Initial Description of the Genome of Aeluropus littoralis, a Halophile Grass

Genomics-assisted breeding for designing salinity-smart future crops

Climate change induces many abiotic stresses, including soil salinity, significantly challenging global agriculture. Salinity stress tolerance (SST) is a complex trait, both physiologically and genetically, and is conferred at various levels of plant functional organization. As both the sustainability and profitability of agricultural production systems are critically dependent on SST, plant breeders are trying to design and develop salinity-smart crop plants capable of thriving under high salinity conditions. The accessibility of extreme-quality reference genomes for cultivated crops, naturally salinity-smart plants, and crop wild relatives has fast-tracked the discovery of key genes and quantitative trait loci (QTLs), marker development, genotyping assays and molecular breeding products with improved SST. Employing fast-forward breeding tools, namely genomic selection (GS), haplotype-based breeding (HBB), artificial intelligence (AI) and high-throughput phenotyping (HTP), has shown influence not only for fast-tracking genetic gains but also for reducing the time and cost of developing commercial cultivars with enhanced SST and yield stability. This review discusses the advancement and prospects of various genomics-assisted breeding (GAB) tools, including genome sequencing, QTL mapping, GWAS, GS, HBB, pan-genomics, single-cell/tissue genomics and phenotyping, epigenomics and transgenomics, to exploit the genetic landscape for improving SST. Additionally, we explore the integration of HTP and AI, which demonstrates how these innovative approaches can optimize breeding efficiency and guide large-scale breeding efforts for designing salinity-smart crops to ensure sustainable agriculture and global food security. The collective adoption of these tools suggests bridging the gap between research and field application to deliver stress-smart varieties designed for saline-affected regions worldwide.

De novo, high-quality assembly and annotation of the halophyte grass Aeluropus littoralis draft genome and identification of A20/AN1 zinc finger protein family

BACKGROUND

Aeluropus littoralis is considered a valuable natural forage plant for ruminant livestock and is highly tolerant to extreme abiotic stresses, especially salinity, drought, and heat. It is a monocotyledonous halophyte, has salt glands, performs C4-type photosynthesis and has a close genetic relationship with cereal crops. Moreover, previous studies have shown its huge potential as a reservoir of genes and promoters to understand and improve abiotic stress tolerance in crops.

RESULTS

The sequencing and hybrid assembly of the A. littoralis genome (2n = 2X = 20) using short and long reads from the BGISeq-500 and PacBio high-fidelity (HiFi) sequencing platforms, respectively. Using the k-mer analysis method, the haploid genome size of A. littoralis was estimated to be 360 Mb (with a heterozygosity rate of 1.88%). The hybrid assembled genome included 4,078 contigs with a GC content of 44% and covered 348 Mb. The longest contig and the N50 values were 5.1 Mb and 133.77 kb, respectively. The Benchmarking Universal Single Copy Ortholog (BUSCO) value was 91.1%, indicating good integrity of the assembled genome. The discovered repetitive elements accounted for 90.6 Mb, representing 26.03% of the total genome, and included a significant component of transposable elements (11.48%, ~40 Mb). Using a homology-based approach, 35,147 genes were predicted from the genome assembly. We next focused our analysis on the zinc-finger A20/AN1 gene family, a member of which (AlSAP) was previously shown to confer increased tolerance to osmotic and salt stresses when it was over-expressed in tobacco, wheat, and rice. Here, we identified the complete set of members of this family in the Aeluropus littoralis genome, thereby laying the foundation for their future functional analysis in cereal crops. In addition, the expression patterns of four novel genes from this family were analyzed by qPCR.

CONCLUSION

This resource and our findings will contribute to improve the current understanding of salinity tolerance in halophytes while providing useful genes and allelic variation to improve salinity and drought tolerance in cereals through genetic engineering and gene editing, respectively.

A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences

Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H+-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22, but no significant difference was found between the two groups. The method successfully identified P-type ATPase family members in raw genomes that are poorly assembled.

Comprehensive Analysis of Calcium Sensor Families, CBL and CIPK, in Aeluropus littoralis and Their Expression Profile in Response to Salinity

Plants have acquired sets of highly regulated and complex signaling pathways to respond to unfavorable environmental conditions during evolution. Calcium signaling, as a vital mechanism, enables plants to respond to external stimuli, including abiotic and biotic stresses, and coordinate the basic processes of growth and development. In the present study, two calcium sensor families, CBL and CIPK, were investigated in a halophyte plant, Aeluropus littoralis, with a comprehensive analysis. Here, six AlCBL genes, and twenty AlCIPK genes were studied. The analysis of the gene structure and conserved motifs, as well as physicochemical properties, showed that these genes are highly conserved during evolution. The expression levels of AlCBL genes and AlCIPK genes were evaluated under salt stress in leaf and root tissue. Based on the real-time RT-PCR results, the AlCIPK gene family had a higher variation in mRNA abundance than the AlCBL gene family. AlCIPK genes were found to have a higher abundance in leaves than in roots. The results suggest that the correlation between AlCBL genes and AlCIPK is tissue-specific, and different correlations can be expected in leaves and roots. Based on these correlations, AlCIPK3.1-AlCBL4.1 and AlCIPK1.2-AlCBL4.4 can be co-expressed in the root tissue, while AlCBL10 has the potential to be co-expressed with AlCIPK5, AlCIPK26, and AlCIPK12.3 in the leaf tissue. Our findings reveal valuable information on the structure and function of calcium sensor families in A. littoralis, a halophyte plant, that can be used in future research on the biological function of CBLs and CIPKs on salt stress resistance.

Genome-wide analysis of the laccase (LAC) gene family in Aeluropus littoralis: A focus on identification, evolution and expression patterns in response to abiotic stresses and ABA treatment

Laccases are plant enzymes with essential functions during growth and development. These monophenoloxidases are involved in lignin polymerization, and their expression respond to environmental stress. However, studies of laccases in some plants and fungi have highlighted that many structural and functional aspects of these genes are still unknown. Here, the laccase gene family in Aeluropus littoralis (AlLAC) is described based on sequence structure and expression patterns under abiotic stresses and ABA treatment. Fifteen non-redundant AlLACs were identified from the A. littoralis genome, which showed differences in physicochemical characteristics and gene structure. Based on phylogenetic analysis, AlLACs and their orthologues were classified into five groups. A close evolutionary relationship was observed between LAC gene family members in rice and A. littoralis. According to the interaction network, AlLACs interact more with proteins involved in biological processes such as iron incorporation into the metallo-sulfur cluster, lignin catabolism, regulation of the symbiotic process and plant-type primary cell wall biogenesis. Gene expression analysis of selected AlLACs using real-time RT (reverse transcription)-PCR revealed that AlLACs are induced in response to abiotic stresses such as cold, salt, and osmotic stress, as well as ABA treatment. Moreover, AlLACs showed differential expression patterns in shoot and root tissues. Our findings indicate that AlLACs are preferentially involved in the late response of A. littoralis to abiotic stress.