Biopolym. Cell. 2020; 36(1):13-21.
Genomics, Transcriptomics and Proteomics
Extreme diversity of SINE families in amphioxus Branchiostoma belcheri
1Kosushkin S. A., 1Vassetzky N. S.
  1. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences
    32, Vavilova Str., Moscow, Russian Federation, 119991


Short INterspersed Elements (SINEs) are an important component of the genome in higher eukaryotes. Commonly, their genomes have one or several SINE families. Aim. Identification and analysis of SINEs in the oriental lancelet Branchistoma belcheri was the goal of this study. Methods. Original and conventional bioinformatics methods were used. Results. Eighteen B. belcheri SINE families have been found and analyzed. Conclusions. Our analysis of the genome of B. belcheri has demonstrated an extreme variation of SINEs. The multitude of retrotransposons in lancelets is discussed in the context of chordate genomes.
Keywords: Short INterspersed Elements, Branchistoma belcheri, retrotransposons


[1] Huang S, Chen Z, Yan X, Yu T, Huang G, Yan Q, Pontarotti PA, Zhao H, Li J, Yang P, Wang R, Li R, Tao X, Deng T, Wang Y, Li G, Zhang Q, Zhou S, You L, Yuan S, Fu Y, Wu F, Dong M, Chen S, Xu A. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun. 2014;5:5896.
[2] Vassetzky NS, Kramerov DA. SINEBase: a database and tool for SINE analysis. Nucleic Acids Res. 2013;41(Database issue):D83-9.
[3] Kramerov DA, Vassetzky NS. Origin and evolution of SINEs in eukaryotic genomes. Heredity (Edinb). 2011;107(6):487-95.
[4] Nishihara H, Smit AF, Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 2006;16(7):864-74.
[5] Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11.
[6] Cañestro C, Albalat R. Transposon diversity is higher in amphioxus than in vertebrates: functional and evolutionary inferences. Brief Funct Genomics. 2012;11(2):131-41.
[7] Holland LZ. A SINE in the genome of the cephalochordate amphioxus is an Alu element. Int J Biol Sci. 2006;2(2):61-5.
[8] Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008;453(7198):1064-71.
[9] Li ZB, Huang YS, Shangguan JB, Ning YF, Yi Y, Dai G. Isolation and characterization of microsatellite loci in Branchiostoma belcheri Gray (Amphioxus). Genet Mol Res. 2015;14(3):10224-7.
[10] You L, Chi J, Huang S, Yu T, Huang G, Feng Y, Sang X, Gao X, Li T, Yue Z, Liu A, Chen S, Xu A. LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species. Database (Oxford). 2019;2019. pii: baz056.
[11] Yamada KD, Tomii K, Katoh K. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics. 2016;32(21):3246-3251.
[12] Nicholas KB, Nicholas HBJ. GeneDoc: a tool for editing and annotating multiple sequence alignment. 1997
[13] Eddy SR. SQUID-C function library for sequence analysis. 2008
[14] Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000;16(6):276-7.
[15] Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int Rev Cytol. 2005;247:165-221.
[16] Kramerov DA, Vassetzky NS. SINEs. Wiley Interdiscip Rev RNA. 2011;2(6):772-86.
[17] Albalat R, Martí-Solans J, Cañestro C. DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates. Brief Funct Genomics. 2012;11(2):142-55.