper Antarc* Antarctic Directory of Open Access Journals: DOAJ Articles Antarctic The Plant Genome 9 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Plant culture SB1-1110 Genetics QH426-470 |
spellingShingle |
Plant culture SB1-1110 Genetics QH426-470 Shu Chen J. Scott McElroy Fenny Dane Leslie R. Goertzen Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth |
topic_facet |
Plant culture SB1-1110 Genetics QH426-470 |
description |
Annual bluegrass ( L.) is one of the most widespread weed species in this world. As a young allotetraploid, has occupied diverse environments from Antarctic area to subtropical regions. To unveil the evolutionary mystery behind ’s wide distribution, extensive adaptability and phenotypic plasticity needs collaboration from multiple research scopes from ecology and plant physiology to population genetics and molecular biology. However, the lack of omic data and reference has greatly hampered the study. This is the first comprehensive transcriptome study on species. Total RNA was extracted from and its two proposed diploid parents, Schrad and Kunth, and sequenced in Illumina Hiseq2000. Optimized, nonredundant transcriptome references were generated for each species using four de novo assemblers (Trinity, Velvet, SOAPdenovo, and CLC Genomics Workbench) and a redundancy-reducing pipeline (CD-HIT-EST and EvidentialGene tr2aacds). Using the constructed transcriptomes together with sequencing reads, we found high similarity in nucleotide sequences and homeologous polymorphisms between and the two proposed parents. Comparison of chloroplast and mitochondrion genes further confirmed as the maternal parent. Less nucleotide percentage differences were observed between and homeologs than between and homeologs, indicating a higher nucleotide substitution rates in homeologs than in homeologs. Gene ontology (GO) enrichment analysis suggested the more compatible cytoplasmic environment and cellular apparatus for homeologs as the major cause for this phenomenon. |
format |
Article in Journal/Newspaper |
author |
Shu Chen J. Scott McElroy Fenny Dane Leslie R. Goertzen |
author_facet |
Shu Chen J. Scott McElroy Fenny Dane Leslie R. Goertzen |
author_sort |
Shu Chen |
title |
Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth |
title_short |
Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth |
title_full |
Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth |
title_fullStr |
Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth |
title_full_unstemmed |
Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth |
title_sort |
transcriptome assembly and comparison of an allotetraploid weed species, annual bluegrass, with its two diploid progenitor species, poa supina schrad and poa infirma kunth |
publisher |
Wiley |
publishDate |
2016 |
url |
https://doi.org/10.3835/plantgenome2015.06.0050 https://doaj.org/article/4f4e9194c66c40a9b07929e142a93d4f |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
The Plant Genome, Vol 9, Iss 1 (2016) |
op_relation |
https://dl.sciencesocieties.org/publications/tpg/articles/9/1/plantgenome2015.06.0050 https://doaj.org/toc/1940-3372 1940-3372 doi:10.3835/plantgenome2015.06.0050 https://doaj.org/article/4f4e9194c66c40a9b07929e142a93d4f |
op_doi |
https://doi.org/10.3835/plantgenome2015.06.0050 |
container_title |
The Plant Genome |
container_volume |
9 |
container_issue |
1 |
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1766028994574024704 |