Abstract
BackgroundPicophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used third-generation sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China.ResultThe 24.23 Mbp nuclear genome of M.homosphaera, harboring 6649 protein-coding genes, is more compact than the genomes of the closely related Sphaeropleales species. This genome streamlining may be caused by a reduction in gene family number, intergenic size and introns. The genome sequence of M.homosphaera reveals the strategies adopted by this organism for environmental adaptation in the eutrophic lake. Analysis of cultures and the protein complement highlight the metabolic flexibility of M.homosphaera, the genome of which encodes genes involved in light harvesting, carbohydrate metabolism, and nitrogen and microelement metabolism, many of which form functional gene clusters. Reconstruction of the bioenergetic metabolic pathways of M.homosphaera, such as the lipid, starch and isoprenoid pathways, reveals characteristics that make this species suitable for biofuel production.ConclusionThe analysis of the whole genome of M. homosphaera provides insights into the genome streamlining, the high lipid yield, the environmental adaptation and phytoplankton evolution.
Highlights
Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes
Using a whole-genome approach, we focused on the gene sets and metabolic pathways of Mychonastes that may facilitate its dominance under the environmental conditions of most eutrophic lakes [4, 5]
The assembly was analyzed regarding its completeness based on sequence homology to the OrthoDB eukaryote dataset, showing 89.4% complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) (Supplementary Table 1), which was higher than the percentages for the sequenced Sphaeropleales species (C.zofingiensis 84.5%, M.neglectum 58.5%, and T.obliquus 79.9%) except for R.subcapitata (91.7%) [10]
Summary
Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used thirdgeneration sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China. As the most urbanized and developed region of China, lake eutrophication is common in the middle-lower reaches of the Yangtze River. Mychonastes species are the dominant eukaryotic picophytoplankton in most eutrophic lakes (e.g., Lake Chaohu and Lake Poyang in China) [2, 3]. The mechanism underlying the dominance of Mychonastes in eutrophic lakes is not clear. Using a whole-genome approach, we focused on the gene sets and metabolic pathways of Mychonastes that may facilitate its dominance under the environmental conditions of most eutrophic lakes [4, 5]. Given the decreasing cost of sequencing [6,7,8], many phytoplankton have been sequenced [9,10,11,12], the genome sequencing of
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