Primers for complete chloroplast genome sequencing in Magnolia.
ABSTRACT: Premise:A new set of primers was developed for sequencing of whole chloroplast genomes of Magnolia species and gap-filling of unfinished genomes. Methods and Results:Two hundred and fifty primers were newly designed based on two previously reported chloroplast genomes from two different genera in Magnoliaceae. A total of 134 primer pairs, including the ones developed in this study and 18 previously reported ones, were enough to cover the entire chloroplast genome sequences in Magnoliaceae. Four species from different sections of Magnolia (M. dealbata, M. fraseri var. pyramidata, M. liliiflora, and M. odora) were used to show the general application of these primers to chloroplast genome sequencing in Magnolia. Conclusions:Using the developed primers, four Magnolia chloroplast genomes were successfully assembled. These results show the utility of these primers across Magnolia and their potential use for phylogenetic studies, DNA barcoding, and population genetics in this group.
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:Magnoliaceae are both economically and ornamentally important trees. Despite extensive studies in this family, the taxonomy of <i>Michelia</i> L. remains unclear, as well as the taxonomical status of <i>Michelia alba</i>. Herein, we report the complete chloroplast genome of <i>M. alba</i> DC. The chloroplast genome was 159,789?bp in length, with a large single-copy (LSC) region of 87,951?bp and a small single-copy (SSC) region of 18,798?bp, separated by two inverted repeat (IRs) regions of 26,570?bp. It contained 156 genes, including 83 coding genes, 68 tRNA genes, and 8 rRNA genes. The overall GC content was 39.3%, and 43.2%, 38.0%, 34.3%, in the IRs, LSC, and SSC regions, respectively. A phylogenetic analysis showed that <i>M. alba</i> is closely related to <i>M. odora</i>, with the genus <i>Michelia</i> nested inside <i>Magnolia</i>.
Project description:In accordance with the previous reduction of the remaining genera of subfamily Magnolioideae (Magnoliaceae) into the genus Magnolia, twenty-six new nomenclatural combinations are formally made by transferring to Magnolia some additional Chinese and Vietnamese taxa from the segregate genera of Manglietia, Michelia and Yulania. The following nine new combinations are created from Manglietia, namely Magnolia admirabilis, M. albistaminea, M. guangnanica, M. jinggangshanensis, M. maguanica, M. pubipedunculata, M. pubipetala, M. rufisyncarpa and M. sinoconifera. Also, twelve new combinations are created from Michelia, namely Magnolia caloptila, M. caudata, M. fallax, M. gelida, M. hunanensis, M. maudiae var. rubicunda, M. multitepala, M. platypetala, M. rubriflora, M. septipetala, M. sonlaensis, M. xinningia. Finally, five new combinations are created from Yulania, namely Magnolia baotaina, M. pendula, M. pilocarpa var. ellipticifolia, M. puberula and M. urceolata.
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.
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>Liriodendron tulifipera</i> L. belongs to Magnoliaceae which is one of the basal angiosperm families. To understand intra-species variations on chloroplast genome in <i>Liriodendron</i> genus, we presented complete chloroplast genome of <i>L. tulifipera,</i> which is 156,387?bp long and has four subregions: 85,606?bp of large single copy (LSC) and 18,778?bp of small single copy (SSC) regions are separated by 26,002?bp of inverted repeat (IR) regions including 129 genes (84 coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.0% and those in the LSC, SSC, and IR regions are 34.9%, 30.5%, and 42.8%, respectively. Twelve single nucleotide polymorphisms (SNPs) located in one region and one insertion and deletion are found between <i>two L. tulifipera</i> genomes. INDEL Phylogenetic trees show that two <i>L. tulifipera</i> chloroplasts are clustered together and are sister to <i>Magnolia</i> species.
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:PISTILLATA (PI) homologs are crucial regulators of flower development in angiosperms. In this study, we isolated the MAwuPI homolog from Magnolia wufengensis, a basal angiosperm belonging to the Magnoliaceae. Molecular phylogenetic analysis suggested that MAwuPI was grouped into the PI/GLO lineages of B-class MADS-box gene with the distinctive PI motif. Further expression profiling analysis showed that MAwuPI was expressed in tepals and stamens but not in juvenile leaves and carpels, similar to the spatial expression pattern of AtPI in Arabidopsis. Interestingly, MAwuPI had higher expression level in inner-tepals than in outer-tepals, whereas the M. wufengensis flower is homochlamydeous. Moreover, ectopic expression of MAwuPI in Arabidopsis pi-1 mutant emerged filament-like structures but had no obvious petals, suggesting a partial phenotypic recovery of pi-1 mutant. The features of MAwuPI in the expression pattern and gene function improved our acknowledgment of B-class genes in M. wufengensis, and contributed to the clarification of M. wufengensis evolution status and relations with other sibling species in molecular perspective.
Project description:BACKGROUND: Magnolia sprengeri Pamp is one of the most highly valuable medicinal and ornamental plants of the Magnolia Family. The natural color of M. sprengeri is variable. The complete genome sequence of M. sprengeri is not available; therefore we sequenced the transcriptome of white and red petals of M. sprengeri using Illumina technology. We focused on the identity of structural and regulatory genes encoding the enzymes involved in the determination of flower color. RESULTS: We sequenced and annotated a reference transcriptome for M. sprengeri, and aimed to capture the transcriptional determinanats of flower color. We sequenced a normalized cDNA library of white and red petals using Illumina technology. The resulting reads were assembled into 77,048 unique sequences, of which 28,243 could be annotated by Gene Ontology (GO) analysis, while 48,805 transcripts lacked GO annotation. The main enzymes involved in the flavonoid biosynthesis, such as phenylalanine ammonia-Lyase, cinnamat-4-Hydroxylase, dihydroflavonol-4-reductase, flavanone 3-hydroxylase, flavonoid-3'-hydroxylase, flavonol synthase, chalcone synthase and anthocyanidin synthase, were identified in the transcriptome. A total of 270 transcription factors were sorted into three families, including MYB, bHLH and WD40 types. Among these transcription factors, eight showed 4-fold or greater changes in transcript abundance in red petals compared with white petals. High-performance liquid chromatography analysis of anthocyanin compositions showed that the main anthocyanin in the petals of M. sprengeri is cyanidin-3-O-glucoside chloride and its content in red petals was 26-fold higher than that in white petals. CONCLUSION: This study presents the first next-generation sequencing effort and transcriptome analysis of a non-model plant from the Family Magnoliaceae. Genes encoding key enzymes were identified and the metabolic pathways involved in biosynthesis and catabolism of M. sprengeri flavonoids were reconstructed. Identification of these genes and pathways adds to the current knowledge of the molecular biology and biochemistry of their production in plant. Such insights into the mechanisms supporting metabolic processes could be used to genetically to enhance flower color among members of the Magnoliaceae.