The complete chloroplast genome sequence of precious tree, Magnolia baillonii.
ABSTRACT: Magnolia baillonii is an important tropical and sub-tropical precious wood tree species in China. In this study, the complete chloroplast genome (cpDNA) sequence of M. baillonii was determined from Illumina HiSeq pair-end sequencing data. The cpDNA is 160,107?bp in length, contains a large single copy region (LSC) of 88,141?bp and a small single copy region (SSC) of 18,905?bp, which were separated by a pair of inverted repeat (IR) regions of 26,574?bp. The genome contains 132 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 39.3%. Further phylogenomic analysis showed that M. baillonii clustered together with Magnolia insignis.
Project description:The first complete chloroplast genome (cpDNA) sequence of <i>Magnolia maudiae</i> was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,205?bp in length, contains a large single-copy region (LSC) of 88,249?bp and a small single-copy region (SSC) of 18,806?bp, which were separated by a pair of inverted repeats (IR) regions of 26,575?bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed that <i>M. maudiae</i> was close to <i>Magnolia odora</i> and <i>Magnolia laevifolia</i> in <i>Magnolia</i> genus.
Project description:As an endangered species, <i>Magnolia kobus</i> is distributed in Jeju island in Korea with only about 500-1000 individuals. In this study, we presented a complete chloroplast genome of <i>M. kobus</i> which is 159,443?bp and has four sub-regions: 87,484?bp of large single copy and 18,783?bp of small single copy regions are separated by 26,588?bp of inverted repeat regions including 113 genes (79 unique genes, four rRNAs and 30 tRNAs). Phylogenetic analysis using chloroplast genomes showed that <i>M. kobus</i> is a sister of <i>M. insignis</i> and <i>M. laevifolia</i> clade.
Project description:<i>Magnolia delavayi</i>, a threatened plant endemic to Southwest China, is of great importance for landscaping because of its lotus-like creamy flowers. In this study, the complete chloroplast (cp) genome of <i>M. delavayi</i> was assembled based on the Illumina sequences. The cp genome of <i>M. delavayi</i> was 159,470?bp in length and contained a pair of inverted regions (IR, 26,409?bp) which were separated by the small single copy (SSC, 18,760?bp) and the large single copy (LSC, 87,892?bp) regions. It encoded 132 genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes. The overall AT content of <i>M. delavayi</i> cp genome is 60.7%. The maximum likelihood phylogenetic analysis revealed that the species of <i>M. delavayi</i> was isolated first among the genus <i>Magnolia</i>. This result will be helpful for the conservation and phylogeny programs of the genus <i>Magnolia</i>.
Project description:Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.
Project description:Plants in Michelia, presented by <i>Magnolia figo</i> DC, are wonderful resources in Magnoliaceae, covering a series of aromatic plants. Despite extensive studies in this family, the <i>M. figo</i> complete chloroplast genome and the taxonomical status based on the whole chloroplast sequences remain unclear. Herein, we report the complete chloroplast genome of <i>M. figo</i>. The chloroplast genome was 160,113?bp in length, with a large single-copy (LSC) region of 88,113?bp and a small single-copy (SSC) region of 18,797?bp, separated by two inverted repeat (protein-coding) regions of 26,602?bp. A total of 135 CDSs were found, including 129 genes, 85 protein-coding mRNAs, 36 tRNA genes, and eight rRNA genes. The overall GC content was 39.3%, and GC percentages range from 34.3% to 43.2% throughout LSC, IRs, and SSC regions. Phylogenetic analysis showed that <i>M. figo</i> is most closely to <i>Michelia odora</i> and displayed a relationship that three <i>Michelia</i> were nested inside <i>Magnolia</i>. This announcement of the complete <i>M. figo</i> cp genome sequence could provide valuable information for further breeding, cp genetic modification, and phylogenetic study in Magnoliaceae.
Project description:Decaisnea insignis is a wild resource plant and is used as an ornamental, medicinal, and fruit plant. High-throughput sequencing of chloroplast genomes has provided insight into the overall evolutionary dynamics of chloroplast genomes and has enhanced our understanding of the evolutionary relationships within plant families. In the present study, we sequenced the complete chloroplast genome of D. insignis and used the data to assess its genomic resources. The D. insignis chloroplast genome is 158,683?bp in length and includes a pair of inverted repeats of 26,167?bp that are separated by small and large single copy regions of 19,162?bp and 87,187?bp, respectively. We identified 83 simple sequence repeats and 18 pairs of large repeats. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited a high A/T content. The D. insignis chloroplast genome bias was skewed towards A/T on the basis of codon usage. A phylogenetic tree based on 82 protein-coding genes of 33 angiosperms showed that D. insignis was clustered with Akebia in Lardizabalaceae. Overall, the results of this study will contribute to better understanding the evolution, molecular biology and genetic improvement of D. insignis.
Project description:Two new species of Lasiodiplodia (Lasiodiplodia endophytica and Lasiodiplodia magnoliae) are described and illustrated from Magnolia forests in Yunnan, China. Endophytic and saprobic Lasiodiplodia pseudotheobromae and endophytic L. thailandica are new records from this host. The internal transcribed spacers (ITS), part of the translation elongation factor-1α (tef1) and partial β-tubulin (tub2) sequence data were analyzed to investigate the phylogenetic relationships of the new species with other Lasiodiplodia species. Lasiodiplodia magnoliae is phylogenetically sister to L. mahajangana and L. pandanicola but morphologically distinct from L. mahajangana in having larger conidia. Lasiodiplodia endophytica is most closely related to L. iraniensis and L. thailandica and the three species can be distinguished from one another by 2 base pair differences in ITS and three or four base pair differences in tef1. The new collections suggest that Magnolia forest plants are good hosts for Lasiodiplodia species with endophytic and saprobic life-styles.
Project description:The first complete chloroplast genome (cpDNA) sequence of <i>Elaeocarpus braceanus</i> was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 158,225?bp in length, contains a large single-copy region (LSC) of 85,731?bp and a small single-copy region (SSC) of 17,654?bp, which were separated by a pair of inverted repeats (IR) regions of 27,420?bp. The genome contains 133 genes, including 88 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed that <i>E. braceanus</i> clustered in a clade in Celastrales order.
Project description:The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure. The available mitochondrial genomes of the early angiosperms show extreme genetic diversity in genome size, structure, and sequences, such as rampant HGTs in Amborella mt genome, numerous repeated sequences in Nymphaea mt genome, and conserved gene evolution in Liriodendron mt genome. However, currently available early angiosperm mt genomes are still limited, hampering us from obtaining an overall picture of the mitogenomic evolution in angiosperms. Here we sequenced and assembled the draft mitochondrial genome of Magnolia biondii Pamp. from Magnoliaceae (magnoliids) using Oxford Nanopore sequencing technology. We recovered a single linear mitochondrial contig of 967,100 bp with an average read coverage of 122 × and a GC content of 46.6%. This draft mitochondrial genome contains a rich 64-gene set, similar to those of Liriodendron and Nymphaea, including 41 protein-coding genes, 20 tRNAs, and 3 rRNAs. Twenty cis-spliced and five trans-spliced introns break ten protein-coding genes in the Magnolia mt genome. Repeated sequences account for 27% of the draft genome, with 17 out of the 1,145 repeats showing recombination evidence. Although partially assembled, the approximately 1-Mb mt genome of Magnolia is still among the largest in angiosperms, which is possibly due to the expansion of repeated sequences, retention of ancestral mtDNAs, and the incorporation of nuclear genome sequences. Mitochondrial phylogenomic analysis of the concatenated datasets of 38 conserved protein-coding genes from 91 representatives of angiosperm species supports the sister relationship of magnoliids with monocots and eudicots, which is congruent with plastid evidence.