Guangdong Ocean University

Sonneratia apetala is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of S. apetala. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (p < 0.001, Q < 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of S. apetala roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in S. apetala response to salt stress.

Salinity is an important environmental factor, and fluctuations in saline-alkali levels that exceed the osmoregulatory capacity of fish may have profound effects on various physiological functions of teleosts. The greater amberjack is highly valued commercially owing to its rapid growth and excellent meat quality. In this study, the juvenile greater amberjack were reared for 30 days under optimal salinity (30 ppt) as well as hypo- (20 ppt) and hyper-salinity (40 ppt) conditions. Histologically, the structure of the kidney was damaged under chronic salinity stress, characterized by hypertrophy at the edges of the columnar epithelial cells in the renal tubules, while the central side was tightened. Through comparative transcriptome analysis of the kidney, a total of 1103, 51, and 1711 differentially expressed genes (DEGs) were identified in the K20 vs. K30 (686 up- and 417 down-regulated), K40 vs. K30 (14 up- and 37 down-regulated), and K20 vs. K40 (1170 up- and 541 down-regulated) salinity stress groups, respectively. Certain DEGs enriched in the cell cytoskeleton (LOC111217621, tubb5, and LOC111234965) and cell apoptosis (tnfrsfa, LOC111218420, LOC111223891, LOC111223286, and bcl2) were identified by kidney transcriptome analysis in response to salinity stress. Furthermore, DEGs associated with lipid and carbohydrate metabolism (elovl6l, acsl4, msmo1, pck1, g6pc1, pfkfb3, and ldha), ion transport (kcnk5, slc4a4, slc9a3, slc41a1, and slc22a2), and immune response (nfkbiaa, nfkbia, and LOC111231462) were identified. These findings suggest that the cytoskeleton was damaged, along with variations in ion transport, lipid and carbohydrate metabolism, and immune responses to salinity stress. The current findings enhance our understanding of the physiological responses of greater amberjack to salinity stress, which could be beneficial in developing strategies to optimize the aquaculture and artificial breeding of this species in environments characterized by fluctuating salinity patterns.

Mitochondrial genomes, with their maternal inheritance, rapid evolution, and compact organization, are ideal for phylogenetic analysis.

This study presents the first comprehensive mitochondrial genome analysis of the rare shrimp Alpheus euphrosyne, a species known for its unique morphological traits and ecological niche.

By sequencing and annotating its entire mitochondrial genome, we provide a detailed genetic blueprint that informs future studies on its evolutionary trajectory, population genetics, and conservation status. Additionally, we conducted phylogenetic genomics studies across multiple Alpheus species to reconstruct the evolutionary history of the genus, identify key evolutionary innovations, and elucidate species relationships. Our findings reveal that the mitochondrial genome of A. euphrosyne is 15,866 bp long, encoding 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 control region. The complete mitochondrial DNA exhibits a positive AT-Skew of 0.048 and a negative CG-Skew of - 0.262. It is noteworthy that among the 22 tRNA genes, trnS1 forms two approximately circular structures in the middle and lacks a Dihydrouracil arm, while the remaining 21 exhibit a normal clover-leaf structure. The gene order of the mitochondrial genomes is highly conserved across the 9 Alpheus species, with the exception of A. lobidens, which has an additional trnQ inserted between nad4L and trnT genes.

In this study, through in-depth analysis of the mitochondrial genome of A. euphrosyne and combined with phylogenetic analysis methods, nine Alpheus species were divided into two major clades, and it was explicitly revealed that A. euphrosyne has the closest genetic relationship with A. randalli. This achievement provides a new scientific basis for the study of species evolution mechanisms and genus-level taxonomic understanding within the Alpheus genus.