Biology subjects

Jia, K.-H.

Publications and source records attributed to Jia, K.-H..

4 recordsLinked to original sources

bioRxiv2024

Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes

With the explosive growth of whole-genome datasets, the accurate detection of orthologous synteny has become crucial for the reconstruction of evolutionary history. However, the currently available methods for the identification of orthologous synteny have great limitations: the methods are difficult to scale with varying polyploidy histories, and the accurate removal of out-paralogy is challenging. In this study, we developed a scalable and robust approach, the Orthology Index (OI), to identify orthologous synteny. Our evaluation of a large-scale dataset with diverse polyploidization events demonstrated that the technique is highly reliable. This discovery highlights OI as a potentially unified criterion for the identification of orthologous synteny, and this is further validated using simulation-based benchmarks. In addition, we explore its broad applications in reconstructing the evolutionary histories of plant genomes, including inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, significantly enhancing our analytical prowess in plant evolutionary genomics.

genomics↗

bioRxiv2024

Telomere-to-telomere, gap-free genome of mung beans (Vigna radiata) provides insights into domestication under structural variation

Mung bean (Vigna radiata), an essential annual legume, holds substantial value in global agriculture due to its short growth cycle, low input requirements, and nutritional benefits. Despite extensive domestication, the genetic mechanisms underlying its morphological and physiological evolution remain incompletely understood. In this study, we present a gap-free, telomere-to-telomere genome assembly of the mung bean cultivar Weilv-9, achieved through the integration of PacBio HiFi, Oxford Nanopore, and Hi-C sequencing technologies. The 500 Mb assembly, encompassing 11 chromosomes and containing 28,740 protein-coding genes, reveals that 49.17% of the genome comprises repetitive sequences. Within the genome, we found the recent amplification of transposable elements significantly impacts the expression of nearby genes. Furthermore, integrating structural variation and SNP data from resequencing, we identified that the fatty acid synthesis, suberin biosynthetic, and phenylpropanoid metabolic processes have undergone strong selection during domestication. These findings provide valuable insights into the genetic mechanisms driving domestication and offer a foundation for future genetic enhancement and breeding programs in mung beans and related species.

genomics↗

bioRxiv2024

Nearly complete genome assembly of a critically endangered pine illuminates evolution and conservation of conifers

Population genetic theory predicts that severe bottlenecks and extremely small effective population sizes (Ne) should reduce the ability of natural selection to eliminate harmful mutations. Under this framework, deleterious alleles are expected to accumulate and even fix, eroding fitness, constraining evolutionary rescue, and potentially precipitating mutational meltdown. Yet, empirical tests of these predictions in species at the extreme lower bound of Ne remain rare. We address this gap using Pinus squamata, one of the rarest tree species on Earth, with only 35 wild individuals remaining. We generated a near-complete reference genome (29.2 Gb) for this species and performed population genomic analyses across nearly all of its extant individuals, together with two closely related species. P. squamata exhibits extraordinarily low nucleotide diversity ({pi} = 3.35 x 10-), the lowest reported for any plant. Demographic inference reveals a recent and severe bottleneck ([~]20 generations ago) that reduced Ne to [~]2.7 and resulted in intense inbreeding. Contrary to theoretical expectations, we uncover evidence for highly efficient purifying selection: strongly deleterious mutations are markedly depleted, indicating substantial purging despite the extremely small Ne. Genome-wide patterns further implicate selection at linked sites--including background selection and pseudo-overdominance--as dominant forces shaping genomic variation in the species. These results challenge the prevailing view that drift overwhelms selection in extremely small populations. Instead, they suggest that, under certain genomic and demographic conditions, purifying selection can remain unexpectedly effective, potentially mitigating the risk of mutational meltdown in the rarest species.

genomics↗

bioRxiv2020

Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 contigs, and includes 31,501 genes. We inferred a male heterogametic sex determining factor on chromosome 7, suggesting that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii X-linked region occupies about 3.21 Mb of chromosome 7, and is probably in a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for studying sex chromosome evolution in Salicaceae family.

genomics↗