The complete chloroplast genome of Magnolia delavayi, a threatened species endemic to Southwest China.
ABSTRACT: Magnolia delavayi, 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 M. delavayi was assembled based on the Illumina sequences. The cp genome of M. delavayi 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 M. delavayi cp genome is 60.7%. The maximum likelihood phylogenetic analysis revealed that the species of M. delavayi was isolated first among the genus Magnolia. This result will be helpful for the conservation and phylogeny programs of the genus Magnolia.
Project description:<i>Rhododendron delavayi</i>, as a member of Ericaceae family, has been widely used as an important garden flower. The cp genome of <i>R. delavayi</i> exhibited a typical quadripartite cycle with 193,798?bp, comprising of a pair of inverted repeats (IRa and IRb) of 15,494?bp intersected by a large single copy (LSC) region of 160,234?bp and a quite small single copy region of 2576?bp. Totally, 123 unique genes were assembled in this cp genome, including 80 protein genes, 35 tRNAs and 8 rRNAs. Out of these assembled genes, 88 genes (71.54%) were single copy. Phylogenetic analysis based on 14?cp genome of related species showed that the <i>R. delavayi</i> was closely related to <i>Vaccinium oldhamii</i>. This study provides important information for future evolution, genetic and molecular biology studies of <i>Rhododendron</i>.
Project description:<i>Paris delavayi</i> Franchet is a perennial herb of the family Melanthiaceae. In this study, the complete chloroplast (cp) genome sequence of <i>P. delavayi</i> was characterized. The cp genome is 164,195?bp in length and contains a pair of inverted repeats (33,415?bp) separated by a large (84,400?bp) and small (12,965?bp) single-copy regions. A total of 112 unique genes were predicted, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that <i>P. delavayi</i> is sister to <i>P. mairei</i> but with low support.
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: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:<i>Magnolia baillonii</i> is an important tropical and sub-tropical precious wood tree species in China. In this study, the complete chloroplast genome (cpDNA) sequence of <i>M. baillonii</i> 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 <i>M. baillonii</i> clustered together with <i>Magnolia insignis</i>.
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>Rhododendron platypodum</i> Diels (Ericaceae) is a Chinese endemic and endangered species with high ornamental value. Here the complete chloroplast (cp) genome of <i>R. platypodum</i> was assembled and characterized. The cp genome is in a total length of 201,047?bp with the typical quadripartite structure of angiosperms, containing two inverted repeats (IRs) of 44,650?bp separated by a large single-copy (LSC) region of 109,134?bp and a small single-copy (SSC) region of 2613?bp. The whole cp genome of <i>R. platypodum</i> contains 143 genes, including 93 protein-coding genes, 42 transfer RNA genes and 8 ribosomal RNA genes. Phylogenetic analysis based on the coding sequences of cp genome within the Ericaceae family suggests that <i>R. platypodum</i> is closely related to <i>R. delavayi</i>.
Project description:Background:Rhododendron delavayi Franch. var. delavayi is a wild ornamental plant species in Guizhou Province, China. The lack of its plastid genome information seriously hinders the further application and conservation of the valuable resource. Methods:The complete plastid genome of R. delavayi was assembled from long sequence reads. The genome was then characterized, and compared with those of other photosynthetic Ericaceae species. Results:The plastid genome of R. delavayi has a typical quadripartite structure, and a length of 202,169 bp. It contains a large number of repeat sequences and shows preference for codon usage. The comparative analysis revealed the irregular recombination of gene sets, including rearrangement and inversion, in the large single copy region. The extreme expansion of the inverted repeat region shortened the small single copy, and expanded the full length of the genome. In addition, consistent with traditional taxonomy, R. delavayi with nine other species of the same family were clustered into Ericaceae based on the homologous protein-coding sequences of the plastid genomes. Thus, the long-read assembly of the plastid genome of R. delavayi would provide basic information for the further study of the evolution, genetic diversity, and conservation of R. delavayi and its relatives.