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Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery

Bryophytes are the first land plants but are scarcely studied at the molecular level. Here, we report transcriptome sequencing and functional annotation of Dumortiera hirsuta, as a representative bryophyte. Approximately 0.5 million reads with ~195 Mb data were generated by sequencing of mRNA using...

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Autores principales: Singh, Harpal, Rai, Krishan Mohan, Upadhyay, Santosh Kumar, Pant, Poonam, Verma, Praveen Chandra, Singh, Ajit Pratap, Singh, Pradhyumna Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611483/
https://www.ncbi.nlm.nih.gov/pubmed/26481431
http://dx.doi.org/10.1038/srep15350
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author Singh, Harpal
Rai, Krishan Mohan
Upadhyay, Santosh Kumar
Pant, Poonam
Verma, Praveen Chandra
Singh, Ajit Pratap
Singh, Pradhyumna Kumar
author_facet Singh, Harpal
Rai, Krishan Mohan
Upadhyay, Santosh Kumar
Pant, Poonam
Verma, Praveen Chandra
Singh, Ajit Pratap
Singh, Pradhyumna Kumar
author_sort Singh, Harpal
collection PubMed
description Bryophytes are the first land plants but are scarcely studied at the molecular level. Here, we report transcriptome sequencing and functional annotation of Dumortiera hirsuta, as a representative bryophyte. Approximately 0.5 million reads with ~195 Mb data were generated by sequencing of mRNA using 454 pyrosequencer. De novo assembly of reads yielded 85,240 unigenes (12,439 contigs and 72,801 singletons). BlastX search at NCBI-NR database showed similarity of 33,662 unigenes with 10-(10) e-value. A total of 23,685 unigenes were annotated at TAIR10 protein database. The annotated unigenes were further classified using the Gene Ontology. Analysis at Kyoto Encyclopedia of Genes and Genomes pathway database identified 95 pathways with significant scores, among which metabolic and biosynthesis of secondary metabolite were the major ones. Phenylpropanoid pathway was elucidated and selected genes were characterized by real time qPCR. We identified 447 transcription factors belonging to 41 families and 1594 eSSRs in 1479 unigenes. D. hirsuta unigenes showed homology across the taxa from algae to angiosperm indicating their role as the connecting link between aquatic and terrestrial plants. This could be a valuable genomic resource for molecular and evolutionary studies. Further, it sheds light for the isolation and characterization of new genes with unique functions.
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spelling pubmed-46114832015-11-02 Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery Singh, Harpal Rai, Krishan Mohan Upadhyay, Santosh Kumar Pant, Poonam Verma, Praveen Chandra Singh, Ajit Pratap Singh, Pradhyumna Kumar Sci Rep Article Bryophytes are the first land plants but are scarcely studied at the molecular level. Here, we report transcriptome sequencing and functional annotation of Dumortiera hirsuta, as a representative bryophyte. Approximately 0.5 million reads with ~195 Mb data were generated by sequencing of mRNA using 454 pyrosequencer. De novo assembly of reads yielded 85,240 unigenes (12,439 contigs and 72,801 singletons). BlastX search at NCBI-NR database showed similarity of 33,662 unigenes with 10-(10) e-value. A total of 23,685 unigenes were annotated at TAIR10 protein database. The annotated unigenes were further classified using the Gene Ontology. Analysis at Kyoto Encyclopedia of Genes and Genomes pathway database identified 95 pathways with significant scores, among which metabolic and biosynthesis of secondary metabolite were the major ones. Phenylpropanoid pathway was elucidated and selected genes were characterized by real time qPCR. We identified 447 transcription factors belonging to 41 families and 1594 eSSRs in 1479 unigenes. D. hirsuta unigenes showed homology across the taxa from algae to angiosperm indicating their role as the connecting link between aquatic and terrestrial plants. This could be a valuable genomic resource for molecular and evolutionary studies. Further, it sheds light for the isolation and characterization of new genes with unique functions. Nature Publishing Group 2015-10-20 /pmc/articles/PMC4611483/ /pubmed/26481431 http://dx.doi.org/10.1038/srep15350 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Singh, Harpal
Rai, Krishan Mohan
Upadhyay, Santosh Kumar
Pant, Poonam
Verma, Praveen Chandra
Singh, Ajit Pratap
Singh, Pradhyumna Kumar
Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery
title Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery
title_full Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery
title_fullStr Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery
title_full_unstemmed Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery
title_short Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery
title_sort transcriptome sequencing of a thalloid bryophyte; dumortiera hirsuta (sw) nees: assembly, annotation, and marker discovery
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611483/
https://www.ncbi.nlm.nih.gov/pubmed/26481431
http://dx.doi.org/10.1038/srep15350
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