Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles

Scientific Reports
Kai WangHuabin Zhao

Abstract

The evolution of bioluminescence has prompted scientific attention to illuminate phylogenetic relationships of luminescent beetles. However, genomic resources are virtually lacking in rhagophthalmids (Rhagophthalmidae) and their related firefly beetles lampyrids (Lampyridae). Here, we employed the Illumina Hiseq 2000 platform and sequenced the whole-body transcriptomes of the four luminescent beetles: one rhagophthalmid (Rhagophthalmus sp.) and three fireflies (Asymmetricata circumdata, Aquatica ficta, and Pyrocoelia pectoralis). We obtained 55.4, 43.4, 38.6, and 36.7 million clean reads for the four species, respectively. All reads were assembled into contigs from which unigenes were derived. All unigenes were annotated by publicly available databases, and a total of 4325 orthologous genes were identified. Using multiple phylogenetic approaches, our transcriptome data confirmed the distinctiveness of Rhagophthalmidae from Lampyridae, which was also supported by our mitogenome analysis using three newly determined mitogenome sequences and 12 previously published ones. Together, this study is the first report of whole transcriptome sequencing data in Rhagophthalmidae and Lampyridae species, representing a valuable genomic resour...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 1, 1987·Journal of Bioluminescence and Chemiluminescence·P J Herring
Apr 2, 1999·Nucleic Acids Research·J L Boore
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Jan 18, 2003·Cellular and Molecular Life Sciences : CMLS·V R Viviani
Mar 27, 2004·Journal of Molecular Evolution·Marta Vila, Mats Björklund
Jan 14, 2005·Bioinformatics·Federico AbascalDavid Posada
Feb 24, 2006·Trends in Genetics : TIG·Olivier JeffroyHervé Philippe
Mar 17, 2007·Systematic Biology·Laura Salter Kubatko, James H Degnan
Jul 24, 2007·Molecular Phylogenetics and Evolution·Kathrin F Stanger-HallDavid M Hillis
Apr 25, 2008·Systematic Biology·Natalia M BelfioreCraig Moritz
May 1, 2008·Nucleic Acids Research·Stefan GötzAna Conesa
Oct 25, 2008·IUBMB Life·Simone M Marques, Joaquim C G Esteves da Silva
Jan 17, 2009·Evolution; International Journal of Organic Evolution·Scott V Edwards
Mar 25, 2009·Trends in Ecology & Evolution·James H Degnan, Noah A Rosenberg
May 28, 2009·Proceedings of the National Academy of Sciences of the United States of America·Huabin ZhaoShuyi Zhang
Jun 9, 2009·Molecular Phylogenetics and Evolution·Liang LiuScott V Edwards
Oct 13, 2010·BMC Evolutionary Biology·Liang LiuScott V Edwards
Dec 15, 2010·Annual Review of Marine Science·Steven H D HaddockJames F Case
Aug 1, 1996·Trends in Ecology & Evolution·J William, O Ballard
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Aug 1, 2012·Nature Methods·Diego DarribaDavid Posada
Aug 30, 2012·Proceedings of the National Academy of Sciences of the United States of America·Sen SongShaoyuan Wu
May 28, 2013·Trends in Plant Science·Bojian ZhongDavid Penny
Jun 7, 2013·Nature·Ewen Callaway
Apr 1, 2014·Molecular Phylogenetics and Evolution·Robin KundrataLadislav Bocak
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
May 8, 2014·Genome Biology and Evolution·Ping FengHuabin Zhao
Jun 27, 2014·Proceedings. Biological Sciences·Wei Hong, Huabin Zhao
Feb 26, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Feng-Juan MuKai Wang
Apr 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Peter W HarrisonJudith E Mank
Sep 6, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kexin LiHuabin Zhao
Sep 6, 2015·Genome Biology and Evolution·Kai Wang, Huabin Zhao
Dec 10, 2015·Genome Biology and Evolution·Martijn J T N TimmermansAlfried P Vogler

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Citations

Jul 17, 2019·Molecular Biology and Evolution·Hengwu JiaoHuabin Zhao
Sep 1, 2019·BMC Evolutionary Biology·Hengwu JiaoHuabin Zhao
May 11, 2018·Frontiers in Zoology·Dominik KusyLadislav Bocak
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Quan Liu, Xinhua Fu
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Min Jee KimIksoo Kim
Oct 20, 2018·International Journal of Biological Macromolecules·Ajaraporn Sriboonlert, Passorn Wonnapinij

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Datasets Mentioned

BETA
X89479
HQ232815

Methods Mentioned

BETA
PCR
RNA-seq

Software Mentioned

ProtTest
MP
jModelTest
RAxML
Trimmomatic
BLASTX
TBLASTN
EST
MEGA
DAMBE

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