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 this...
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ftpubmed:oai:pubmedcentral.nih.gov:8521055 2023-05-15T17:01:11+02:00 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. 2021-10-04 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8521055/ http://www.ncbi.nlm.nih.gov/pubmed/34671379 https://doi.org/10.3389/fgene.2021.625764 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8521055/ http://www.ncbi.nlm.nih.gov/pubmed/34671379 http://dx.doi.org/10.3389/fgene.2021.625764 Copyright © 2021 Shestibratov, Baranov, Mescherova, Kiryanov, Panteleev, Mozharovskaya, Krutovsky and Padutov. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. CC-BY Front Genet Genetics Text 2021 ftpubmed https://doi.org/10.3389/fgene.2021.625764 2021-10-24T00:38:36Z 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. Text karelia* PubMed Central (PMC) Frontiers in Genetics 12 |
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PubMed Central (PMC) |
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Genetics |
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Genetics 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 |
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Genetics |
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 |
Text |
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. |
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 S.A. |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8521055/ http://www.ncbi.nlm.nih.gov/pubmed/34671379 https://doi.org/10.3389/fgene.2021.625764 |
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karelia* |
genre_facet |
karelia* |
op_source |
Front Genet |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8521055/ http://www.ncbi.nlm.nih.gov/pubmed/34671379 http://dx.doi.org/10.3389/fgene.2021.625764 |
op_rights |
Copyright © 2021 Shestibratov, Baranov, Mescherova, Kiryanov, Panteleev, Mozharovskaya, Krutovsky and Padutov. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2021.625764 |
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Frontiers in Genetics |
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12 |
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