The first draft genome assembly of the MHR genome is presented, providing a foundation to understand the genetic architecture underlying key phenotypic traits and identifying potential novel gene sources in MHR for rice improvement in the Caribbean region.
Abstract
Moruga Hill Rice (MHR) is an African rice (Oryza glaberrima Steud.) brought to Trinidad by formerly enslaved African Americans and has been grown for many generations in Trinidad at subsistence and commercial scale. Despite its historical and agricultural significance, genomic resources specific to MHR remain unexplored, and its genetic composition, evolutionary history, and potential agronomic traits have not been characterized. This current study presents the first draft genome assembly of the MHR genome using a hybrid sequencing approach. The MHR genome size was found to be ~372.9 Mb with 56,073 predicted genes. Variant analysis revealed a total of 3,318,242 variants, of which 2,440,476 were SNPs, and 877,766 were InDels. Several candidate genes encoding proteins with orthology to previously characterized biotic resistance and abiotic stress-responsive genes in rice were identified. Potential gene families identified prompt further investigation of their roles in MHR drought and salt stress responses. Phylogenomic analysis of O. glaberrima landraces suggests that MHR shares close genetic affinity with the IRGC−104595 Malian landrace, consistent with historical records. This assembly thus expands the African rice genomic repository, providing a foundation to understand the genetic architecture underlying key phenotypic traits and identifying potential novel gene sources in MHR for rice improvement in the Caribbean region.
This study provides new insights into the pangenome of Magnaporthe oryzae and introduces a method for the identification of functionally important genes in fungal species.
Yi Wang, Qi Wu, Jin-bin Li et al.· Journal of Advanced Research· 0 citations
Variants associated with stress-responsive transporters, kinase signalling proteins, transcription factors and regulatory genes were also detected, indicating potentially important adaptive genomic signatures within the Iluppai Poo Samba genome.
Einstein Mariya David, Theivasigamani Parthasarathi· Agricultural Science Digest...· 0 citations
Orosanga japonica (Hemiptera: Ricaniidae) is an invasive, polyphagous planthopper established in Türkiye since 2007 that threatens economically important perennial and field crops across the Black Sea region. Although its establishment and rapid spread suggest considerable adaptive capacity, the genomic basis of this potential remains unexplored. We combined whole-genome sequencing with RNA-Seq data to generate a functionally annotated genome, recovering 92.5% of conserved single-copy orthologs. Utilizing these resources, we performed comparative genomic analyses across 20 additional hemipteran and thysanopteran species, investigating gene family dynamics and genome-wide positive selection. These analyses revealed 52 gene families with statistically significant, lineage-specific size changes (24 expansions and 28 contractions): expanded families were enriched for C2H2 zinc-finger transcription factors, α/β-hydrolases, major facilitator transporters, serpins, and chemosensory proteins, whereas contracted families included a cytochrome P450 family. Additionally, branch site tests identified 122 candidate genes under lineage-specific positive selection. These loci fall into three functional categories potentially associated with invasion-related traits: host detection and neuronal excitability, stress tolerance (xenobiotic, oxidative, and proteostatic), and barrier remodeling. Together, these genomic signatures highlight candidate molecular mechanisms that may contribute to host detection, xenobiotic tolerance, and ecological plasticity, providing a framework for evolutionary analysis and the targeted management of this emerging agricultural pest.
Yusuf Ulaş Çınar, Mehmet Ali Balcı, Onur Obut et al.· Insects· 0 citations
We present the de novo whole-genome assembly of a deepwater rice variety (Oryza sativa cv. Pin Gaew 56). Although the submergence escape response is a vital survival strategy in deepwater rice, current reference genomes lack sufficient genetic information to fully understand the molecular mechanisms behind this complex physiological process. Pin Gaew 56 (PG56) is a well-studied genetic resource with extensively documented physiological and molecular traits related to internode elongation under partial submergence. This study provides a cultivar-specific genomic resource for PG56 that can support further investigation of the genetic basis of the submergence escape response. A de novo whole-genome assembly of the deepwater rice cultivar PG56 was generated to support genomic studies of the submergence escape response. The final assembly has a total length of 407.7 Mb, comprising 138 scaffolds with an N50 of 32.5 Mb. Genome completeness assessed by BUSCO showed 94.5% complete BUSCOs, and continuity in LTR-rich regions was supported by an LTR Assembly Index of 28.2. Assembly quality was further supported by k-mer-based quality assessment and whole-genome synteny alignment against the MH63 reference genome. Together, these data provide a useful genomic resource for investigating the genetic mechanisms underlying internode elongation and flooding adaptation in deepwater rice.
Hoon Je Seong, Sung Un Huh, Tae-Ho Lee et al.· BMC Genomic Data· 0 citations
White rust disease elicited by the biotrophic pathogen
Albugo candida
is a leading cause of yield losses in oilseed
Brassica
crops, especially in the widely cultivated
Brassica juncea
. In the present investigation, the high-quality draft genome of a virulent Ac2V race of
A. candida
infecting
B. juncea
was sequenced using Illumina and Nanopore technologies. The raw data were assembled into a genome of 36.88 Mb with 415 scaffolds and N50 = 301.91 kb. The variant analysis showed 124,974 single nucleotide polymorphisms (SNPs) with an average density of 3.3 SNP per kb genome against the Ac2VPB reference assembly. Approximately 24.29% of the genome was constituted of repetitive elements, including 1,039 SSRs. A total number of 13,715 coding genes were revealed in the genome with an average distribution of 359.03 genes per Mb. Out of these predicted genes, 11,556 were annotated based on sequence homology and 355 were predicted as effectors with no transmembrane domain and N-terminal signal peptide. The annotation of 355 effectors revealed that 141 of them had homologs, while the remaining 214 were novel. Depending on the conserved motifs, these effectors were characterized, and their role in pathogenesis was established through qPCR in
B. juncea
. Additionally, phylogenetic analysis through average nucleotide identity revealed a similarity of 99.6% between the Canadian and Indian Ac2V isolate. Furthermore, 62 new contigs were identified in the Indian isolate that showed no sequence similarity to the Canadian isolate, suggesting variation within the race. Altogether, the present work provides genomic resources and framework for the dissection of this pathogen, which will refine our understanding of the
Albugo
–
Brassica
interaction.
Samridhi Mehta, Laxmi Awasthi, Rakhi Tomar et al.· Frontiers in Fungal Biology· 0 citations
Comparative genomic analyses revealed that F. brachygibbosum TZ1MST22 harbors more biomass-degrading enzymes than other pathogenic and endophytic Fusarium species, which will support efforts to optimize its cultivation for the high-yield production of useful metabolites.
Amani ben Alaya, Abdelmalek Lekired, M. Chaouachi et al.· Functional & Integrative Gen...· 0 citations
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