Complete mitochondrial genome of an oleaginous microalga Vischeria punctata (Eustigmatophyceae: Chlorobotryaceae) and phylogenetic analysis

References

• Abuduaini A, Wang YB, Zhou HY, Kang RP, Ding ML, Jiang Y, Suo FY, Huang LD. 2021. The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species. IMA Fungus. 12(1):31. doi:10.1186/s43008-021-00081-z.
   PubMed Web of Science ®Google Scholar
• Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol. 27(6):1436–1448. doi:10.1093/molbev/msq029.
   PubMed Web of Science ®Google Scholar
• Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, et al. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 306(5693):79–86. doi:10.1126/science.1101156.
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. doi:10.1089/cmb.2012.0021.
   PubMed Web of Science ®Google Scholar
• Barcytė D, Zátopková M, Němcová Y, Richtář M, Yurchenko T, Jaške K, Fawley KP, Škaloud P, Ševčíková T, Fawley MW, et al. 2022. Redefining Chlorobotryaceae as one of the principal and most diverse lineages of eustigmatophyte algae. Mol Phylogenet Evol. 177:107607 doi:10.1016/j.ympev.2022.107607.
   PubMed Web of Science ®Google Scholar
• Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319. doi:10.1016/j.ympev.2012.08.023.
   PubMed Web of Science ®Google Scholar
• Bi G, Mao Y, Xing Q, Cao M. 2018. HomBlocks: a multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching. Genomics. 110(1):18–22. doi:10.1016/j.ygeno.2017.08.001.
   PubMed Web of Science ®Google Scholar
• Chan PP, Lowe TM. 2019. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol Biol. 1962:1–14.
   PubMedGoogle Scholar
• Chesnick JM, Goff M, Graham J, Ocampo C, Lang BF, Seif E, Burger G. 2000. The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus: complete sequence, gene content and genome organization. Nucleic Acids Res. 28(13):2512–2518. doi:10.1093/nar/28.13.2512.
   PubMed Web of Science ®Google Scholar
• Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE. 2019. Apollo: democratizing genome annotation. PLoS Comput Biol. 15(2):e1006790. doi:10.1371/journal.pcbi.1006790.
   PubMed Web of Science ®Google Scholar
• Eliáš M, Amaral R, Fawley KP, Fawley MW, Němcová Y, Neustupa J, Přibyl P, Santos LMA, Ševčíková T. 2017. Eustigmatophyceae. In: Handbook of the protists. Cham: Springer. Vol. 1; p. 367–406. doi:10.1007/978-3-319-28149-0_39
   Google Scholar
• Gao B, Xu M, Shan D, Zhang C, Yang Y, Dong Z, Zhang H, Han B, Huang L, Zhang C. 2023. The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids. BMC Biol. 21(1):133. doi:10.1186/s12915-023-01618-x.
   PubMed Web of Science ®Google Scholar
• Gao B, Yang J, Lei X, Xia S, Li A, Zhang C. 2016. Characterization of cell structural change, growth, lipid accumulation, and pigment profile of a novel oleaginous microalga, Vischeria stellata (Eustigmatophyceae), cultured with different initial nitrate supplies. J Appl Phycol. 28(2):821–830. doi:10.1007/s10811-015-0626-1.
   Web of Science ®Google Scholar
• Hibberd DJ. 1981. Notes on the taxonomy and nomenclature of the algal classes Eustigmatophyceae and Tribophyceae (synonym Xanthophyceae). Bot J Linn Soc. 82(2):93–119. doi:10.1111/j.1095-8339.1981.tb00954.x.
   Web of Science ®Google Scholar
• Huang L, Gao B, Wang F, Zhang C. 2019. The complete mitochondrial genome of an oleaginous microalga Vischeria stellata strain SAG 33.83 (Eustigmatophyceae). Mitochondrial DNA Part B. 4(1):301–302. doi:10.1080/23802359.2018.1542993.
   Web of Science ®Google Scholar
• Jagadevan S, Banerjee A, Banerjee C, Guria C, Tiwari R, Baweja M, Shukla P. 2018. Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production. Biotechnol Biofuels. 11(1):185. doi:10.1186/s13068-018-1181-1.
   PubMedGoogle Scholar
• Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14):3059–3066. doi:10.1093/nar/gkf436.
   PubMed Web of Science ®Google Scholar
• Kryvenda A, Rybalka N, Wolf M, Friedl T. 2018. Species distinctions among closely related strains of Eustigmatophyceae (Stramenopiles) emphasizing ITS2 sequence-structure data: Eustigmatos and Vischeria. Eur J Phycol. 53(4):471–491. doi:10.1080/09670262.2018.1475015.
   Web of Science ®Google Scholar
• Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35(9):3100–3108. doi:10.1093/nar/gkm160.
   PubMed Web of Science ®Google Scholar
• Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. doi:10.1093/molbev/msu300.
   PubMed Web of Science ®Google Scholar
• Okonechnikov K, Golosova O, Fursov M. 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 28(8):1166–1167. doi:10.1093/bioinformatics/bts091.
   PubMed Web of Science ®Google Scholar
• Oudot-Le SMP, Green BR. 2011. Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Gene. 476(1–2):20–26. doi:10.1016/j.gene.2011.02.001.
   PubMed Web of Science ®Google Scholar
• Ševčíková T, Klimeš V, Zbránková V, Strnad H, Hroudová M, Vlček Č, Eliáš M. 2016. A Comparative analysis of mitochondrial genomes in eustigmatophyte algae. Genome Biol Evol. 8(3):705–722. doi:10.1093/gbe/evw027.
   PubMed Web of Science ®Google Scholar
• She Y, Gao X, Jing X, Wang J, Dong Y, Cui J, Xue H, Li Z, Zhu D. 2022. Effects of nitrogen source and NaCl stress on oil production in Vischeria sp. WL1 (Eustigmatophyceae) isolated from dryland biological soil crusts in China. J Appl Phycol. 34(3):1281–1291. doi:10.1007/s10811-022-02720-3.
   Web of Science ®Google Scholar
• Sinetova MA, Sidorov RA, Medvedeva AA, Starikov AY, Markelova AG, Allakhverdiev SI, Los DA. 2021. Effect of salt stress on physiological parameters of microalgae Vischeria punctata strain IPPAS H-242, a superproducer of eicosapentaenoic acid. J Biotechnol. 331:63–73. doi:10.1016/j.jbiotec.2021.03.001.
   PubMed Web of Science ®Google Scholar
• Tang X, Bi G. 2016. Complete mitochondrial genome of Fistulifera solaris (Bacillariophycidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(6):4405–4406. doi:10.3109/19401736.2015.1089545.
   PubMedGoogle Scholar
• Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. doi:10.1093/nar/gkx391.
   PubMed Web of Science ®Google Scholar
• Wang FF, Gao BY, Huang LD, Su M, Dai CM, Zhang CW. 2018. Evaluation of oleaginous eustigmatophycean microalgae as potential biorefinery feedstock for the production of palmitoleic acid and biodiesel. Bioresour Technol. 270:30–37. doi:10.1016/j.biortech.2018.09.016.
   PubMed Web of Science ®Google Scholar
• Wei L, Xin Y, Wang D, Jing X, Zhou Q, Su X, Jia J, Ning K, Chen F, Hu Q, et al. 2013. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. BMC Genomics. 14(1):534. doi:10.1186/1471-2164-14-534.
   PubMedGoogle Scholar
• Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352. doi:10.1093/bioinformatics/btv383.
   PubMedGoogle Scholar
• Yang HP, Wenzel M, Hauser DA, Nelson JM, Xu X, Eliáš M, Li FW. 2021. Monodopsis and Vischeria genomes shed new light on the biology of eustigmatophyte algae. Genome Biol Evol. 13(11):evab233.
   PubMed Web of Science ®Google Scholar
• Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355. doi:10.1111/1755-0998.13096.
   PubMed Web of Science ®Google Scholar