Subjects: Biology >> Botany >> Applied botany submitted time 2024-04-17 Cooperative journals: 《广西植物》
Abstract： The taxonomy of Tacca remains controversial. Schizocapsa guangxiensis is considered to be the same species as T. plantanginea, but some taxonomists classify them into different species based on their morphological differences. In order to clarify the genetic differences and phylogenetic relationship between S. guangxiensis and T. plantanginea, this study conducted high-throughput DNA sequencing of S. guangxiensis, assembled a complete chloroplast genome using bioinformatics software, and compared it with the published T. plantanginea chloroplast genome. The results showed that: (1) The chloroplast genome size of S. guangxiensis and T. plantanginea is 162 149 bp and 160 749 bp, respectively, and they have the same GC content (36.90%). Notably, the gene types and gene amount are exactly the same in these two species, including 89 proteincoding genes and 37 tRNA genes, and 6 rRNA genes. (2) Codon preference analysis shows that there are certain differences in the codon frequencies used by the two species, but they both prefer codons ending in A/T(U). (3) Compared with T. plantanginea, the SSC boundary of S. guangxiensis has obvious expansion, which is the main factor leading to the length variant in chloroplast genome between the two species. (4) There are some sequence divergences between S. guangxiensis and T. plantanginea in the LSC and SSC regions, especially the intergenic region, which can be exploited as species-specific molecular marker. (5) Phylogenetic results show that S. guangxiensis and T. plantanginea have a rather distant genetic relationship. Although S. guangxiensis is placed in Tacca, they belong to two different species. This study enriches the genetic information of the chloroplast genome of S. guangxiensis and provides a theoretical basis for species classification, genetic diversity analysis and species protection of S. guangxiensis.
Subjects: Biology >> Botany >> Applied botany submitted time 2023-12-26 Cooperative journals: 《广西植物》
Abstract： Camellia minima, a rare and endangered species of Sect. Chrysantha, has not been previously explored in terms of its chloroplast genome. Utilizing the Illumina HiSeq 2000 platform, the chloroplast genome sequence of C. minima was sequenced, assembled, annotated, and analysed, The results showed that: (1) The chloroplast genome of C. minima was 156 961 bp in length, embodies a typical tetrad structure, and contains 136 annotated genes, including 87 protein-coding genes, 41 tRNA genes, and 8 rRNA genes. (2) The analysis identified 66 SSR loci and 39 repetitive sequences. (3) Codons prefer to use codons ending in A/U. Comprehensive ENC mapping, PR2-plot, and neutral analyses suggest natural selection as a primary factor shaping codon usage patterns. (4) Boundary analysis indicated variation in the length and position of the ycf1 gene among different species of yellow Camellia. (5) Phylogenetic analysis of the chloroplast genomes of published species of Sect. Chrysantha revealed that C. minima was most closely related to C. micrantha. This study provides crucial insights for exploring species evolution and enhancing exogenous gene expression, establishing a theoretical foundation for the conservation and utilization of species of Sect. Chrysantha in the future.
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