Zhang, J.-J. | Search bioRxiv

bioRxiv2022

Chinese fir genome and the evolution of gymnosperms

Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families and 70 genera. Their distinctiveness has triggered much debate on their origin, evolution, and phylogenetic placement among seed plants. To better understand the evolution of gymnosperms and their relation to other seed plants, we report here a high-quality genome sequence for a tree species, Chinese fir (Cunninghamia lanceolata), which has excellent timber quality and high aluminum adaptability and is a member of Cupressaceae with high levels of heterozygosity. We assembled an 11.24 Gb genome with a contig N50 value of 2.15 Mb and anchored the 10.89 Gb sequence to 11 chromosomes. Phylogenomic analyses showed that cycads sister to Ginkgo, which place to sister in all gymnosperm lineages, and Gnetales within conifers sister to Pinaceae. Whole-genome duplication (WGD) analysis showed that the ancestor of seed plants has differentiated into angiosperms and gymnosperms after having experienced a WGD event. The ancestor of extant gymnosperm has experienced a gymnosperm-specific WGD event and the extant angiosperms do not share a common WGD before their most recent common ancestor diverged into existing angiosperms lineages. Analysis of the MADS-box gene family of C. lanceolata revealed the developmental mechanism of the reproductive organs in C. lanceolata, which supported the (A)B(C) model of the development of gymnosperms reproductive organs. In addition, astringent seeds and shedding of whole branches (with withered leaves) might be a strategy of C. lanceolata that evolved during long-term adaptation to an aluminum-rich environment. The findings also reveal the molecular regulation mechanism of shade tolerance in C. lanceolata seedlings. Our results improve the resolution of ancestral genomic features within seed plants and the knowledge of genome evolution and diversification of gymnosperms.

genomics↗

bioRxiv2020

Lnc-ECAL-1 controls cerebrovascular homeostasis by targeting endothelium-specific tight junction protein Cldn5b

Cerebrovascular disorder-induced brain blood flow interruption or intracranial hemorrhage pose a great threaten to health. Emerging roles of long-noncoding RNAs (lncRNAs) in diagnosis and treatment of cardiovascular diseases have been recognized. However, whether and how lncRNAs modulate vascular homeostasis, especially network formation remain largely unknown. Here, we identified ECAL-1, a long non-coding RNA, as an important determinant for cerebrovascular homeostasis. Using the morpholino- and CRISPR /Cas9-based genetic modifications in combination with in vivo confocal imaging in zebrafish, we claimed that inactivation of ECAL-1 induced the apparent distortion of cerebral vascular pattern accompanied by intracranial hemorrhage. These cerebrovascular abnormalities were associated with decreased proliferation and anomalous interconnection of endothelial cells. Importantly, overexpression of Cldn5b, an endothelial cell-specific tight junction protein-encoding gene, could partially rescued the phenotype induced by ECAL-1 deficiency. Furthermore, bioinformatic analysis and experimental validation revealed that ECAL-1 sponged miR-23a, which targeted Cldn5b 3UTR and modulated Cldn5b expression, to maintain cerebrovascular pattern formation and integrity. Our results presented here revealed that ECAL-1 specifically controls cerebrovascular network formation and integrity through targeting miR-23a-Cldn5b axis. These findings provide a new regulation modality for cerebrovascular patterning and the potential neurovascular disorders, and ECAL-1-miR-23a axis represents as an attractive therapeutic target for cerebrovascular diseases.

developmental biology↗