The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution

Abstract

Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only six copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content, and small animal size. Here, we report the seventh representative copepod genome and the first genome and the first transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology, and behavior of A. tonsa have been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCR-free whole genome sequence and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate that A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The nonrepetitive fraction of the genome assembly is estimated to be 566 Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod whole genome sequence data sets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.

The whole genome sequence and mRNA transcriptome of the tropical cyclopoid copepod Apocyclops royi

“…After bacterial contamination removal, the WGS assembly consists of scaffolds up to 116 Kb in length, with an average GC% of 33.5% (Fig. 1B), which is similar to other available copepod WGS assemblies, such as Acartia tonsa [13]. The uniformity of the length and GC% in Fig.…”

“…For example, we removed several contigs in the size range 100 kb to 1 Mb, all with a GC content between 56 % and 58 % and highly similar to known bacterial sequences. In order to estimate the genome size of A. royi including the unassembled and repetitive fraction, we used the preQC program which has previously been used for copepod genome size estimation [13]. The result shows that the expected complete genome size of A. royi is 450 Mb (supplementary material 3 preQC report).…”

“…Much of the unassembled sequence is can presumably be found in scaffolds smaller than the 1kb cutoff, though repeats also would be collapsed in these scaffolds. In a recent publication on the Acartia tonsa WGS assembly, the genome sizes of all copepod WGS projects was estimated and in all cases showed that less than half of the expected genome size was included in the WGS assembly [13]. The difference between the assembled and the actual size of the A. royi genome is thus expected, similar to the differences in other species, and hypothesized to be largely caused by unassembled repetitive/non-coding regions or collapsed scaffolds [13].…”

“…In a recent publication on the Acartia tonsa WGS assembly, the genome sizes of all copepod WGS projects was estimated and in all cases showed that less than half of the expected genome size was included in the WGS assembly [13]. The difference between the assembled and the actual size of the A. royi genome is thus expected, similar to the differences in other species, and hypothesized to be largely caused by unassembled repetitive/non-coding regions or collapsed scaffolds [13]. For example, if a repeat of 500 nt is found 1.000 times scattered throughout the genome, the sequence is unlikely to show up more than once in the assembly, which means that the assembly size is 500.000 nt smaller than the template genome.…”

“…Copepod genomes are infamously difficult to assemble [10, 11]. This is likely caused by high repetitiveness, a low GC content of around 30% [12] and very variable genome sizes [13], which means that it is difficult to assess the costs before undertaking whole genome sequencing (WGS). This is compounded by the often small physical size of the animals, which makes it necessary to use a collection of animals rather than a single individual for nucleic acid purification, adding to the complexity of genome assembly.…”