The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

Abstract

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.

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…The most abundant were mononucleotide repeats, located in non-coding regions, and contributed to AT richness ( Figure 3). These results are consistent with most reported angiosperms [23][24][25][26][28][29][30]. The total number of SSRs was 237 in A. katsumadai, 244 in A. oxyphylla sampled from Guangdong, 247 in A. pumila, 236 in A. zerumbet, and 241 in A. oxyphylla sampled from Hainan ( Figure 3A).…”

“…The contractions and expansions at the borders of IR regions were common evolutionary events and may cause size variations of chloroplast genomes [13,[23][24][25][26][27][28][29][30]. We compared the IR-SC boundaries information of the five Alpinia chloroplast genomes ( Figure 5).…”

“…Typical chloroplast genomes of angiosperms have a generally conserved quadripartite circular structure, which consists of a large single copy (LSC) region, a small single copy (SSC) region, and two copies of inverted repeats (IRs) [16][17][18]. With the rapid development of high-throughput sequencing technologies, such as Illumina and PacBio sequencing platforms, it is now convenient to acquire complete chloroplast genome sequences [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. The chloroplast genomes have been widely utilized for species identification, the reconstruction of phylogenetic relationships, the resolution of origin problems, and the development of molecular markers [19][20][21][22][23][24][25][26][27][28][29][30].…”

The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae

“…The unequal using frequencies of synonymous codons detected in most sequenced genomes was termed synonymous codons usage bias [30], and is now considered crucial in shaping gene expression and cellular function [31]. RSCU indicates the relative probability of a particular codon encoding the synonymous codon of the corresponding amino acid.…”

Chloroplast characterizations and phylogenetic location of a common ornamental cherry cultivar, Prunus campanulata ‘Kanhizakura-plena’ (Rosaceae)

“…High-quality complete chloroplast genome (cp) helps differentiate the cultivars and focus on vital functional gene loss or gain in plastome. Comparative genome of inner or outer species in genus level also provided a new promising method for phylogeny, population dynamics, and species evolution (Li et al 2019). Thus, it is interesting to assemble and characterize the cp genome of P. campanulata 'Kanhizakura-plena' to provide a better understanding of the domestication and genetics in this genus.…”