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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ftdoajarticles:oai:doaj.org/article:e132be149f4249ecb699546afe9e47b9 2023-05-15T17:01:11+02:00 Structure and Phylogeny of the Curly Birch Chloroplast Genome Konstantin A. Shestibratov Oleg Yu. Baranov Eugenia N. Mescherova Pavel S. Kiryanov Stanislav V. Panteleev Ludmila V. Mozharovskaya Konstantin V. Krutovsky Vladimir E. Padutov 2021-10-01T00:00:00Z https://doi.org/10.3389/fgene.2021.625764 https://doaj.org/article/e132be149f4249ecb699546afe9e47b9 EN eng Frontiers Media S.A. https://www.frontiersin.org/articles/10.3389/fgene.2021.625764/full https://doaj.org/toc/1664-8021 1664-8021 doi:10.3389/fgene.2021.625764 https://doaj.org/article/e132be149f4249ecb699546afe9e47b9 Frontiers in Genetics, Vol 12 (2021) Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers Genetics QH426-470 article 2021 ftdoajarticles https://doi.org/10.3389/fgene.2021.625764 2022-12-31T09:08:09Z 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. Article in Journal/Newspaper karelia* Directory of Open Access Journals: DOAJ Articles Frontiers in Genetics 12 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers Genetics QH426-470 |
spellingShingle |
Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers Genetics QH426-470 Konstantin A. Shestibratov Oleg Yu. Baranov Eugenia N. Mescherova Pavel S. Kiryanov Stanislav V. Panteleev Ludmila V. Mozharovskaya Konstantin V. Krutovsky Vladimir E. Padutov Structure and Phylogeny of the Curly Birch Chloroplast Genome |
topic_facet |
Betula pendula var. carelica chloroplast curly birch genome microsatellites Molecular markers Genetics QH426-470 |
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 |
Article in Journal/Newspaper |
author |
Konstantin A. Shestibratov Oleg Yu. Baranov Eugenia N. Mescherova Pavel S. Kiryanov Stanislav V. Panteleev Ludmila V. Mozharovskaya Konstantin V. Krutovsky Vladimir E. Padutov |
author_facet |
Konstantin A. Shestibratov Oleg Yu. Baranov Eugenia N. Mescherova Pavel S. Kiryanov Stanislav V. Panteleev Ludmila V. Mozharovskaya Konstantin V. Krutovsky Vladimir E. Padutov |
author_sort |
Konstantin A. Shestibratov |
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 |
https://doi.org/10.3389/fgene.2021.625764 https://doaj.org/article/e132be149f4249ecb699546afe9e47b9 |
genre |
karelia* |
genre_facet |
karelia* |
op_source |
Frontiers in Genetics, Vol 12 (2021) |
op_relation |
https://www.frontiersin.org/articles/10.3389/fgene.2021.625764/full https://doaj.org/toc/1664-8021 1664-8021 doi:10.3389/fgene.2021.625764 https://doaj.org/article/e132be149f4249ecb699546afe9e47b9 |
op_doi |
https://doi.org/10.3389/fgene.2021.625764 |
container_title |
Frontiers in Genetics |
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12 |
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1766054249273229312 |