De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth

Abstract

These authors contributed equally to this work. SUMMARYCasuarina 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 therefore 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 1983 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 N 6 -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 were associated with secondary growth and contained different DNA modifications. The high-quality genome sequence and annotation of C. equisetifolia in this study provide a valuable resource to strengthen our understanding of the diverse traits of trees.

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

“…More recently, since the introduction of high-throughput sequencing technologies, the number of genome sequencing projects has increased at an exponential rate, leading to genome assemblies for organisms previously considered too low a priority to be sequenced. For instance, high-quality genome assemblies have been released for Potentilla micrantha (Buti et al, 2017), Salvia splendens (Dong et al, 2018), Cuscuta campestris (Vogel et al, 2018) and Casuarina equisetifolia (Ye et al, 2019).…”

“…Our genome-wide analysis of fig has identified the majority of eukaryotic species conserved motifs and one species-specific motif, ANHGA. For those 6mA sites of which it was not possible to infer a defined motif, we retrieved some conserved motifs: GAGG, that is present in both plants and animals (Wu et al, 2016), ACCT, already identified in Arabidopsis (Liang et al, 2018), and CAAG, found in Casuarina equisetifolia (Ye et al, 2019).…”

“…The emergence of third-generation sequencing (TGS) technologies (Ansorge et al, 2016) including single-molecule, real-time (SMRT) sequencing developed by Pacific Biosciences (PacBio, Tucson, AZ, USA), has led to the production of high-quality genome assemblies (Daccord et al, 2017;Vogel et al, 2018;Ye et al, 2019). Long-read sequencing has overcame the problems with short-read sequencing assembly, that is resolution of repetitive components of the genome (Veeckman et al, 2016) and phasing of heterozygous regions (Low et al, 2019).…”

Harnessing Current Knowledge of DNA N6-Methyladenosine From Model Plants for Non-model Crops

“…SMRT can detect every DNA modification at single base resolution ( Zhu et al, 2018 ). Recently, 6mA has been detected on genome-wide level in eudicot model Arabidopsis thaliana ( Liang et al, 2018b ) and monocot model rice ( Oryza sativa ) ( Zhang et al, 2018 ; Zhou et al, 2018 ), as well as in non-model plants Casuarina equisetifolia ( Ye et al, 2019 ), woodland strawberry ( Fragaria vesca ) ( Xie et al, 2020 ), and soyabeans ( Glycine max) ( Yuan et al, 2020 ), and fig ( Ficus carica ) ( Usai et al, 2021 ). While combined SMRT sequencing and 6mA-IP-Seq have been used to detect genome wide 6mA levels in Arabidopsis and rice ( Liang et al, 2018b ; Zhang et al, 2018 ; Zhou et al, 2018 ), and they reveals more efficient information for dynamic distribution and pattern of 6mA compared to these 6mA studies in non-model plants.…”

Characterization, Cultivation, and Chloroplast Genome Analysis of Betula Fujianensis

“…Scanning electron microscope (Model TM3030Plus Tabletop microscope, Hitachi, Japan) was used to visualize the leaf surfaces of the 1.5 y forest trees, corresponding to samples in light response photosynthesis curve. Free-hand transverse sections from random branches and were stained with phloroglucinol-HCl (1% (weight/volume) phloroglucinol in 6 mol/l HCl) for 5 min for lignin visualization (Ye et al 2019;Zhang et al 2018) using stereomicroscope (Leica M205FA, Germany).…”