Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes

Abstract

Background Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role. Results We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication. Conclusions Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.

The copy number of the eukaryotic rRNA gene can be counted comprehensively

“…The obtained copy number of the 18S rRNA gene of each species from the three replicates was consistent (Table 1; Figure 1b); however, it differed among the species: the largest was approximately 77 ( Sulcionema specki ) and the smallest was approximately 2 ( Hemistasia phaeocysticola) . As 20 copies of the 18S rRNA gene have been counted from the nuclear genome of Diplonema papillatum (Valach et al, 2023), our estimated score (i.e., approximately 17 in D. papillatum ) is comparable to it and one‐sample t‐test also supported that there is no significant difference between two scores (t = −1.548, p = 0.262; Appendix). Hence, the estimation of the other four species can be expected to be reasonable.…”

Functional differentiation of Sec13 paralogues in the euglenozoan protists

“…Using sequences of COPII subunits from other members of the Euglenozoa and Naegleria gruberi, a representative of the Euglenozoan sister lineage Heterolobosea [8], we used homology-searching to identify genes encoding homologous proteins in the genome of P. papillatum [21] and recently available transcriptomes from six additional diplonemid species, namely Diplonema japonicum, Rhynchopus humris, Lacrimia lanifica, Sulcionema specki, Artemidia motanka and Namystynia karyoxenos [22]. We identified orthologues for Sar1, Sec13, Sec23, Sec24 and Sec31 (figure 1; electronic supplementary material, tables S1 and S2), whereas the less conserved Sec12 and Sec16 were not found, even with more sensitive hidden Markov model searches.…”

“…COPII subunits were retrieved by BLAST+v2.8.1 [42] searches using discobid sequences [8] as queries in the genome of Paradiplonema papillatum [21], transcriptomes of diplonemids Diplonema japonicum, Rhynchopus humris, Lacrimia lanifica, Sulcionema specki, Artemidia motanka and Namystynia karyoxenos [22], genome of the kinetoplastid Bodo saltans [43], and transcriptomes of the euglenids Euglena longa [44] and Eutreptiella gymnastica [45] (reassembly available at https://doi.org/10.5281/zenodo.257410) [46]. To identify more divergent sequences, more sensitive searches by HMMER v3.3 based on profile hidden Markov models [47] were performed in parallel.…”

Current Status of Marine Animal Derived Polysaccharides in Sustainable Food Packaging

“…Marine animals are a rich source of polysaccharides, namely chitosan, hyaluronan, chondroitin sulfate, and gelatin. , The efficacy of chitosan-based packaging in maintaining the quality and prolonging the shelf life of diverse food items, such as fruits, vegetables, meat, and seafood, has been reported. , Modern research efforts have been directed toward the alteration of chitosan films with the aim of enhancing their mechanical and barrier characteristics. , The combination of chitosan with other natural polymers, such as alginate or pectin, has been reported to augment its properties. , The utilization of hyaluronan-based packaging has attracted significant interest as a prospective substitute for synthetic packaging materials. , The film-forming properties of hyaluronan films, coupled with their high water-absorbing capacity, make them an appropriate choice for implementation in food packaging applications. , Chondroitin sulfate has also been explored as a potential natural polymer for food packaging. Chondroitin sulfate films have been shown to have good barrier properties against moisture and oxygen, as well as good mechanical properties. , The utilization of gelatin as a potential natural polymer for food packaging has been subject to extensive research. , The film-forming properties of gelatin films are admirable, and they exhibit satisfactory barrier properties against oxygen and moisture. , …”