The complete chloroplast genome of Betula costata (Betulaceae).
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ABSTRACT:
SUBMITTER: Lee MW
PROVIDER: S-EPMC7748461 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Betula microphylla (Betulaceae) is a species widely distributed in Xinjiang China and in Mongolia and Siberia of Russia. In this study, we described the complete chloroplast genome of B. microphylla based on Illumina paired-end sequencing. The chloroplast genome of B. microphylla is 160,489 bp long, including two inverted repeats (IRs, 26,070 bp), separated by a large single-copy region (LSC, 89,306 bp), and a small single-copy region (SSC, 19,045 bp). The overall GC content of the whole genome is 36.1%, and the corresponding values of the LSC, SSC, and IR regions are 33.7%, 29.7%, and 42.5%. The phylogenetic analysis indicated that B. microphylla is closely related to Betula occidentalis.
| S-EPMC7510756 | biostudies-literature
Project description:Betula chichibuensis is a critically endangered limestone birch confined to the Chichibu and Kitakami mountains in central and northeastern Japan, respectively. In this study, we assembled and characterized the complete chloroplast genome of B. chichibuensis. The whole chloroplast genome was 160,791 bp in length, consisting of a large single-copy (LSC) region of 89,504 bp and a small single-copy (SSC) region of 19,175 bp, separated by a pair of inverted repeat (IR) regions of 26,056 bp. It contained 133 genes, including 88 protein-coding genes (80 PCG types), 37 tRNA genes (30 tRNA types), and eight rRNA genes (four rRNA types). The overall GC content of the chloroplast genome was 36.01%. Phylogenetic analysis resolved B. chichibuensis as sister to the clade containing B. pendula.
| S-EPMC7510759 | biostudies-literature
Project description:The complete chloroplast genome of Carpinus tibetana was a circular DNA molecule of 158,762 bp in length, containing a large single copy region (LSC) of 87,825 bp and small single copy region (SSC) of 18,797 bp, which were separated by a pair of 26,071 bp and 26,069 bp inverted repeat regions (IRs). The all GC content of C. tibetana chloroplast genome was 36.47%. It encoded totally 127 genes, including 83 protein-coding genes, 35 tRNA genes and eight rRNA genes. The chloroplast genome of C. tibetana will provide useful genetic information for future conservation genetics and phylogenetic studies.
| S-EPMC7832502 | biostudies-literature
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.
| S-EPMC4866320 | biostudies-literature
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.
| S-EPMC6302522 | biostudies-literature
Project description:Costaria costata is a commercially and industrially important brown alga. In this study, we used next-generation sequencing to determine the complete plastid genome of C. costata. The genome consists of a 129,947 bp circular DNA molecule with an A+T content of 69.13% encoding a standard set of six ribosomal RNA genes, 27 transfer RNA genes, and 137 protein-coding genes with two conserved open reading frames (ORFs). The overall genome structure of C. costata is nearly the same as those of Saccharina japonica and Undaria pinnatifida. The plastid genomes of these three algal species retain a strong conservation of the GTG start codon while infrequently using TGA as a stop codon. In this regard, they differ substantially from the plastid genomes of Ectocarpus siliculosus and Fucus vesiculosus. Analysis of the nucleic acid substitution rates of the Laminariales plastid genes revealed that the petF gene has the highest substitution rate and the petN gene contains no substitution over its complete length. The variation in plastid genes between C. costata and S. japonica is lower than that between C. costata and U. pinnatifida as well as that between U. pinnatifida and S. japonica. Phylogenetic analyses demonstrated that C. costata and U. pinnatifida have a closer genetic relationship. We also identified two gene length mutations caused by the insertion or deletion of repeated sequences, which suggest a mechanism of gene length mutation that may be one of the key explanations for the genetic variation in plastid genomes.
| S-EPMC4596871 | biostudies-literature
Project description:Alnus formosana (Betulaceae) is an important ecological and economic deciduous tree species widely distributed throughout subtropical regions of Taiwan province, China. At the present study, the complete chloroplast genome of A. formosana was assumbled using next-generation sequencing technology. The complete chloroplast sequence is 161,029 bp in length, which consisted of a large single copy (LSC, 89,720 bp) and a small single copy (SSC; 19,205 bp) separated a pair of inverted repeats (IRs; 26,052 bp). The overall guanine-cytosine (GC) content was 36.4%. A total of 131 genes were annotated, including 85 protein-coding genes, 37 tRNAs, eight rRNAs and one pseudogene (ψycf1). The phylogenetic analysis fully resolved A. formosana in a clade with A. japonica. The plastome of A. formosana will provide informative genomic resources for further phylogenetic application and genetic improvement.
| S-EPMC8425680 | biostudies-literature
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.
| S-EPMC6348958 | biostudies-literature
Project description:Microsatellite markers were developed and characterized for the critically endangered birch Betula chichibuensis (Betulaceae) to investigate the genetic structure of this species for conservation purposes. Sixteen microsatellite markers with di-, tri-, and tetranucleotide repeat motifs were developed and optimized using MiSeq paired-end sequencing. Of these, 14 were polymorphic, with two to five alleles per locus, in 47 individuals from two newly discovered populations of B. chichibuensis in Japan. Observed and unbiased expected heterozygosities per locus ranged from 0.000 to 0.617 and from 0.000 to 0.629, respectively. These markers were tested for cross-species amplification in B. maximowicziana, B. platyphylla var. japonica, and B. schmidtii. This set of microsatellite markers, the first developed for B. chichibuensis, will help elucidate spatial patterns of gene flow and levels of inbreeding in this species to aid its conservation.
| S-EPMC5435406 | biostudies-literature
Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads
| PRJNA723268 | ENA