Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species
            <i>Scenedesmus obliquus</i>
            Strain DOE0152z

Starkenburg, Shawn R.; Hovde, Blake T.; Daligault, Hajnalka E.; Davenport, Karen W.; Huang, Andy; Neofotis, Peter; McKie‐Krisberg, Zaid

doi:10.1128/genomea.00617-17

Cited by 24 publications

(20 citation statements)

References 14 publications

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“…Results using the MECAT software showed a better assembly ability than that of SMRT Portal in S. obliquus AS-6-11, in which the contig numbers are 58.1% less, and the N50 value is 1.5-fold higher (Additional file 1 : Table S1). The genome sizes of the released Scenedesmus strains [ 20 – 24 ] range from 23.4 to 208.0 Mbp (Table 1 ). Among the available results, the N50 contig sizes of S. obliquus AS-6-11 reported in this study and S. obliquus strain DOE0152z using Pacbio technology are significantly higher than the other Scenedesmus strains using SGS (Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…ARA 93.2 56.8 4727 37,561 Illumina HiSeq – [ 20 ] Scenedesmus sp. MC-1 38.2 61.4 – 42,815 Illumina HiSeq 2000 8652 [ 21 ] S. vacuolatus 23.4 53.6 20,139 1571 454 20,139 PRJNA498405 S. quadricauda isolate LWG 002611 65.4 63.2 13,425 8094 Ion Proton 13,514 [ 22 ] Tetradesmus obliquus UTEX393 108.7 56.8 9191 – Illumina Hiseq2000 – [ 23 ] S. obliquus strain DOE0152z 208.0 56.7 2705 155,544 PacBio – [ 24 ] S. obliquus AS-6-11 172.3 52.0 2772 94,410 PacBio 31,964 This study a - means information not available …”

Section: Resultsmentioning

confidence: 99%

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Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

Chen

Mhuantong

et al. 2020

BMC Genomics

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Background Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been very limited. Cell self-flocculation of microalgal cells can be used as a simple and economic method for harvesting biomass, and it is of great importance to perform genome-scale studies for the self-flocculating S. obliquus strains to promote their biotechnological applications. Results We employed the Pacific Biosciences sequencing platform for sequencing the genome of the self-flocculating microalga S. obliquus AS-6-11, and used the MECAT software for de novo genome assembly. The estimated genome size of S. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Gene Ontology (GO) and KEGG pathway analyses revealed 65 GO terms and 428 biosynthetic pathways. Comparing to the genome sequences of the well-studied green microalgae Chlamydomonas reinhardtii, Chlorella variabilis, Volvox carteri and Micractinium conductrix, the genome of S. obliquus AS-6-11 encodes more unique proteins, including one gene that encodes D-mannose binding lectin. Genes encoding the glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, and proteins with fasciclin domains that are commonly found in cell wall proteins might be responsible for the self-flocculating phenotype, and were analyzed in detail. Four genes encoding both GPI-anchored cell wall proteins and fasciclin domain proteins are the most interesting targets for further studies. Conclusions The genome sequence of the self-flocculating microalgal S. obliquus AS-6-11 was annotated and analyzed. To our best knowledge, this is the first report on the in-depth annotation of the S. obliquus genome, and the results will facilitate functional genomic studies and metabolic engineering of this important microalga. The comparative genomic analysis here also provides new insights into the evolution of green microalgae. Furthermore, identification of the potential genes encoding self-flocculating proteins will benefit studies on the molecular mechanism underlying this phenotype for its better control and biotechnological applications as well.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

Chen

Mhuantong

et al. 2020

BMC Genomics

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show abstract

“…MECAT showed a better assembly ability than that of SMRT Portal in S. obliquus AS-6-11, in which the contig numbers are 58.1% less, and the N50 value is 1.5-fold higher (Additional le 1: Table S1). The genome sizes of the released Scenedesmus strains [20][21][22][23][24] range from 23.4 to 208.0 Mbp (Table 1). Among the available results, the N50 contig sizes of S. obliquus AS-6-11 reported in this study and S. obliquus strain DOE0152z using Pacbio technology are signi cantly higher than the other Scenedesmus strains using SGS ( Table 1).…”

Section: Morphological Features and Genome Assemblymentioning

confidence: 99%

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

Chen

Mhuantong²,

et al. 2020

Preprint

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Background Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been very limited. Cell self-flocculation of microalgal cells can be used as a simple and economic method for harvesting biomass, and it is of great importance to perform genome-scale studies for the self-flocculating S. obliquus strains to promote their biotechnological applications. Results We sequenced the genome of the self-flocculating microalga S. obliquus AS-6-11 employing the Pacific Biosciences sequencing platform, and used the MECAT software for de novo genome assembly. The estimated genome size of S. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Gene Ontology (GO) and KEGG pathway analysis revealed 65 GO terms and 428 biosynthetic pathways. Comparing to the well-studied green microalgae Chlamydomonas reinhardtii, Chlorella variabilis, Volvox carteri and Micractinium conductrix, the genome of S. obliquus AS-6-11 encodes more unique proteins, and some of them might be responsible for the self-flocculating phenotype. These genes encode D-mannose binding lectin, glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, and proteins with fasciclin domains that are commonly found in cell surface proteins, respectively. Four genes encoding both GPI-anchored cell wall proteins and fasciclin domain proteins are the most interesting targets for further studies. Conclusions To our best knowledge, this is the first report on the in-depth annotation of the S. obliquus genome, and the results will facilitate functional genomic studies of this important microalga. The comparative genomic analysis here also provides new insights into the evolution of green microalgae. Furthermore, identification of the potential genes encoding proteins for the self-flocculation of microalgal cells will benefit studies on the molecular mechanism underlying this phenotype for its better control and biotechnological applications as well.

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“…Efforts to increase Haematococcus productivity by targeting transformation to both nuclear and chloroplast genomes ( 4 , 5 ) have been limited by the lack of high-quality genome assemblies. The use of PacBio single-molecule real-time (SMRT) sequencing has gained traction recently for improving genome assemblies, including for algal chloroplasts, due to the long reads that are generated ( 6 , 7 ). Floydiella and Volvox species have some of the largest chloroplasts known among members of the Viridiplantae at ∼500 kb ( 8 , 9 ); previously, the largest known chloroplast (1.13 Mb) of any lineage belonged to the red alga Corynoplastis japonica ( 10 ).…”

Section: Genome Announcementmentioning

confidence: 99%

Next-Generation Sequencing of Haematococcus lacustris Reveals an Extremely Large 1.35-Megabase Chloroplast Genome

et al. 2018

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Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z

Abstract: The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

Cited by 24 publications

References 14 publications

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

Next-Generation Sequencing of Haematococcus lacustris Reveals an Extremely Large 1.35-Megabase Chloroplast Genome

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