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The complete chloroplast genome of Betula costata (Betulaceae).

ABSTRACT: In the present study, we analyzed the complete chloroplast genome sequence of Betula costata using the Ion Torrent platform. The chloroplast genome of B. costata was found to be 160,547 bp in length, with a large single-copy (LSC) region of 89,385 bp, a small single-copy (SSC) region of 19,038 bp, and a pair of inverted repeats (IRs) of 26,062 bp each. The overall GC content of the chloroplast genome was 36.1%. It contained 132 genes, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic analysis indicated that B. costata is closely related to Betula nana and Betula pubescens.

SUBMITTER: Lee MW

PROVIDER: S-EPMC7748461 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Betula costata (Betulaceae).

Lee Min Woo MW Kim Sang-Chul SC Lee Jei-Wan JW Ahn Ji-Young JY

Mitochondrial DNA. Part B, Resources 20200203 1

In the present study, we analyzed the complete chloroplast genome sequence of Betula costata using the Ion Torrent platform. The chloroplast genome of B. costata was found to be 160,547 bp in length, with a large single-copy (LSC) region of 89,385 bp, a small single-copy (SSC) region of 19,038 bp, and a pair of inverted repeats (IRs) of 26,062 bp each. The overall GC content of the chloroplast genome was 36.1%. It contained 132 genes, including 87 protein-coding genes, 8 rRNA genes ...[more]

PMID: 33366834

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Project description:Background and aimsBetula L. (birch) is a genus of approx. 60 species, subspecies or varieties with a wide distribution in the northern hemisphere, of ecological and economic importance. A new classification of Betula has recently been proposed based on morphological characters. This classification differs somewhat from previously published molecular phylogenies, which may be due to factors such as convergent evolution, hybridization, incomplete taxon sampling or misidentification of samples. While chromosome counts have been made for many species, few have had their genome size measured. The aim of this study is to produce a new phylogenetic and genome size analysis of the genus.MethodsInternal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced for 76 Betula samples verified by taxonomic experts, representing approx. 60 taxa, of which approx. 24 taxa have not been included in previous phylogenetic analyses. A further 49 samples from other collections were also sequenced, and 108 ITS sequences were downloaded from GenBank. Phylogenetic trees were built for these sequences. The genome sizes of 103 accessions representing nearly all described species were estimated using flow cytometry.Key resultsAs expected for a gene tree of a genus where hybridization and allopolyploidy occur, the ITS tree shows clustering, but not resolved monophyly, for the morphological subgenera recently proposed. Most sections show some clustering, but species of the dwarf section Apterocaryon are unusually scattered. Betula corylifolia (subgenus Nipponobetula) unexpectedly clusters with species of subgenus Aspera Unexpected placements are also found for B. maximowicziana, B. bomiensis, B. nigra and B. grossa Biogeographical disjunctions were found within Betula between Europe and North America, and also disjunctions between North-east and South-west Asia. The 2C-values for Betula ranged from 0·88 to 5·33 pg, and polyploids are scattered widely throughout the ITS phylogeny. Species with large genomes tend to have narrow ranges.ConclusionsBetula grossa may have formed via allopolyploidization between parents in subgenus Betula and subgenus Aspera. Betula bomiensis may also be a wide allopolyploid. Betula corylifolia may be a parental species of allopolyploids in the subsection Chinenses Placements of B. maximowicziana, B. michauxii and B. nigra need further investigation. This analysis, in line with previous studies, suggests that section Apterocaryon is not monophyletic and thus dwarfism has evolved repeatedly in different lineages of Betula Polyploidization has occurred many times independently in the evolution of Betula.

Project description:BackgroundBetula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the divergence of species, RNA editing and phylogeny. In this study, we sequenced and analyzed the complete chloroplast (cp) genome sequence of B. platyphylla.ResultsThe complete cp genome of B. platyphylla was 160,518 bp in length, which included a pair of inverted repeats (IRs) of 26,056 bp that separated a large single copy (LSC) region of 89,397 bp and a small single copy (SSC) region of 19,009 bp. The annotation contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. There were 3 genes using alternative initiation codons. Comparative genomics showed that the sequence of the Fagales species cp genome was relatively conserved, but there were still some high variation regions that could be used as molecular markers. The IR expansion event of B. platyphylla resulted in larger cp genomes and rps19 pseudogene formation. The simple sequence repeat (SSR) analysis showed that there were 105 SSRs in the cp genome of B. platyphylla. RNA editing sites recognition indicated that at least 80 RNA editing events occurred in the cp genome. Most of the substitutions were C to U, while a small proportion of them were not. In particular, three editing loci on the rRNA were converted to more than two other bases that had never been reported. For synonymous conversion, most of them increased the relative synonymous codon usage (RSCU) value of the codons. The phylogenetic analysis suggested that B. platyphylla had a closer evolutionary relationship with B. pendula than B. nana.ConclusionsIn this study, we not only obtained and annotated the complete cp genome sequence of B. platyphylla, but we also identified new RNA editing sites and predicted the phylogenetic relationships among Fagales species. These findings will facilitate genomic, genetic engineering and phylogenetic studies of this important species.

Project description:BackgroundPrevious phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history.MethodsChloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data.ResultsBetulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia.DiscussionsThis research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

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The complete chloroplast genome of Betula costata (Betulaceae).

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The complete chloroplast genome of <i>Betula costata</i> (Betulaceae).

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