Genome Article

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Recently, the Plant Diversity Protection Research Group of Luoyang Normal University and Fraser Gene published a publication entitled Genome Assembly at Chromosome Scale in the international mainstream journal Molecular Ecological Resources (if = 7.09, the first district of Chinese Academy of Sciences). Annotation and evolution of Rhododendron subspecies in Henan Province. Lingbao In this study, PacBio+Hi-C technology was used for the first time to construct a high-quality reference genome of Rhododendron Lingbao, an endemic plant in China. Then, based on comparative genome analysis, the linear relationship between Rhododendron Lingbao and other rhododendrons was revealed, and the molecular mechanism of adversity adaptability of Rhododendron Lingbao was preliminarily revealed, which provided a new idea for the protection and evolution research of Rhododendron Lingbao germplasm resources.

Rhododendron has high ornamental, horticultural and medicinal value. In recent years, a large number of reports about rhododendron genome and transcriptome have appeared, which is of great significance to the evolution of rhododendron gene family and the extensive phenotypic plasticity research. But so far, the genome of Rhododendron Lingbao, an endemic plant in China, has not been reported, which limits the research on its genetic resources, environmental adaptability and molecular evolution. Therefore, it is of great theoretical significance to construct the genome of Rhododendron Lingbao.

Materials: Rhododendron subspecies in Henan. Lingbao

Sequencing strategy: PacBio (220 times) +Hi-C (100 times) +Illumina (90 times).

According to the investigation and analysis, it is estimated that the genome size of Rhododendron Lingbao is 654. 12Mb and the heterozygosity is 0.72%. Subsequently, the researchers constructed a high-quality genome of Rhododendron Lingbao at the chromosome level by using deep PacBio sequencing and Hi-C-assisted assembly. The genome size was 622.72Mb, Contig N50=2.54Mb, and the scaffold N50=50. 18Mb. Then, the researchers confirmed the integrity and accuracy of genome assembly through various methods. The comparison rate of the third generation data is 97.85%, the genome integrity assessed by BUSCO is 97%, and the single base error rate of the second generation data is only 0.0003%. Compared with other published Rhododendron species, the genome assembled in this study has the best integrity and accuracy.

Combining ab initio annotation, homologous annotation and full-length transcriptome annotation, the researchers identified 365,438+0,098 protein coding genes in Lingbao Rhododendron species, with an average length of 6393.37 bp, of which 88.77% genes can be functionally annotated. 65.76% of the genome of Rhododendron Lingbao is repetitive, with the highest LTR content. In addition, the researchers also identified 22,565,438+0 rrna, 448 tRNAs, 488 snRNAs and 94 miRNAs in Lingbao Rhododendron.

The researchers selected 14 related species for comparative genome analysis of Rhododendron Lingbao, and * * * identified 15483 gene families, among which 168 is unique to Rhododendron Lingbao. Phylogenetic tree analysis showed that rhododendrons were closely related, and their differentiation time was about12.3 ~199,000 years ago, while the differentiation time of kiwifruit, camellia and rhododendron was about 64.6 ~ 73.8 million years ago.

* * * Linear analysis showed that the * * linearity among Rhododendron Maying, Rhododendron Xing 'an, Rhododendron West and Rhododendron Lingbao was very good, and the * * * linearity between single chromosomes was dominant, but there were chromosome rearrangement events among different rhododendrons. Through WGD analysis, it is found that Rhododendron and Camellia have similar WGD peaks (Ks value ranges from 0.637 to 0.715). Combined with the molecular clock, the researchers determined that Rhododendron first had a WGD event (79.2 million years ago), and then differentiated from its related species Camellia. Gene amplification and contraction analysis showed that 2257 gene families of Rhododendron Lingbao were amplified, and the amplified genes were significantly enriched in the pathways related to salicylic acid response, cell response to acid chemistry, regulation of defense response and regulation of stress response, which confirmed that Rhododendron Lingbao had strong stress resistance. The contracted genes were significantly enriched in the pathways related to terpene synthase activity, carbon-oxygen lyase activity and ADP binding.

Previous studies have shown that MYB homologous genes play an important role in regulating plant development, flower color and stress response, and researchers subsequently identified the changes of MYB gene family in Lingbao Rhododendron. The results showed that Rhododendron Lingbao had 1 10 MYB homologous genes distributed on 13 chromosomes. The number of MYB genes is less than that of cotton, rape and other species, and some MYB genes of Lingbao Rhododendron exist tandem duplication. In addition, the phylogenetic tree based on MYB gene showed that MYB gene of Rhododendron Lingbao and MYB gene of Arabidopsis belong to different classifications. These results will help to verify the function of MYB gene in the future.

summary

In this study, PacBio and Hi-C techniques were used to construct the genome of Rhododendron Lingbao at chromosome level. On this basis, compared with other Rhododendron plants and related plants, the genome evolution, WGD events, expansion and classification of genes related to adversity adaptability of Rhododendron Lingbao were expounded, which provided new insights for germplasm resources protection, new variety breeding and genetic evolution research of Rhododendron Lingbao.