Structure and Phylogeny of the Curly Birch Chloroplast Genome

Описание

Тип публикации: статья из журнала

Год издания: 2021

Идентификатор DOI: 10.3389/fgene.2021.625764

Ключевые слова: betula pendula var. carelica, chloroplast, curly birch, genome, microsatellites, molecular markers, phylogeny, plastome

Аннотация: 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 geneПоказать полностьюtic 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. © Copyright © 2021 Shestibratov, Baranov, Mescherova, Kiryanov, Panteleev, Mozharovskaya, Krutovsky and Padutov.

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Издание

Журнал: Frontiers in Genetics

Выпуск журнала: Vol. 12

Номера страниц: 625764

ISSN журнала: 16648021

Издатель: Frontiers Media S.A.

Персоны

  • Shestibratov Konstantin A. (Russian Acad Sci, Branch Shemyakin & Ovchinnikov Inst Bioorgan Chem, Forest Biotechnol Grp, Pushchino, Russia; GF Morozov Voronezh State Univ Forestry & Technol, Forestry Fac, Voronezh, Russia)
  • Baranov Oleg Yu (Natl Acad Sci Belarus, Forest Res Inst, Lab Genom & Bioinformat, Gomel, BELARUS)
  • Mescherova Eugenia N. (Russian Acad Sci, Branch Shemyakin & Ovchinnikov Inst Bioorgan Chem, Forest Biotechnol Grp, Pushchino, Russia)
  • Kiryanov Pavel S. (Natl Acad Sci Belarus, Forest Res Inst, Lab Genom & Bioinformat, Gomel, BELARUS)
  • Panteleev Stanislav (Natl Acad Sci Belarus, Forest Res Inst, Lab Genom & Bioinformat, Gomel, BELARUS)
  • Mozharovskaya Ludmila (Natl Acad Sci Belarus, Forest Res Inst, Lab Genom & Bioinformat, Gomel, BELARUS)
  • Krutovsky Konstantin (GF Morozov Voronezh State Univ Forestry & Technol, Forestry Fac, Voronezh, Russia; George August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, Gottingen, Germany; Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Moscow, Russia; Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk, Russia)
  • Padutov Vladimir E. (Natl Acad Sci Belarus, Forest Res Inst, Dept Genet Tree Breeding & Biotechnol, Gomel, BELARUS)

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