Project description:Premise of the study:Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Methods and Results:Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis. One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively. Interestingly, in cross-varietal amplification, 13 out of the 16 loci were successfully amplified in O. acuminata var. acuminata, and 12 amplified in each of the other three varieties of O. acuminata. Conclusions:These newly developed SSR markers will facilitate further study of genetic variation and provide important genetic data needed for appropriate conservation of natural populations of all varieties of O. acuminata.
Project description:<i>Musa acuminata</i> var. <i>chinensis</i> is one of the most important wild banana species native to China which has huge potential breeding value by its cold tolerance and disease resistance. In this study, we first reported the complete chloroplast genome of <i>M. acuminata</i> var. <i>chinensis</i> and explore its phylogenetic position using a maximum likelihood phylogenetic tree. The chloroplast genome of <i>M. acuminata</i> var. <i>chinensis</i> is 170,402?bp in length and the overall GC content of the whole genome is 36.8%. It consisting of a pair of inverted repeat (IR, 35,320?bp) regions, a large single-copy (LSC, 88,870?bp) and a small single-copy (SSC, 10,900?bp). The chloroplast genome contained 112 genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA ribosomal genes. The most genes occur as a single copy, while 23 gene species occur in double copies. Phylogenetic analysis of 7 selected chloroplast genomes revealed that <i>M. acuminata</i> var. <i>chinensis</i> was closely related to <i>M. acuminata</i> ssp. <i>malaccensis</i>. The complete chloroplast genome of <i>M. acuminata</i> var. <i>chinensis</i> will greatly enhance precious gene resources for banana breeding programs in the future.
Project description:Diarrhetic Shellfish Poisoning (DSP) is a globally significant human health syndrome most commonly caused by dinoflagellates within the genus Dinophysis. While blooms of harmful algae have frequently been linked to excessive nutrient loading, Dinophysis is a mixotrophic alga whose growth is typically associated with prey availability. Consequently, field studies of Dinophysis and nutrients have been rare. Here, the temporal dynamics of Dinophysis acuminata blooms, DSP toxins, and nutrients (nitrate, ammonium, phosphate, silicate, organic compounds) were examined over four years within two New York estuaries (Meetinghouse Creek and Northport Bay). Further, changes in the abundance and toxicity of D. acuminata were assessed during a series of nutrient amendment experiments performed over a three year period. During the study, Dinophysis acuminata blooms exceeding one million cells L-1 were observed in both estuaries. Highly significant (p<0.001) forward stepwise multivariate regression models of ecosystem observations demonstrated that D. acuminata abundances were positively dependent on multiple environmental parameters including ammonium (p = 0.007) while cellular toxin content was positively dependent on ammonium (p = 0.002) but negatively dependent on nitrate (p<0.001). Nitrogen- (N) and phosphorus- (P) containing inorganic and organic nutrients significantly enhanced D. acuminata densities in nearly all (13 of 14) experiments performed. Ammonium significantly increased cell densities in 10 of 11 experiments, while glutamine significantly enhanced cellular DSP content in 4 of 5 experiments examining this compound. Nutrients may have directly or indirectly enhanced D. acuminata abundances as densities of this mixotroph during experiments were significantly correlated with multiple members of the planktonic community (phytoflagellates and Mesodinium). Collectively, this study demonstrates that nutrient loading and more specifically N-loading promotes the growth and toxicity of D. acuminata populations in coastal zones.
Project description:Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.