Subjects: Biology >> Botany >> Applied botany submitted time 2021-08-09 Cooperative journals: 《广西植物》
Abstract： In order to investigate the good genes, cultivate the main superior cultivars and discover phylogenetic relationships of Magnolia officinalis, M. officinalis subsp. biloba and M. hypoleuca, we compared the differences among the cp (chloroplast) genomes of three Magnolia species and performed a phylogenetic tree of 14 species. Illumina HiSeq platform was used to sequence and assemble the cp genome of M. hypoleuca. Then the cp genomes of three Magnolia species were annotated by online platform and performed with three Magnolia species cp gene cycles. Moreover, the cp genomes of other 11 Magnolia species were downloaded from the NCBI database and phylogenetic tree of 14 all species cp genomes was constructed based on NJ method. The results indicated that Clean Reads of M. hypoleuca were 19 791 019, and Q30 was 91.33%. The total length of cp genome of M. hypoleuca was 160 051 bp, its GC content was 39.2%, including 37 tRNA and 8 rRNA. Besides, there were respectively six and four more functional gene numbers of M. hypoleuca than the other two Magnolia species, which indicated it had stronger viability. Compared with the cp genome structure of three Magnolia species, it showed that three Magnolia species had similar IR, LSC and SSC structures, GC content and tRNA number, but there were differences in the type and number of coding genes, the number and structure of introns and exons. Besides, the differential functional genes of three Magnolia species were mainly located in LSC region and IR region, involving large ribosomal subunits, small ribosomal subunits and unknown functional genes groups. Furthermore, based on NJ phylogenetic tree, M. hypoleuca was closely related to M. officinalis subsp. biloba, next to M. officinalis. In this study, M. hypoleuca had more abundant cp genome structure, composition and variation characteristics, which was the molecular mechanism of its adaptation to low light and low temperature environment in high latitude area. And it will also provide strong guidance for molecular breeding of excellent Magnolia varieties.
Subjects: Biology >> Botany >> Applied botany submitted time 2020-05-28 Cooperative journals: 《广西植物》
Abstract： Magnolia officinalis is a famous traditional medicinal plant, belonging to the Magnoliaceae family and Magnolia genus and being widely cultivated in China. Its bark, root bark, branch bark, leaves, flowers and fruits could be used as medicine or food. However, the whose genome information is little known for this plant species. In order to obtain the whole genome sequence information of M. officinalis, the leaf DNA was used as the material, and the third-generation sequencing technology of Pacbio Sequel was used to establish its nucleotide sequence database. Then genome assembly, function annotation and evolution analysis were carried out by bioinformatic methods. The experimental results showed that 140.91 Gb third-generation data were obtained after the original sequencing data, with the Read N50 about 13 784 bp. The assembled M. officinalis genome size was 1.68 Gb, Contig N50 being about 222 069 bp, and the integrity of single copy gene being 78.05 %. 98.40% of the genes from the assembled sequence got gene annotation after being compared with functional databases such as NR, KOG and KEGG. The result of KOG gene annotation was that the protein function of M. officinalis concentrated in the general functional prediction only, posttranslational modification, protein turnover, chaperones signal transduction mechanisms. GO functional classification indicated that the genes of M. officinalis concentrated on cell components and biological processes. KEGG analysis found that the M. Officinalis genes mostly involved in metabolic pathways. By comparative genomics analysis, the genomes of Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Poplar trichocarpa, Ginkgo biloba, Amborella trichopoda, Camellia sinensis and Cinnamomum kanehirae were aligned. It was found that 20 801 of 23 424 genes in M. officinalis could be classified into 12 129 families, 515 gene families being unique to M. officinalis. The genetic evolution tree constructed from the genomes of the selected reference species pointed that the M. officinalis (Magnoliaceae) was closely related to Cinnamomum kanehirae (Lauraceae), and the divergence time between the two species was about 122.5 mya. It is the first time to use the third-generation sequencing technology to analyze the whole genome of M. officinalis in the study. The study is conducive to its further development and utilization, and also provides the information for the study of the whole genome of other medicinal plants.
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