Biology subjects

Zhao, J.-L.

Publications and source records attributed to Zhao, J.-L..

4 recordsLinked to original sources

bioRxiv2026

CNS diseases cerebrospinal fluid single-cell atlas reveals immune characteristics of neuropsychiatric systemic lupus erythematosus

Neuropsychiatric systemic lupus erythematosus (NPSLE) is a potentially severe complication of systemic lupus erythematosus (SLE), yet its pathogenesis remains largely elusive. By jointly probing the immune dynamics of subjects cerebrospinal fluid (CSF) and peripheral blood, we showed that both innate and adaptive immune responses jointly contribute to the pathogenesis of NPSLE. In particular, we found the remarkable enrichment of BAM-CCL3, a subtype of border-associated macrophages with strong recruitment capacity, implicating its potential role in central nervous system (CNS) inflammation. We also observed pronounced activation of memory B cells and CD4+ regulatory T cells in NPSLE CSF, along with the preferential blood-to-CSF migration and subsequent within-CSF clonal expansion of CD8+ effector memory T cells in NPSLE patients, suggesting a persistent CNS-localized adaptive immune dysregulation. Finally, we developed the single-cell CNS disease CSF-Blood Atlas (scCDCB), a comprehensive collection for CSF and peripheral blood of multiple CNS diseases, which is publicly available at (https://sccdcb.gao-lab.org) to serve as a reference for future research on CNS diseases.

genomics↗

bioRxiv2025

The small genome size ensures adaptive flexibility for an alpine ginger

Understanding the proximate and ultimate causes of genome size (GS) variation is the focus of much research. However, the extent and causes of intraspecific variation in GS is debated and poorly understood. This study aims to test the large-genome constraint hypothesis through the variations of intraspecific GS. GS was measured in 53 Roscoea tibetica populations from the Hengduan Mountains using flow cytometry. Stomatal size and density were collected from the wild populations and common garden populations. Associations between GS and environmental factors, stomatal traits were explored. We found that high GS variability was positively correlated with most environmental factors but negatively correlated with solar radiation during the growing season. The environment, rather than geography, significantly influenced the variations in GS. The stomatal traits measured in the wild were significantly correlated with GS, but no such correlations were detected in the common garden. Populations in the common garden have larger stomatal size and lower stomatal density. Populations with smaller GS present larger degree of stomatal traits variation from wild to common garden. Our findings suggests that intraspecific GS has experienced adaptive evolution driven by environmental stress and the evolution of intraspecific GS can be explained by the large-genome constraint hypothesis. Smaller GS is more advantageous to the alpine ginger to adapt to alpine habitat and thrive in changing habitat.

ecology↗

bioRxiv2021

Transcriptome-based phylogeny and whole-genome duplication in Theaceae

Theaceae, with three tribes and nine genera, is a family of great economic and ecological importance. Recent phylogenetic analyses based on plastid genome resolved the relationship among three tribes and the intergeneric relationships within Gordonieae and Stewartieae. However, generic level relationships within the largest tribe Theeae were not fully resolved and potential hybridization among genera within Theeae revealed previously also remains to be tested further. Here we conducted a comprehensive phylogenomic study of Theaceae based on transcriptomes and low-depth whole-genome sequencing of 57 species as well as additional plastome sequence data from previous work. Phylogenetic analyses suggested that Stewartieae was the first-diverging clade in Theaceae, consistent with previous study using plastomic data. Within Theeae, the highly supported Apterosperma-Laplacea clade grouped with Pyrenaria with maximum support based on the partitioned and unpartitioned concatenation analyses using the 610 low-copy nuclear genes, leaving Camellia and Polyspora as another sister genera in the tribe. PhyloNet analyses suggested one reticulation event within Camellia and Pyrenaria respectively, but no intergeneric reticulations were detected in Theeae. Another introgression was found between Gordonia lasianthus and the common ancestor of Gordonieae during the Late Oligocene. The existing land bridges (e.g. Bering land bridge) might have facilitated this ancient introgression. Further researches need to be conducted to uncover the interspecific introgression pattern within Camellia. Ks distribution analyses supported the tea family shared one whole-genome duplication (WGD) event Ad-{beta}, which was recently mapped to the clade containing core Ericales, Primuloids, Polemonioids and Lecythidaceae.

evolutionary biology↗

bioRxiv2018

Mitochondrial genome annotation and phylogenetic placement of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa

Genetic characterization of southern African cichlids has not received much attention. Here, we describe the mitogenome sequences and phylogenetic positioning of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa. The complete mitochondrial DNA sequences were determined for O. andersonii and O. macrochir, two important aquaculture and fisheries species endemic to southern Africa. The complete mitogenome sequence lengths were 16642 bp and 16644 bp for O. andersonii and O. macrochir respectively. The general structural organization follows that of other teleost species with 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a non-coding control region. Phylogenetic placement of the two species among other African cichlids was performed using Maximum Likelihood (ML) and Bayesian Markov-Chain-Monte-Carlo (MCMC). The consensus trees confirmed the relative positions of the two cichlid species with O. andersonii being very closely related to O. mossambicus and O. macrochir showing a close relation to both species. Among the 13 mitochondrial DNA protein coding genes ND6 may have evolved more rapidly and COIII was the most conserved. There are signs that ND6 may have been subjected to positive selection in order for these cichlid lineages to diversity and adapt to new environments. More work is needed to characterize the southern Africa cichlids as they are important species for capture fisheries, aquaculture development and understanding biogeographic history of African cichlids. Bioconservation of some endangered cichlids is also essential due to the threat by invasive species.

genomics↗