Introduction to Broad-Leaf Fern (Dipteris shenzhenensis)
Dipteris, commonly known as Broad-Leaf Fern, is an ancient plant genus that serves as a vital indicator of global climate warming and plant geography during the Mesozoic era. Despite its significance, the limited genomic resources available have posed challenges in studying the paleoclimate, systematic evolution, and medicinal value of this genus. In a groundbreaking effort, scientists have succeeded in sequencing and assembling the first chromosome-level genome of Dipteris shenzhenensis, a critically endangered species endemic to China.
Significance and Distribution of Dipteris
Dipteris represents an early divergent genus of leptosporangiate ferns, boasting only eight species globally. Its distribution is confined to the Indo-Malay archipelago, stretching from northeastern India and southern China to the southern Ryukyu Islands, northeastern Queensland, and Fiji Islands. Unlike its extant relatives, Dipteris fossils are found globally in abundance, providing crucial insights into climate and plant distribution patterns during the Mesozoic. The genus also plays a key role in the evolutionary transition of the “sporangial annulus” from horizontal to vertical—a subject of significant debate within fern phylogeny. Furthermore, the rhizomes of Dipteris have recognized medicinal properties, promoting their potential in treating an array of health conditions including edema, kidney deficiency, and even Alzheimer’s disease due to their antioxidant and antibacterial activities.
Genomic Insights of Dipteris shenzhenensis
Dipteris shenzhenensis, with its distinctively split fan-shaped leaves, is not only a fascinating plant but also a critical subject of genomic research. It possesses a chromosome number of 2n = 2x = 66, and its genome size has been estimated at approximately 2.14 Gb by flow cytometry and 1.94 Gb by genome survey. This study presents the sequencing and assembly of its chromosome-level genome utilizing cutting-edge technologies including Illumina short-read sequencing, PacBio SMRT long-read sequencing, and high-throughput chromosome conformation capture (Hi-C).
Genome Assembly and Composition
The assembled genome of Dipteris shenzhenensis spans 1.9 Gb, with a contig N50 length of 4.75 Mb and a GC content of 42.28%. Impressively, 98.37% of the assembled sequences are anchored to 33 pseudochromosomes. The genome predominantly consists of repetitive sequences, accounting for 71.97% of the total genome. Key components include 36.82% LTR retrotransposons and 22.33% DNA transposons, providing insights into the evolutionary history of the species.
The study identified 45 telomeres across the pseudochromosomes, with 15 of them paired, 15 featuring a single telomere, and three lacking identifiable telomeres altogether. A total of 26,471 protein-coding genes were predicted, with an impressive 92.5% being functionally annotated. Additionally, the genome encompasses 11,215 non-coding RNAs including miRNAs, tRNAs, rRNAs, and snRNAs.
Implications for Research and Conservation
The first high-quality genome of Dipteris shenzhenensis opens new avenues for understanding plant evolution, particularly in tracing back to the Mesozoic era. It provides crucial genomic resources that will enhance our understanding of the systematic evolution and paleoclimate adaptations of ferns. Furthermore, the ornamental and medicinal values of this genus could be unlocked further, emphasizing its importance in both scientific research and biodiversity conservation.
The findings are monumental in advancing our comprehension of Dipteris shenzhenensis and could potentially lead to groundbreaking discoveries about its evolutionary lineage, climatic adaptations, and medicinal properties. With this genomic blueprint, researchers are now better equipped to explore the fascinating world of ferns and their resilience through climatic shifts over millions of years.
