Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx
Curly birch [Betula pendula var. carelica (Merckl.) Hämet-Ahti] is a relatively rare variety of silver birch (B. pendula Roth) that occurs mainly in Northern Europe and northwest part of Russia (Karelia). It is famous for the beautiful decorative texture of wood. Abnormal xylogenesis underlying this...
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Online Access: | https://doi.org/10.3389/fgene.2021.625764.s002 |
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ftsmithonian:oai:figshare.com:article/16728244 2023-05-15T17:01:12+02:00 Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx Konstantin A. Shestibratov (9939543) Oleg Yu. Baranov (11518363) Eugenia N. Mescherova (11518366) Pavel S. Kiryanov (11518369) Stanislav V. Panteleev (11518372) Ludmila V. Mozharovskaya (11518375) Konstantin V. Krutovsky (7852592) Vladimir E. Padutov (11518378) 2021-10-04T04:33:45Z https://doi.org/10.3389/fgene.2021.625764.s002 unknown https://figshare.com/articles/dataset/Data_Sheet_2_Structure_and_Phylogeny_of_the_Curly_Birch_Chloroplast_Genome_docx/16728244 doi:10.3389/fgene.2021.625764.s002 CC BY 4.0 CC-BY Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers phylogeny plastome Dataset 2021 ftsmithonian https://doi.org/10.3389/fgene.2021.625764.s002 2021-12-20T00:57:18Z Curly birch [Betula pendula var. carelica (Merckl.) Hämet-Ahti] is a relatively rare variety of silver birch (B. pendula Roth) that occurs mainly in Northern Europe and northwest part of Russia (Karelia). It is famous for the beautiful decorative texture of wood. Abnormal xylogenesis underlying this trait is heritable, but its genetic mechanism has not yet been fully understood. The high number of potentially informative genetic markers can be identified through sequencing nuclear and organelle genomes. Here, the de novo assembly, complete nucleotide sequence, and annotation of the chloroplast genome (plastome) of curly birch are presented for the first time. The complete plastome length is 160,523 bp. It contains 82 genes encoding structural and enzymatic proteins, 37 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The chloroplast DNA (cpDNA) is AT-rich containing 31.5% of A and 32.5% of T nucleotides. The GC-rich regions represent inverted repeats IR1 and IR2 containing genes of rRNAs (5S, 4.5S, 23S, and 16S) and tRNAs (trnV, trnI, and trnA). A high content of GC was found in rRNA (55.2%) and tRNA (53.2%) genes, but only 37.0% in protein-coding genes. In total, 384 microsatellite or simple sequence repeat (SSR) loci were found, mostly with mononucleotide motifs (92% of all loci) and predominantly A or T motifs (94% of all mononucleotide motifs). Comparative analysis of cpDNA in different plant species revealed high structural and functional conservatism in organization of the angiosperm plastomes, while the level of differences depends on the phylogenetic relationship. The structural and functional organization of plastome in curly birch was similar to cpDNA in other species of woody plants. Finally, the identified cpDNA sequence variation will allow to develop useful genetic markers. Dataset karelia* Unknown |
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Open Polar |
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Unknown |
op_collection_id |
ftsmithonian |
language |
unknown |
topic |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers phylogeny plastome |
spellingShingle |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers phylogeny plastome Konstantin A. Shestibratov (9939543) Oleg Yu. Baranov (11518363) Eugenia N. Mescherova (11518366) Pavel S. Kiryanov (11518369) Stanislav V. Panteleev (11518372) Ludmila V. Mozharovskaya (11518375) Konstantin V. Krutovsky (7852592) Vladimir E. Padutov (11518378) Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx |
topic_facet |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers phylogeny plastome |
description |
Curly birch [Betula pendula var. carelica (Merckl.) Hämet-Ahti] is a relatively rare variety of silver birch (B. pendula Roth) that occurs mainly in Northern Europe and northwest part of Russia (Karelia). It is famous for the beautiful decorative texture of wood. Abnormal xylogenesis underlying this trait is heritable, but its genetic mechanism has not yet been fully understood. The high number of potentially informative genetic markers can be identified through sequencing nuclear and organelle genomes. Here, the de novo assembly, complete nucleotide sequence, and annotation of the chloroplast genome (plastome) of curly birch are presented for the first time. The complete plastome length is 160,523 bp. It contains 82 genes encoding structural and enzymatic proteins, 37 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The chloroplast DNA (cpDNA) is AT-rich containing 31.5% of A and 32.5% of T nucleotides. The GC-rich regions represent inverted repeats IR1 and IR2 containing genes of rRNAs (5S, 4.5S, 23S, and 16S) and tRNAs (trnV, trnI, and trnA). A high content of GC was found in rRNA (55.2%) and tRNA (53.2%) genes, but only 37.0% in protein-coding genes. In total, 384 microsatellite or simple sequence repeat (SSR) loci were found, mostly with mononucleotide motifs (92% of all loci) and predominantly A or T motifs (94% of all mononucleotide motifs). Comparative analysis of cpDNA in different plant species revealed high structural and functional conservatism in organization of the angiosperm plastomes, while the level of differences depends on the phylogenetic relationship. The structural and functional organization of plastome in curly birch was similar to cpDNA in other species of woody plants. Finally, the identified cpDNA sequence variation will allow to develop useful genetic markers. |
format |
Dataset |
author |
Konstantin A. Shestibratov (9939543) Oleg Yu. Baranov (11518363) Eugenia N. Mescherova (11518366) Pavel S. Kiryanov (11518369) Stanislav V. Panteleev (11518372) Ludmila V. Mozharovskaya (11518375) Konstantin V. Krutovsky (7852592) Vladimir E. Padutov (11518378) |
author_facet |
Konstantin A. Shestibratov (9939543) Oleg Yu. Baranov (11518363) Eugenia N. Mescherova (11518366) Pavel S. Kiryanov (11518369) Stanislav V. Panteleev (11518372) Ludmila V. Mozharovskaya (11518375) Konstantin V. Krutovsky (7852592) Vladimir E. Padutov (11518378) |
author_sort |
Konstantin A. Shestibratov (9939543) |
title |
Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx |
title_short |
Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx |
title_full |
Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx |
title_fullStr |
Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx |
title_full_unstemmed |
Data_Sheet_2_Structure and Phylogeny of the Curly Birch Chloroplast Genome.docx |
title_sort |
data_sheet_2_structure and phylogeny of the curly birch chloroplast genome.docx |
publishDate |
2021 |
url |
https://doi.org/10.3389/fgene.2021.625764.s002 |
genre |
karelia* |
genre_facet |
karelia* |
op_relation |
https://figshare.com/articles/dataset/Data_Sheet_2_Structure_and_Phylogeny_of_the_Curly_Birch_Chloroplast_Genome_docx/16728244 doi:10.3389/fgene.2021.625764.s002 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2021.625764.s002 |
_version_ |
1766054260443709440 |