The Fascinating Flying Spider Monkey Tree Fern

So far, not much is known about how fern genomes have changed over time. Two small genomes from the heterosporous Salviniales have been published. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. Even though it happened during a whole-genome duplication over 100 million years ago, synteny has been preserved in a way that has never been seen before in plants. This is likely what makes tree ferns special. Our in-depth studies of stem anatomy and lignin biosynthesis have given us new information about how stem formation in tree ferns has changed over time. We found a phenolic compound called alsophilin that is found in large amounts in xylem and explained how it is made at the molecular level. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. The spinulosa genome fills in an important gap in the library of plant genomes and helps us understand many unique aspects of tree fern biology.

Genome assembly and annotation

The genome of A. spinulosa (Fig. 1a) was estimated to be 6. 23 Gb in size and had a heterozygosity of 0. 28% (Extended Data Fig. 1). We conducted de novo genome assembly of A. chromosome level using 902 Gb (145× coverage) of corrected single-molecular real-time (SMRT) long reads, 386 Gb (62× coverage) of clean Illumina short reads, and 399 Gb (63× coverage) of high-throughput chromatin conformation capture (Hi-C) data (Supplementary Table 1). The assembled genome size was 6. 27 Gb, with 6. 23 Gb anchored to 69 pseudochromosomes, and N50 sizes were 1. 80 Mb and 92. 48 Mb, respectively, for contigs and scaffolds (Extended Data Fig. 1, Supplementary Table 2 and Supplementary Fig. 1). The mapping rates of Illumina and RNA-seq reads to the genome were 97. 9% and 95. 8%, respectively. The interspersed long terminal repeat (LTR) retrotransposons10 were used to judge the assembly. The LTR assembly index score was 17. 32, comparable to that of Arabidopsis (TAIR10). BUSCO (Benchmarking Universal Single-Copy Orthologs) assessment11 using the Eukaryota_odb10 database (10 September 2020) showed that 249 (97. 6% of 255) complete BUSCO genes were covered in the assembly (Supplementary Table 3).

a, A. spinulosa’s arborescent habit. b, the amounts of DNA methylation in three areas: the genome, the gene body, and the TE space (Gypsy, Copia, and EnSpm) Are Shown TSS, transcription start site; TTS, transcription termination site. The gene family grew and shrunk in 12 plant species, including 3 bryophytes, 3 ferns, 1 lycophyte, 4 seed plants, and one outgroup species, Chara braunii. The tree was constructed using 134 single-copy orthologous genes. The red and blue numbers above the branches represent expansion and contraction events, respectively. The number at each node represents divergence time. d, WGD analysis. The cladogram shows the relative phylogenetic positions of two ancient WGDs in A. along the right edge are Ks plots for each species in the genus Cyatheales. Below that is a summary of the experimental and simulated MAPS analyses. The shaded area in the MAPS summary shows the standard deviation for the gene tree simulations. Pj, Plagiogyria japonica; Da, Dicksonia antarctica; Sl, Sphaeropteris lepifera; As, A. spinulosa; Gp, Gymnosphaera podophylla; Gg, Gymnosphaera gigantea. e, Intragenomic synteny among 69 chromosomes in the A. spinulosa genome.

A total of 4. 68 Gb was identified as repetitive sequences, with retrotransposons (2. 52 Gb) as the main transposable elements (TEs). Within the LTR family, the Gypsy and Copia families were predominant, accounting for 24. 91% and 12. 47% of the genome (Supplementary Table 4). Using the Geta pipeline to predict genes on the repeat-masked genome led to 67,831 high-confidence protein-coding genes, of which 95 36% can be functionally annotated (Supplementary Tables 5 and 6). The average intron length was 11. 46 times that in Arabidopsis thaliana (Supplementary Table 7). The predicted proteome included 72. 1% complete and 21. 6% fragmented BUSCO genes against the Eukaryota_odb10 database (Supplementary Table 3). We also sequenced small RNAs in leaves and found 182 microRNAs that were already known and 181 that might be new (Supplementary Text).

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Land plants evolved from charophycean algae in water 470 million years ago (Ma), and they have since changed the ecosystem on land. Land plants’ bodies have changed over time due to developmental, biochemical, and physiological changes. One of these changes is the appearance of vascular tissues. In seed plants, xylem has thickened cell walls that help the trunk carry water efficiently and support itself strongly. Lignin is an important part of the secondary cell walls in xylem. It supports fiber cells mechanically and creates a water-repellent surface in vessels to help water move2

Outside of seed plants, the fern order Cyatheales is one of the few lineages having arborescent trunks. The fossil record of Cyatheaceae in Cyatheales is the most complete from the Jurassic period. More recently, there have been changes that have led to the creation of about 643 species in four genera3. Like most homosporous ferns, members of Cyatheaceae have large genomes (1C = 6. 48–9. 63 picogram) and a high chromosome base number (X = 69)4. However, in contrast to many other groups of ferns, recent polyploidy is rare in Cyatheaceae5,6.

Tree ferns are also very pretty to look at and are thought to be a good source for natural products that can be used in medicine. Some chemicals found in the tree fern Alsophila spinulosa (Cyatheaceae) have been shown to fight cancer and bacteria7,8,9. However, these chemicals probably only make up a small part of the plant’s natural product diversity. A lot of tree fern species are also being taken from the wild too much, which, along with climate change, makes it very unlikely that they will survive. A better understanding of their recent demographic history will help guide future conservation efforts.

In this study, we generated a chromosomal-scale genome assembly for the tree fern A. spinulosa. We characterized its genome in detail, including DNA methylation, repeat landscape and the history of whole-genome duplications (WGDs). We then carried out genome-powered investigations into vascular tissues and metabolic diversity in A. spinulosa. Finally, from genome resequencing data, we reconstructed the demographic history of A. spinulosa.

Amami-Oshima – Living in Biodiversity