De novo transcriptome assembly of the green alga Ankistrodesmus falcatus

Abstract

Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.

Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?

“…Diamond was used to align all contigs to the GenBank nr and KEGG databases for taxonomic assignment and KEGG ID annotation, respectively (Buchfink et al, 2015; Kanehisa & Goto, 2000). We performed differential gene expression analyses as described above for Daphnia , after we mapped, using Kallisto (Bray et al, 2016), eRNA reads to the reference genomes and transcriptomes of species known a priori to persist in the communities ( A. falcatus, S. quadricauda , and P. subcapitata ) and highly abundant species identified by SqueezeMeta ( Brachionus plicatilis , Volvox cateri , Stylonychia lemnae , Chlamydomonas eustigma ) (Aeschlimann et al, 2014; Han et al, 2019; Hirooka et al, 2017; Nag Dasgupta et al, 2018; Prochnik et al, 2010; Schomaker & Dudycha, 2021; Suzuki et al, 2018). We used the SQMtools R package to further analyze the SqueezeMeta data and created stacked-bar plots to represent the most relatively abundant taxa (Puente-Sánchez et al, 2020).…”

“…With default parameters, STAR [78] was used to map all eRNA and oRNA reads that passed quality control and trimming to the Daphnia pulex reference genome [45]. Using Kallisto [79], we also mapped eRNA reads to the reference genomes and transcriptomes of species known a priori to persist in the communities and highly abundant species identified by alignment of eRNA reads to NCBI nr database [80][81][82][83][84][85][86][87]. FeatureCounts [88] was used on the STAR resulting BAM file to quantify gene counts.…”

Genotypic variation in an ecologically important parasite is associated with host species, lake and spore size

“…in a beaker to which we had not added Metschnikowia spores). On the day of exposure, we added algal food, 12 500 cells Ankistrodesmus falcatus /mL (‘AJT’ strain; Schomaker and Dudycha, 2021 ), to each beaker. On the second day of exposure, an additional 18 750 cells Ankistrodesmus falcatus /mL were added to each beaker.…”

Lake water chemistry and population of origin interact to shape fecundity and growth in Daphnia ambigua

“…Algal media and vitamin supplement constituents were reagent grade (Fisher Scientific). Our Ankistrodesmus strain originated from the lab of C. E. Goulden at the Academy of Natural Sciences in Philadelphia, PA, USA and has been designated the AJT strain (Schomaker & Dudycha, 2021). To ensure consistent feeding levels throughout the experiment and to minimize any effects of feeding on water chemistry, algae were settled and resuspended with filtered lake water, maintaining a density of 1,000,000 cells/mL using a hemocytometer.…”