Biology subjects

Zoclanclounon, Y. A. B.

Publications and source records attributed to Zoclanclounon, Y. A. B..

5 recordsLinked to original sources

bioRxiv2026

Transcriptome profiling reveals gene regulatory network governing seed size in Brassica napus

Seed size is a critical trait influencing yield and quality in oilseed crops such as Brassica napus. Despite their economic importance, the genetic and molecular mechanisms regulating seed size remain unclear, particularly in polyploid species, such as B. napus. To deepen our understanding of seed size regulation, we performed a comprehensive transcriptomic analysis across four developmental stages (heart, torpedo, green, and mature) and three distinct seed organs: the seed coat, embryo, and endosperm. Differential expression analysis between B. napus var. Zhongshuang (ZS11) and B. napus cv. Ragged Jack (RJ) was performed to uncover regulatory networks involved in seed size control. Our results uncovered dynamic gene regulatory networks (GRNs) and pinpointed key regulators, including well-established factors like ABI5 and BRI1, as well as novel candidate genes such as KNAT5, ARF11, SUS2, UGT72B1, UGT89A2, and SBT1.7. The present research provides an understanding of the regulatory networks governing seed size in B. napus. These findings not only enhance our knowledge of seed biology but also offer valuable resources for future breeding strategies aimed at optimizing seed size and yield in polyploid oilseed crops.

genomics↗

bioRxiv2026

The impact of long-read sequencing on fungal genome assemblies: progress and disparity

Fungal genomics has expanded rapidly over the past 30 years, and recently the pace and breath has further quickened for many taxa, although many taxonomic gaps persist. With three decades of rapid growth, fungal genomics now merits a re-examination of its history, progress, and unresolved taxonomic gaps. Here, we review the development of fungal genomics from early efforts such as the Fungal Genome Initiative to current progress driven by third-generation long-read sequencing. We have compiled and summarised publicly available fungal genomes to highlight trends in assembly quality, adoption of long-read technologies, and taxonomic representation. Notably, substantial phylogenetic gaps remain, particularly outside Dikarya, and significant challenges persist for unculturable taxa. This review identifies priorities for the fungal community, including: (1) coordinated efforts to close major taxonomic gaps across the fungal tree of life; (2) improved repository metrics to facilitate identification of high-quality assemblies; and (3) improved and standardised genome annotation which is lacking for most assemblies. Together, these steps will support the development of reliable genomic resources that capture the full breadth of diversity across the fungal kingdom, generating foundational data for comparative genomics, evolutionary biology, functional studies, genetic studies and applied research.

genomics↗

bioRxiv2023

Detecting the genetic variants associated with key culinary traits in Dioscorea alata

Quality attributes play a pivotal role in determining consumers acceptability and market value of food crops. Dioscorea alata is a major yam species for food security in tropical areas, but our understanding of the genetic factors underlying tuber culinary traits is limited. This study aimed at elucidating the genetic basis of key culinary attributes, including dry matter content, cooking time, boiled yam hardness, and moldability, through genome-wide association studies (GWAS). Phenotypic assessments revealed notable variations among the D. alata genotypes across two locations as well as significant correlations among the quality traits. The GWAS identified 25 significant associations distributed across 14 chromosomes. Allele segregation analysis of the identified loci highlighted favorable alleles associated with desired traits, such as reduced cooking time, increased dry matter content, enhanced hardness, and good moldability. Within the set of 42 putative candidate genes, we identified specific genes differentially expressed in tubers of distinct genotypes with contrasting quality attributes. Furthermore, we conducted a comparative analysis with previously reported quantitative trait loci for dry matter content and showed that multiple genomic regions govern this trait in D. alata. Our study offers valuable insights into the links between these key culinary traits and the underlying genetic basis in D. alata. These findings have practical implications for breeding programs aimed at enhancing the quality attributes of greater yam.

plant biology↗

bioRxiv2023

Haplotype-resolved telomere-to-telomere assembly of the African catfish (Clarias gariepinus) provides insights for semi-terrestrial adaptation of airbreathing catfishes

Airbreathing catfishes are a group of stenohaline freshwater fish that can withstand various environmental conditions and farming practices, including the ability to breathe atmospheric oxygen. This unique ability has allowed them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological conditions remain poorly understood. Here, we sequenced the genome of the African catfish Clarias gariepinus, one of the most commonly farmed clariids. By integrating different long reads sequencing technologies, we generated a chromosome-level assembly with high-resolution haplotypes, including the male-specific haplotype. The diploid assembly yielded 58 contigs spanning 969.72 Mb with a contig N50 of 33.71 Mb. We report 25,655 predicted protein-coding genes and 49.94% repetitive elements in the African catfish genome. Several gene families involved in ion transport, osmoregulation, oxidative stress response, and muscle metabolism were expanded or positively selected in clariids, suggesting a potential role in their transition to terrestrial life. The reported findings expand our understanding of the genomic mechanisms underpinning the resilience and adaptive mechanisms of C. gariepinus to adverse environments. These insights will serve as a valuable resource for future studies in elucidating these unique biological traits in related teleosts and leverage these insights for aquaculture improvement.

genomics↗

bioRxiv2023

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

BackgroundMicrosatellite markers represent a low-cost and efficient tool for rapid genotyping as compared to single nucleotide polymorphism markers in laboratories with limited resources. For the economically important yam species widely cultivated in developing countries, very few microsatellite markers are available and no marker database has been developed to date. Herein, we conducted a genome-wide microsatellite marker development among four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam breeder community. ResultsThe screening of yam genomes resulted in 318,713; 322,501; 307,040 and 253,856 microsatellites in Dioscorea alata, D. rotundata, D. dumetorum, and D. zingiberensis, respectively. Mono-, di- and tri-nucleotides were the most important types of repeats in the different species and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, a subset of 17 markers were experimentally validated with good discriminatory power regarding the species and the ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at http://yamdb.42web.io/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. ConclusionsThe present work is the first comprehensive microsatellite marker mining across several yam species and will contribute to advance yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam breeders, especially those in developing countries.

genomics↗