Biology subjects

Hsu, C.-y.

Publications and source records attributed to Hsu, C.-y..

2 recordsLinked to original sources

bioRxiv2024

Genomic diversity and evolution in the Hawaiian Islands endemic Kokia (Malvaceae)

Island species are highly vulnerable due to habitat destruction and their often small population sizes with reduced genetic diversity. The Hawaiian Islands constitute the most isolated archipelago on the planet, harboring many endemic species. Kokia is an endangered flowering plant genus endemic to these islands, encompassing three extant and one extinct species. Recent studies provided evidence of unexpected genetic diversity within Kokia. Here, we provide high quality genome assemblies for all three extant Kokia species, including an improved genome for K. drynarioides. All three Kokia genomes contain 12 chromosomes exhibiting high synteny within and between Kokia and the sister taxon Gossypioides kirkii. Gene content analysis revealed a net loss of genes in K. cookei compared to other species, whereas the gene complement in K. drynarioides remains stable and that of K. kauaiensis displays a net gain. A dated phylogeny estimates the divergence time from the last common ancestor for the three Kokia species at [~]1.2 million years ago (mya), with the sister taxa [K. cookei + K. drynarioides] diverging [~]0.8 mya. Kokia appears to have followed a stepping-stone pattern of colonization and diversification of the Hawaiian Archipelago, likely starting on low or now submerged older islands. The genetic resources provided may benefit conservation efforts of this endangered endemic genus.

genomics↗

bioRxiv2022

Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification

We present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes optimally sized restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Library amplification and barcoding are completed in one PCR step, and magnetic beads are used to purify the genomic fragments from the ligation and library generation steps. Our protocol increases the efficiency and decreases the time to complete a ddRAD-Seq experiment. To demonstrate its utility, we compared SNPs from our protocol with those from whole genome resequencing data from Gossypium herbaceum and Gossypium arboreum. Principal component analysis demonstrated that the variability of the combined data was explained by the genotype (PC1) and methodology applied (PC2). Phylogenetic analysis showed that the SNPs from our method clustered with SNPs from the resequencing data of the corresponding genotype. Sequence alignments illustrated that for homozygous loci, more than 90% of the SNPs from the resequencing data were discovered by our method. Our analyses suggest that our ddRAD-Seq method is reliable in identifying SNPs suitable for phylogenetic and association genetic studies while reducing cost and time over known methods.

genomics↗