Liu et al. BMC Genomics (2020) 21:477 https://doi.org/10.1186/s12864-020-06891-6 RESEARCH ARTICLE Open Access Genome analyses provide insights into the evolution and adaptation of the eukaryotic Picophytoplankton Mychonastes homosphaera Changqing Liu1,2†, Xiaoli Shi1*†, Fan Wu1,2, Mingdong Ren1,2, Guang Gao1 and Qinglong Wu1,2 Abstract Background: 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 third- generation sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China. Result: The 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. Conclusion: The analysis of the whole genome of M. homosphaera provides insights into the genome streamlining, the high lipid yield, the environmental adaptation and phytoplankton evolution. Keywords: Picophytoplankton, Mychonastes, Genome, Adaptation Background Mychonastes species are the dominant eukaryotic pico- As the most urbanized and developed region of China, phytoplankton in most eutrophic lakes (e.g., Lake lake eutrophication is common in the middle-lower Chaohu and Lake Poyang in China) [2, 3]. However, the reaches of the Yangtze River. Picophytoplankton (with mechanism underlying the dominance of Mychonastes in cell diameters < 3 μm) are abundant and can contribute eutrophic lakes is not clear. Using a whole-genome ap- 9–55% of primary productivity in eutrophic lakes [1, 2]. proach, we specifically focused on the gene sets and metabolic pathways of Mychonastes that may facilitate * Correspondence: [email protected] its dominance under the environmental conditions of †Changqing Liu and Xiaoli Shi contributed equally to this work. most eutrophic lakes [4, 5]. Although given the decreas- 1 State Key Laboratory of Lake Science and Environment, Nanjing Institute of ing cost of sequencing [6–8], many phytoplankton have Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China been sequenced [9–12], the genome sequencing of Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Liu et al. BMC Genomics (2020) 21:477 Page 2 of 18 picophytoplankton has only targeted marine species thus Results far [13, 14]. The absence of genome information for Phylogenetic analyses picophytoplankton in freshwater lakes prevents us from We performed phylogenetic analyses using 18S rRNA to recognizing the picophytoplankton niche and its eco- verify the phylogenetic position of M.homosphaera logical role in the lake. within Viridiplantae, with red algae as an outgroup Mychonastes belong to the order Sphaeropleales within (Fig. 1). In the tree, M.homosphaera was clustered by the class Chlorophyceae. Sphaeropleales is a large group family, forming a monophyletic group with the other that contains some of the most common freshwater Mychonastaceae species. There was robust support (BP = algae [15]. The genome sequences of Sphaeropleales are 95) for the inclusion of M.homosphaera in Mychonasta- a hot research topic because some of these species show ceae, where it was positioned closest to Mychonastes enormous potential for biofuel production [10, 11, 16], homosphaera (AB025423) isolated from Lake Kinneret, with robust growth and a high lipid content. Thus far, Israel [19]. six genomes of Sphaeropleales, belonging to Scenedes- mus quadricauda [9], Raphidocelis subcapitata [10], General features of the nuclear genome Monoraphidium neglectum [11], Tetradesmus obliquus We sequenced 5.8 Gbp reads using the PacBio Sequel [12], Chromochloris zofingiensis [17], and Coelastrella sp. system. Based on assembly and correction, we obtained [18], have been sequenced. These Sphaeropleales ge- M.homosphaera genome statistics (genome size: 24.23 nomes provide much information for Mychonastes gen- Mb, contig N50: 2 Mb, contig number: 31) (Table 1). ome research and contribute to explaining the evolution The assembly was analyzed regarding its completeness and adaptation of Mychonastes. Comparative analyses of based on sequence homology to the OrthoDB eukaryote genomes would provide insights into the environmental dataset (www.orthodb.org), showing 89.4% complete adaptation and genome evolution of Sphaeropleales. BUSCOs (Benchmarking Universal Single-Copy Ortho- In order to further increase knowledge about the evo- logs) (Supplementary Table 1), which was higher than lution and adaptation of freshwater picophytoplankton, the percentages for the sequenced Sphaeropleales spe- we isolated a Mychonastes strain from Lake Chaohu, a cies (C.zofingiensis 84.5%, M.neglectum 58.5%, and highly eutrophic lake, and sequenced its complete gen- T.obliquus 79.9%) except for R.subcapitata (91.7%) [10]. ome by using third-generation sequencing (PacBio Se- Therefore, we obtained a nearly complete genome for quel). Here, we conducted combined analysis of the M.homosphaera. complete genome sequences of M.homosphaera and A total of 53,016 SSRs (simple sequence repeats) were other Sphaeropleales species as well as picophytoplank- masked by MISA (MIcroSAtellite identification tool), ton species to investigate the evolutionary history and which accounted for 20.13% of the M.homosphaera gen- environmental adaptation of M.homosphaera. ome. There were six types of SSR in the M.homosphaera Fig. 1 Phylogenetic tree of 18S rDNA sequences using the maximum likelihood method Liu et al. BMC Genomics (2020) 21:477 Page 3 of 18 Table 1 Mychonastes homosphaera genome statistics Out of these, 5711 protein-coding genes (85.89% of the Assembly statistics for the nuclear genome predicted genes) were annotated, and coding sequences Assembly genome size (Mbp) 24.23 constituted 43.1% of the genome, with a mean exon length and mean intron length of 323.36 and 358.88 bp, Genomic G + C content (%) 72.4 respectively. The protein-coding genes contained 25,628 Contig number 31 introns, with a density of 3.85 introns per gene, and 32, Number of Contig N50 5 277 exons, with a density of 4.85 introns per gene. Length of Contig N50 (kbp) 2001 The nuclear genome of M.homosphaera was the smal- miRNA number 0 lest among those known for Sphaeropleales, at less than rRNA number 26 half of the size of the known whole genome sequences from Sphaeropleales. Unlike other Sphaeropleales spe- snRNA number 11 cies, M.homosphaera exhibited small intergenic regions tRNA number 64 and a high coding rate, which is common in other pico- Gene statistics phytoplankton (Fig. 2); therefore, the coding percentage Predicted number of nuclear genes 6649 of M.homosphaera (43.1%) was higher than that of other Number of annotated genes 5711 (85.89%) Sphaeropleales (expect R.subcapitata). Furthermore, Average transcript length (bp) 2952.98 M.homosphaera exhibited the highest GC content (72.4%) among the Sphaeropleales species examined to Average CDS length (bp) 1569.72 date. Exon number 32,277 Average exon number per gene 4.85 General features of chloroplast and mitochondrial Average exon length (bp) 323.36 genomes Intron number 25,628 M.homosphaera is the Sphaeropleales picophytoplank- Average intron number per gene 3.85 ton, we compared its organelle genomes with those of other Sphaeropleales species (M.neglectum and R.subca- Average intron length (bp) 358.88 pitata) and those of two marine picophytoplanktons Coding (%) 43.1% (Ostreococcus tauri and Micromonas commoda), to understand the genome features of M.homosphaera. The genome (Supplementary Table 2), and the vast majority complete chloroplast genome of M.homosphaera was of SSR (52,206 repeat sequences) belong