Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study in Spartina alterniflora.

Salt stress poses a significant threat to global cereal crop production, emphasizing the need for a comprehensive understanding of salt tolerance mechanisms. Accurate functional annotations of differentially expressed genes are crucial for gaining insights into the salt tolerance mechanism. The challenge of predicting gene functions in under-studied species, especially when excluding infrequent GO terms, persists. Therefore, we proposed the use of NetGO 3.0, a machine learning-based annotation method that does not rely on homology information between species, to predict the functions of differentially expressed genes under salt stress. Spartina alterniflora, a halophyte with salt glands, exhibits remarkable salt tolerance, making it an excellent candidate for in-depth transcriptomic analysis. However, current research on the S. alterniflora transcriptome under salt stress is limited. In this study we used S. alterniflora as an example to investigate its transcriptional responses to various salt concentrations, with a focus on understanding its salt tolerance mechanisms. Transcriptomic analysis revealed substantial changes impacting key pathways, such as gene transcription, ion transport, and ROS metabolism. Notably, we identified a member of the SWEET gene family in S. alterniflora, SA_12G129900.m1, showing convergent selection with the rice ortholog SWEET15. Additionally, our genome-wide analyses explored alternative splicing responses to salt stress, providing insights into the parallel functions of alternative splicing and transcriptional regulation in enhancing salt tolerance in S. alterniflora. Surprisingly, there was minimal overlap between differentially expressed and differentially spliced genes following salt exposure. This innovative approach, combining transcriptomic analysis with machine learning-based annotation, avoids the reliance on homology information and facilitates the discovery of unknown gene functions, and is applicable across all sequenced species.

The Spartina alterniflora genome sequence provides insights into the salt-tolerance mechanisms of exo-recretohalophytes.

Spartina alterniflora is an exo-recretohalophyte Poaceae species that is able to grow well in seashore, but the genomic basis underlying its adaptation to salt tolerance remains unknown. Here, we report a high-quality, chromosome-level genome assembly of S. alterniflora constructed through PacBio HiFi sequencing, combined with high-throughput chromosome conformation capture (Hi-C) technology and Illumina-based transcriptomic analyses. The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb. Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA). Moreover, whole-genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments. Comparative genomics analyses identified numerous species-specific genes, significantly expanded genes and positively selected genes that are enriched for 'ion transport' and 'response to salt stress'. RNA-seq analysis identified several ion transporter genes including the high-affinity K+ transporters (HKTs), SaHKT1;2, SaHKT1;3 and SaHKT1;8, and high copy number of Salt Overly Sensitive (SOS) up-regulated under high salt conditions, and the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant, suggesting specialized roles for S. alterniflora to adapt to saline environments. Integrated metabolomics and transcriptomics analyses revealed that salt stress activate glutathione metabolism, with differential expressions of several genes such as γ-ECS, GSH-S, GPX, GST and PCS in the glutathione metabolism. This study suggests several adaptive mechanisms that could contribute our understanding of evolutional basis of the halophyte.

A micro-electroporation/electrophoresis-based vaccine screening system reveals the impact of vaccination orders on cross-protective immunity.

The constant emergence of mutated pathogens poses great challenges to the existing vaccine system. A screening system is needed to screen for antigen designs and vaccination strategies capable of inducing cross-protective immunity. Herein, we report a screening system based on DNA vaccines and a micro-electroporation/electrophoresis system (MEES), which greatly improved the efficacy of DNA vaccines, elevating humoral and cellular immune responses by over 400- and 35-fold respectively. Eighteen vaccination strategies were screened simultaneously by sequential immunization with vaccines derived from wildtype (WT) SARS-CoV-2, Delta, or Omicron BA.1 variant. Sequential vaccination of BA.1-WT-Delta vaccines with MEES induced potent neutralizing antibodies against all three viral strains and BA.5 variant, demonstrating that cross-protective immunity against future mutants can be successfully induced by existing strain-derived vaccines when a proper combination and order of sequential vaccination are used. Our screening system could be used for fast-seeking vaccination strategies for emerging pathogens in the future.

Deep learning-enabled discovery and characterization of HKT genes in Spartina alterniflora.

Spartina alterniflora is a halophyte that can survive in high-salinity environments, and it is phylogenetically close to important cereal crops, such as maize and rice. It is of scientific interest to understand why S. alterniflora can live under such extremely stressful conditions. The molecular mechanism underlying its high-saline tolerance is still largely unknown. Here we investigated the possibility that high-affinity K+ transporters (HKTs), which function in salt tolerance and maintenance of ion homeostasis in plants, are responsible for salt tolerance in S. alterniflora. To overcome the imprecision and unstable of the gene screening method caused by the conventional sequence alignment, we used a deep learning method, DeepGOPlus, to automatically extract sequence and protein characteristics from our newly assemble S. alterniflora genome to identify SaHKTs. Results showed that a total of 16 HKT genes were identified. The number of S. alterniflora HKTs (SaHKTs) is larger than that in all other investigated plant species except wheat. Phylogenetically related SaHKT members had similar gene structures, conserved protein domains and cis-elements. Expression profiling showed that most SaHKT genes are expressed in specific tissues and are differentially expressed under salt stress. Yeast complementation expression analysis showed that type I members SaHKT1;2, SaHKT1;3 and SaHKT1;8 and type II members SaHKT2;1, SaHKT2;3 and SaHKT2;4 had low-affinity K+ uptake ability and that type II members showed stronger K+ affinity than rice and Arabidopsis HKTs, as well as most SaHKTs showed preference for Na+ transport. We believe the deep learning-based methods are powerful approaches to uncovering new functional genes, and the SaHKT genes identified are important resources for breeding new varieties of salt-tolerant crops.

A fourth dose of the inactivated SARS-CoV-2 vaccine redistributes humoral immunity to the N-terminal domain.

The effectiveness of a 3rd dose of SARS-CoV-2 vaccines waned quickly in the Omicron-predominant period. In response to fast-waning immunity and the threat of Omicron variant of concern (VOC) to healthcare workers (HCWs), we conduct a non-randomized trial (ChiCTR2200055564) in which 38 HCWs volunteer to receive a homologous booster of inactivated vaccines (BBIBP-CorV) 6 months after the 3rd dose. The primary and secondary outcomes are neutralizing antibodies (NAbs) and the receptor-binding domain (RBD)-directed antibodies, respectively. The 4th dose recalls waned immunity while having distinct effects on humoral responses to different antigens. The peak antibody response to the RBD induced by the 4th dose is inferior to that after the 3rd dose, whereas responses to the N-terminal domain (NTD) of spike protein are further strengthened significantly. Accordingly, the 4th dose further elevates the peak level of NAbs against ancestral SARS-CoV-2 and Omicron BA.2, but not BA.1 which has more NTD mutations. No severe adverse events related to vaccination are recorded during the trial. Here, we show that redistribution of immune focus after repeated vaccinations may modulate cross-protective immune responses against different VOCs.

The complete chloroplast genome of Damnacanthus indicus C.F.Gaertn. (Rubiaceae).

Damnacanthus indicus C.F.Gaertn. is an understorey shrub widely distributed in East Asia. In this study, the complete chloroplast genome of D. indicus was assembled and annotated. The chloroplast genome is 153,997 bp in total length, consisting of a large single-copy region (LSC 85,159 bp), a small single-copy region (SSC 17,584 bp) and two inverted repeat regions (25,627 bp for IRA and IRB,respectively). It contains 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that D. indicus is sister to Mitchella repens, suggesting a close relationship of the two genera.

The complete chloroplast genome of the extremely drought-resistant plant Primulina ophiopogoides.

Primulina ophiopogoides is a perennial herb of Gesneriaceae distributed on the limestone rocks. Here, the complete chloroplast (cp) genome of P. ophiopogoides was assembled and characterized. The cp genome is in a total length of 152,718 bp with the typical quadripartite structure, containing 2 inverted repeats (IRs) of 25,472 bp separated by a large single-copy (LSC) region of 83,615 bp and a small single-copy (SSC) region of 18,159 bp. The whole cp genome of P. ophiopogoides contains 131 genes, including 86 protein-coding genes, 37 tRNAs genes, and 8 rRNAs. The phylogenetic analysis indicated that P. ophiopogoides displayed a closer kinship to Primulina linearifolia.

The complete chloroplast genome of Semiaquilegia guangxiensis, a rare and endemic herb in Guangxi, China.

The complete chloroplast genome sequence of Semiaquilegia guangxiensis was assembled and the phylogenetic relationship with other species in Trib. Isopyreae was inferred in this study. The chloroplast genome is 164,047 bp in length. A typical quadripartite structure was detected, including two inverted repeats (IRs) of 29,581 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 87,490 bp and 17,395 bp, respectively. Moreover, The genome comprises 132 genes, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome is 38.9%. The phylogenetic analysis indicated that S. guangxiensis is most closely related to its congener S. adoxoides, and Semiaquilegia is most closely related to Aquilegia in Ranunculaceae.