Biology subjects

Yang, H.-P.

Publications and source records attributed to Yang, H.-P..

3 recordsLinked to original sources

bioRxiv2021

Monodopsis and Vischeria genomes elucidate the biology of eustigmatophyte algae

Members of eustigmatophyte algae, especially Nannochloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. While extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis (60 Mb) and Vischeria (106 Mb), which are the sister groups to Nannochloropsis. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis, LINE repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and non-mevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis that has only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.

genomics↗

bioRxiv2021

Underwater CAM photosynthesis elucidated by Isoetes genome

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigated the underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identified several key differences. Notably, for carboxylation of PEP, Isoetes recruited the lesser-known "bacterial-type" PEPC, along with the "plant-type" exclusively used in other terrestrial CAM and C4 plants. Furthermore, we found that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.

plant biology↗

bioRxiv2020

Metagenomic characterization of a harmful algal bloom using nanopore sequencing

Water bodies around the world are increasingly threatened by harmful algal blooms (HABs) under current trends of rising water temperature and nutrient load. Metagenomic characterization of HABs can be combined with water quality and environmental data to better understand and predict the occurrence of toxic events. However, standard short-read sequencing typically yields highly fragmented metagenomes, preventing direct connection of genes to a single genome. Using Oxford Nanopore long-read sequencing, we were able to obtain high quality metagenome-assembled genomes, and show that dominant organisms in a HAB are readily identified, though different analyses disagreed on the identity of rare taxa. Genes from diverse functional categories were found not only in the most dominant genera, but also in several less common ones. Using simulated datasets, we show that the Flongle flowcell may provide an option for HAB monitoring with less data, at the expense of failing to detect rarer organisms and increasing fragmentation of the metagenome. Based on these results, we believe that Nanopore sequencing provides a fast, portable, and affordable method for studying HABs.

genomics↗