The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis.

Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis has been used as a traditional medicine for more than 2000 years in China and many other Asian countries. The pharmacological activities of C. chinensis have been validated by research. Here, we present a de novo high-quality genome of C. chinensis with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50 of 4.53 Mb. We found that the relatively large genome size of C. chinensis was caused by the amplification of long terminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales was discovered. Comparative genomic analysis revealed that the tyrosine decarboxylase (TYDC) and (S)-norcoclaurine synthase (NCS) genes were expanded and that the aspartate aminotransferase gene (ASP5) was positively selected in the berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highest in the roots of C. chinensis in the third and fourth years. The chromosome-level reference genome of C. chinensis provides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.

[Variation in physicochemical properties and bacterial community structure in rhizosphere soil of Coptis chinensis tow cropping modes].

The natural forest and artificial shed are the main cropping modes of Coptis chinensis. This study is aimed to reveal the rhizosphere soil bacterial community structure difference between under tow C. chinensis cropping modes-natural forest and artificial shed, and to assist us to completely understand soil quality condition,and provide theoretical guidance for soil improvement and C. chinensis planting. The rhizosphere soil samples of 1-5-year-old C. chinensis under tow cropping modes-natural forest and artificial shed were collected. Illumina high-throughput sequencing technology was used to analyze the alpha diversity, community composition, community structure of soil bacteria under the tow cropping modes,and the effects of soil nutriment indices on soil bacterial community structure. Through the analysis of species number, Shannon, Chao1 index and ACE index of bacterial community, it was found that the bacterial diversity of 1-year-old C. chinensis soil under natural forest cropping mode was significantly lower than that under artificial shed cropping mode, and the diversity of bacterial communities in soil of 2-5-years old C. chinensis were not significant different between two cropping modes. A total of 53 phyla,60 classes,140 orders and 266 families were detected in the rhizosphere soil of C. chinensis under the cropping modes of natural forest, respectively. The rhizosphere soil of C. chinensis under the cropping modes of artificial shed included 54 phyla,65 classes,140 orders and 264 families, respectively. Under the two cropping modes, the top 10 dominant species of bacterial community abundance are the same, they are Proteobacteria, Acidobacteria, Actinobacteria,Bacteroidetes, Planctomycetes, Chloroflexi, Verrucomicrobia, Gemmatimonadetes, Firmicutes and Cyanobacteria, but there are differences in the abundance sequence. The top 10 dominant species of bacterial community abundance accounted for 74.36% to 74.30% of the total bacteria, and 3.15% to 3.92% of the bacteria are unclassified. The results of Metastat analysis showed that the abundance of Gemmatimonadetes in the rhizosphere soil of C. chinensis under the cropping modes the artificial shed was significantly higher than that under the natural forest cropping mode(P<0.05). MRPP analysis of community structure differences showed that under tow cropping modes, there were significant differences in the bacterial community structure of 1-4-year-old soil bacteria, among which the difference between 1-year-old soil samples was the largest. With the increase of cropping years, the difference gradually decreases, and there is no significant difference in the bacterial community structure between 5-year-old soil samples. RDA analysis and correlation analysis of bacterial community structure and soil physical and chemical properties showed that the order of environmental factors on the rhizosphere soil bacteria of Coptis chinensis was: pH>available P> total P> total K>bulk density>total N>available N>organic matter. The results are helpful to understand the soil health of C. chinensis and provide scientific basis and theoretical guidance for soil improvement and C. chinensis planting.

Variation in fungal community structures in rhizosphere soil of Coptis chinensis with cropping mode under natural forest and artificial shed / 中国中药杂志

This study is aimed to reveal the rhizosphere soil fungal community structure difference of Coptis chinensis cropping between natural forest and artificial shed modes, and provide theoretical guidance for soil improvement and C. chinensis planting. The rhizosphere soil samples of 1-5-year-old C. chinensis under natural forest and artificial shed modes were collected. Illumina high-throughput sequencing technology was used to analyze the community structure and diversity of soil fungi under the tow cropping modes,and the effects of soil nutriment indices on soil fungal community structure. The results suggested that the abundance and diversity of fungal communities in soil of 2-5-year-old C. chinensis were not significant different in both two cropping modes, but it was significantly higher than that in the 1-year-old C. chinensis. Comparing soil samples from the same year-old C. chinensis under the two cropping modes, it was found that there was no significant difference in the abundance and diversity of fungal communities. The fungal community of the rhizosphere soil was different in composition and abundance between tow cropping modes, and between different planting years. The 17 phyla,59 classes and 155 orders,and 17 phyla,59 classes and 157 orders were detected in the rhizosphere soil of C. chinensis under the cropping modes of natural forest and the artificial shed, respectively. Ascomycota, Basidiomycota and Mortierellomycota were dominant phyla in rhizosphere soil, and the average abundance of the 3 phyla accounted for 74.36% and 74.30% of the total fungi. The results of analysis of similarities showed that there were significant differences in the fungal community structure of 1-year-old and 2-year-old C. chinensis soil fungi, and there was no significant difference in the community structure of 3-5-year-old samples. Under the natural forest cropping mode, there were significant differences among the samples of different years. Under the artificial shed cropping, there were significant differences in fungal community structure between 1-year-old and 3-5-year-old C. chinensis soil, and between 2-year-old and 3-5-year-old C. chinensis soil. The results of canonical correlation analysis showed that soil pH and soil organic matter content were the main factors affecting the soil fungal community structure. Soil organic matter content was positively correlated with Basidiomycota and Cryptomycota, pH was negatively correlated with Basidiomycota and C. ryptomycota. The planting of C. chinensis has promoted the diversity and abundance of rhizosphere fungal community significantly. For the same year-old C. chinensis soil, abundance of fungal community was no significant difference between two cropping modes. There are significant differences in the rhizosphere soil fungal community structure between tow cropping modes in the first two years of planting. Through the interaction between the rhizosphere and the soil and the continuous selection of the rhizosphere to the fungal community, the fungal community structure tended to be the same between the two cropping modes in rhizosphere soil of 3-5-year old C. chinensis. The soil pH and orga-nic matter content were the main factors affecting the change of fungal community structure.

[Study on preferred food of adult Mylabris phalerata in different geographical populations].

With the deterioration of environment, and the excessive collection of wild resources, the wild populations of Myla- bris phalerata Pallas are less and less, almost extincted in many traditional distribution areas. It is necessary to breed M. phalerata artificially for sustainable utilization. Food preference of adult M. phalerata is the key to its provenance screening and domestication in the artificial breeding. In this paper, the food preference of 3 geographical populations of M. phalerata was studied. The results showed that the food preferences of adult M. phalerata in different geographical populations were different. The adult M. phalerata in Wuming preferred cucumber flowers, gourd flowers and melon flowers. The adult M. phalerata in Tianlin preferred cowpea flowers. And the adult M. phalerata in Guangzhou preferred cowpea flowers and gourd flowers. Gourd flowers were the most attractive food for the adult M. phalerata of 3 geographical populations of M. phalerata.