Determination and Analysis of Complete Mitochondrial Genome of Ozobranchus jantseanus： Based on Pacbio and Illumina Sequencing

Abstract

Abstract:

The complete mitochondrial genome of Ozobranchus jantseanus was sequenced and annotated accurately through a combination of Illumina and Pacbio technology, and the comparative analysis of the gene order and phylogenetic relationship with other species in the Hirudinea were performed. The results showed that the complete mitochondrial genome length of O. jantseanus was 14 868 bp, and there were two kinds of start codon, ATG and ATT, and four types of stop codon, TAA, TAG, TA and T in the coding gene of O. jantseanus. Comparative analysis showed that mitochondrial genes orders of 10 species in the Hirudinea were divided into two types, and the differences were reflected in the exchange of tRNA gene order and the length of long noncoding region (LNR). All Rhynchobdellida species, including O. jantseanus, belonged to the b-type, and most of the Arhynchobdellida species to a-type. The Neighbor-Joining (NJ) evolution analysis of 13 protein coding genes (PCGs) from species in the Hirudinea showed that O. jantseanus and others species in Rhynchobdellid formed a monophyletic group.

Key words: Ozobranchus jantseanus, complete mitochondrial genome, Hirudinea, Pacbio and Illumina sequencing

GU Shengli, LIU Jianjun, SUN Entao, ZHAN Xiaodong, NIE Liuwang. Determination and Analysis of Complete Mitochondrial Genome of Ozobranchus jantseanus： Based on Pacbio and Illumina Sequencing[J]. Journal of Jishou University（Natural Sciences Edition).

References

[1] 杨潼.中国动物志,环节动物门,蛭纲[M].北京:科学出版社,1996:85-87.
[2] 李良华,边书京,蔡军,等.乌龟寄生性鳃蛭病的防治探讨[J].动物科学与动物医学,2002,19(5):22-24.
[3] YAMAUCHI T, SUZUKI D. Geographical Distribution of Ozobranchus jantseanus (Annelida: Hirudinida: Ozobranchidae) in Japan[J]. Medical Entomology and Zoology, 2008, 59(4): 345-349.
[4] SUZUKI D, MIYAMOTO T, KIKAWADA T, et al. A Leech Capable of Surviving Exposure to Extremely Low Temperatures[J]. PLoS ONE, 2014, 9(1): e86807.
[5] LIU Xinhua, LUO Dan, ZHAOYuanli, et al. Complete Mithochondrial Genome of Ozobranchus jantseanus (Hirudinida: Arhychobdellida: Ozobranchidae)[J]. Mitochondrial DNA Part B, 2017, 2(1): 232-233.
[6] NAKANO T, NAKAMURA R, OHTSUKA S, et al. Low Genetic Diversity in Ozobranchus jantseanus (Hirudinida: Ozobranchidae) in Japan: Possibility of Introduction with Their Host Turtles[J]. Parasitology International, 2017, 66(6): 798-801.
[7] DUMONCEAUX T, HILL J, CHABAN B, et al. Modified Paired End Rapid Library Preparation Protocol for 454 GS Junior 8 kb Library Preparation Using Covaris G-Tubes and Bluepippin Electrophoresis[J]. Protoc Exch, 2014: 1-12.
[8] BOLGER A M, LOHSE M, USADEL B. Trimmomatic: A Flexible Trimmer forIllumina Sequence Data[J]. Bioinformatics, 2014, 30(15): 2114-2120.
[9] JACKMAN S D, VANDERVALK B P, MOHAMADI H, et al. ABySS2.0: Resource-Efficient Assembly of Large Genomes Using a Bloom Filter[J]. Genome Research, 2017, 27(5): 768-777.
[10] NURK S, BANKEVICH A, ANTIPOV D, et al. Assembling Genomes and Mini-Metagenomes from Highly Chimeric Reads[C]∥Proceedings of the 17th International Conference on Research in Computational Molecular Biology. Berlin: Springer Link, 2013: 158-170.
[11] BERNT M, DONATH A, JHLING F, et al. MITOS: Improved De Novo Metazoan Mitochondrial Genome Annotation[J]. Molecular Phylogenetics and Evolution, 2013, 69(2): 313-319.
[12] GRIN I, LINKE D. GCView: The Genomic Context Viewer for Protein Homology Searches[J]. Nucleic Acids Research, 2011, 39(S): W353-W356.
[13] KATOH K, STANDLEY D M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability[J]. Molecular Biology and Evolution, 2013, 30(4): 772-780.
[14] KOICHIRO T, GLEN S, DANIEL P, et al. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0[J]. Molecular Biology and Evolution, 2013, 30(12): 2725-2729.
[15] WANG Yongbo, HUANG Min, WANG Rongxia, et al. Complete Mitochondrial Genome of the Fish Leech Zeylanicobdella arugamensis[J]. Mitochondrial DNA Part B, 2018, 3(2): 659-660.
[16] 潘宝平，卜文俊.线粒体基因组的遗传与进化研究进展[J].生物学通报，2005，40(8):5-7.
[17] JENNINGS R M, HALANYCH K M. Mitochondrial Genomes of Clymenella torquata (Maldanidae) and Riftia pachyptila(Siboglinidae): Evidence for Conserved Gene Order in Annelida[J]. Molecular Biology and Evolution, 2004, 22(2): 210-222.
[18] 徐云玲.无吻蛭目五种水蛭线粒体基因组注释分析[D].武汉：湖北中医药大学,2013.
[19] MAHMOUD M, ZYWICKI M, TWARDOWSKI T, et al. Efficiency of Pacbio Long Read Correction by 2nd Generation Illumina Sequencing[J]. Genomics, 2019, 111(1): 43-49.
[20] WAGNER J, COUPLAND P, BROWNE H P, et al. Evaluation of PacBio Sequencing for Full-Length Bacterial 16S rRNA Gene Classification[J]. BMC Microbiology, 2016, 16(1): 274.
[21] 王继文.动物线粒体假基因的识别及其在进化生物学中的应用[J].动物学杂志，2004，39(3):103-108.
[22] BOORE J L, BROWN W M. Big Trees from Little Genomes: Mitochondrial Gene Order as a Phylogenetic Tool[J]. Current Opinion in Genetics & Development, 1998, 8(6): 668-674.
[23] LE TH, BLAIR D, MCMANUS D P. Mitochondrial Genomes of Parasitic Flatworms[J]. Trends in Parasitology, 2002, 18(5): 206-213.
[24] NOVIKOVA N, GUSEV N, POLIKARPOV N, et al. Survival of Dormant Organisms After Long-Term Exposure to the Space Environment[J]. Acta Astronautica, 2011, 68(9): 1574-1580.
[25] JONSSON K I, RABBOW E, SCHILL R O, et al. Tardigrades Survive Exposure to Space in Low Earth Orbit[J]. Current Biology, 2008, 18(17): R729-R731.
[26] GUSEV O, SUETSUGU Y, CORNETTE R, et al. Comparative Genome Sequencing Reveals Genomic Signature of Extreme Desiccation Tolerance in the Anhydrobiotic Midge[J]. Nature Communications, 2014, 5(1): 15-31.
[27] HASHIMOTO T, HORIKAWA DD, SAITO Y, et al. Extremotolerant Tardigrade Genome and Improved Radiotolerance of Human Cultured Cells by Tardigrade-Unique Protein[J]. Nature Communications, 2016, 7: 12808.
[28] STOREY K B, STOREY J M. Molecular Biology of Freezing Tolerance[J]. Comprehensive Physiology, 2013, 3(3): 1283-1308.
[29] LISA F D, BERNARDI P. Mitochondrial Function as a Determinant of Recovery or Death in Cell Response to Injury[J]. Molecular and Cellular Biochemistry, 1998, 184(1/2): 379-391.