Casuarinaceae SMRT
 About this Site
      Casuarina equisetifolia (C. equisetifolia), a conifer‐like angiosperm with resistance to typhoon and stress tolerance, is mainly cultivated in the coastal areas of Australasia. C. equisetifolia, making it a valuable model to study secondary growth associated genes and stress‐tolerance traits. However, the genome sequence is unavailable and thus wood‐associated growth rate and stress resistance at the molecular level is largely unexplored. We therefore constructed a high‐quality draft genome sequence of C. equisetifolia by a combination of Illumina second‐generation sequencing reads and Pacific Biosciences single‐molecule real time (SMRT) long reads to advance the investigation of this species. Here, we report the genome assembly, which contains approximately 300 megabases (Mb) and scaffold size of N50 is 1.06 Mb. Additionally, gene annotation, assisted by a combination of prediction and RNA‐seq data, generated 29,827 annotated protein‐coding genes and 1,983 non‐coding genes, respectively. Furthermore, we found that the total number of repetitive sequences account for one third of the genome assembly. Here we also construct the genome‐wide map of DNA modification, such as two novel forms N6‐Adenine (6mA) and N4‐methylcytosine (4mC) at the level of single‐nucleotide resolution using single‐molecule real‐time (SMRT) sequencing. Interestingly, we found that 17% of 6mA modification genes and 15% of 4mC modification genes also included alternative splicing events. Finally, we investigated cellulose, hemicellulose, and lignin‐related genes, which associated with secondary growth and contained different DNA modification. The high‐quality genome sequence and annotation of C. equisetifolia of this study provide valuable resources to strengthen our understanding of the diverse traits of trees.

Publication:

This project has been published in Plant Journal https://doi.org/10.1111/tpj.14159


 The background of Casuarinaceae SMRT project
      Genomic DNA was obtained from branchlets of C. equis. subsp. incana, which were collected from CHIHU state-owned protection forest farm of Fujian province (24°35’N, 118°55’E). Following figures included several different subspecies:
Bamboo
Populus trichocarpa
Pinus taeda
Eucalyptus grandis
Glycine max
Solanum lycopersicum<