Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis.

The protein-coding genes and pseudogenes of Cuscuta australis had the diverse contribution to the formation and evolution of parasitism. The codon usage pattern analysis of these two type genes could be used to understand the gene transcription and translation. In this study, we systematically analyzed the codon usage patterns of protein-coding sequences and pseudogenes sequences in C. australis. The results showed that the high frequency codons of protein coding sequences and pseudogenes had the same A/U bias in the third position. However, these two sequences had converse bias at the third base in optimal codons: the protein coding sequences preferred G/C-ending codons while pseudogene sequences preferred A/U-ending codons. Neutrality plot and effective number of codons plot revealed that natural selection played a more important role than mutation pressure in two sequences codon usage bias. Furthermore, the gene expression level had a significant positive correlation with codon usage bias in C. australis. Highly-expressed protein coding genes exhibited a higher codon bias than lowly-expressed genes. Meanwhile, the high-expression genes tended to use G/C-ending synonymous codons. This result further verified the optimal codons usage bias and its correlation with the gene expression in C. australis.

[Natural distribution and community ecological characteristics of Taxus chinensis var. mairei in Shanxi Province, China.] / 山西省南方红豆杉自然分布与群落生态学特征.

Taxus chinensis var. mairei is a national Category 1 protective species in China, with its northernmost natural distribution to the southeast of Shanxi Province, China. This study was conducted to investigate the natural distribution of T. chinensis var. mairei in Shanxi Province. The community classification, species diversity, population structure and competition intensity of T. chinensis var. mairei were studied. The results showed that T. chinensis var. mairei mainly formed four community types, including the community of T. chinensis var. mairei + Carpinus turczaninowii, the community of T. chinensis var. mairei - Vitex negundo var. heterophylla, the community T. chinensis var. mairei - Clerodendrum trichotomum and the community of T. chinensis var. mairei + Quercus variabilis. T. chinensis var. mairei was concentratedly distributed in Mohe of Linchuan County and Manghe Nature Reserve of Yangcheng County, and scattered in some other areas. The communities had an obviously vertical structure, with T. chinensis var. mairei trees growing into main canopy which were about 8-10 m high in mixed forests and 5-6 m high in pure forests. The species diversity index and evenness index had significant difference among the four community types. The average height of T. chinensis var. mairei was 5.16 m. The individuals in tree layer and succession layer were 43.4% and 56.6%, respectively, while they were scarce in the regeneration layer. 67.6% of the trees were small-diameter (DBH＜16 cm) and only 4.0% were large-diameter (32 cm≤DBH＜40 cm). T. chinensis var. mairei was considered to be lack of seedlings because only 4 seedlings were found, which might result in the declination of this species in future. T. chinensis var. mairei in Shanxi Province showed relatively concentrated distribution, with most individuals being small-diameter, resulting in tense intraspecific competition which accounted for 61.8% of the total intensity. The interspecific competition to T. chinensis var. mairei was mainly from C. turczaninowii and Q. variabilis, which were two dominant tree species with larger population in this area.