Structure and Phylogeny of the Curly Birch Chloroplast Genome
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 th...
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crfrontiers:10.3389/fgene.2021.625764 2024-05-19T07:43:21+00:00 Structure and Phylogeny of the Curly Birch Chloroplast Genome Shestibratov, Konstantin A. Baranov, Oleg Yu. Mescherova, Eugenia N. Kiryanov, Pavel S. Panteleev, Stanislav V. Mozharovskaya, Ludmila V. Krutovsky, Konstantin V. Padutov, Vladimir E. Ministry of Science and Higher Education of the Russian Federation Belarusian Republican Foundation for Fundamental Research 2021 http://dx.doi.org/10.3389/fgene.2021.625764 https://www.frontiersin.org/articles/10.3389/fgene.2021.625764/full unknown Frontiers Media SA https://creativecommons.org/licenses/by/4.0/ Frontiers in Genetics volume 12 ISSN 1664-8021 journal-article 2021 crfrontiers https://doi.org/10.3389/fgene.2021.625764 2024-04-24T07:12:48Z 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 ( trn V, trn I, and trn A). 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. Article in Journal/Newspaper karelia* Frontiers (Publisher) Frontiers in Genetics 12 |
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Open Polar |
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Frontiers (Publisher) |
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crfrontiers |
language |
unknown |
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 ( trn V, trn I, and trn A). 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. |
author2 |
Ministry of Science and Higher Education of the Russian Federation Belarusian Republican Foundation for Fundamental Research |
format |
Article in Journal/Newspaper |
author |
Shestibratov, Konstantin A. Baranov, Oleg Yu. Mescherova, Eugenia N. Kiryanov, Pavel S. Panteleev, Stanislav V. Mozharovskaya, Ludmila V. Krutovsky, Konstantin V. Padutov, Vladimir E. |
spellingShingle |
Shestibratov, Konstantin A. Baranov, Oleg Yu. Mescherova, Eugenia N. Kiryanov, Pavel S. Panteleev, Stanislav V. Mozharovskaya, Ludmila V. Krutovsky, Konstantin V. Padutov, Vladimir E. Structure and Phylogeny of the Curly Birch Chloroplast Genome |
author_facet |
Shestibratov, Konstantin A. Baranov, Oleg Yu. Mescherova, Eugenia N. Kiryanov, Pavel S. Panteleev, Stanislav V. Mozharovskaya, Ludmila V. Krutovsky, Konstantin V. Padutov, Vladimir E. |
author_sort |
Shestibratov, Konstantin A. |
title |
Structure and Phylogeny of the Curly Birch Chloroplast Genome |
title_short |
Structure and Phylogeny of the Curly Birch Chloroplast Genome |
title_full |
Structure and Phylogeny of the Curly Birch Chloroplast Genome |
title_fullStr |
Structure and Phylogeny of the Curly Birch Chloroplast Genome |
title_full_unstemmed |
Structure and Phylogeny of the Curly Birch Chloroplast Genome |
title_sort |
structure and phylogeny of the curly birch chloroplast genome |
publisher |
Frontiers Media SA |
publishDate |
2021 |
url |
http://dx.doi.org/10.3389/fgene.2021.625764 https://www.frontiersin.org/articles/10.3389/fgene.2021.625764/full |
genre |
karelia* |
genre_facet |
karelia* |
op_source |
Frontiers in Genetics volume 12 ISSN 1664-8021 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3389/fgene.2021.625764 |
container_title |
Frontiers in Genetics |
container_volume |
12 |
_version_ |
1799483075835461632 |