Annotated genome sequences of the carnivorous plantRoridula gorgoniasand a non-carnivorous relative,Clethra arborea

被引:6
作者
Hartmann, Stefanie [1 ]
Preick, Michaela [1 ]
Abelt, Silke [1 ]
Scheffel, Andre [2 ]
Hofreiter, Michael [1 ]
机构
[1] Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany
[2] Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany
关键词
Carnivorous plant; Roridula gorgonias; Clethra arborea; Genome assembly; Transcriptome assembly; Phylogenomics; Orthologous Matrix (OMA) Project; EVOLUTION; TOOL;
D O I
10.1186/s13104-020-05254-4
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorousRoridula gorgoniasand that of a non-carnivorous relative, Madeira's lily-of-the-valley-tree,Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2% and 89.5%, respectively. We used their predicted genes together with publicly available data from other Ericales' genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies.
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共 37 条
[1]   A Y-chromosome-encoded small RNA acts as a sex determinant in persimmons [J].
Akagi, Takashi ;
Henry, Isabelle M. ;
Tao, Ryutaro ;
Comai, Luca .
SCIENCE, 2014, 346 (6209) :646-650
[2]   OMA standalone: orthology inference among public and custom genomes and transcriptomes [J].
Altenhoff, Adrian M. ;
Levy, Jeremy ;
Zarowiecki, Magdalena ;
Tomiczek, Bartlomiej ;
Vesztrocy, Alex Warwick ;
Dalquen, Daniel A. ;
Mueller, Steven ;
Telford, Maximilian J. ;
Glover, Natasha M. ;
Dylus, David ;
Dessimoz, Christophe .
GENOME RESEARCH, 2019, 29 (07) :1152-1163
[3]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[4]   The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba [J].
Barta, Jiri ;
Stone, James D. ;
Pech, Jiri ;
Sirova, Dagmara ;
Adamec, Lubomir ;
Campbell, Matthew A. ;
Storchova, Helena .
BMC PLANT BIOLOGY, 2015, 15
[5]   UniProt: a worldwide hub of protein knowledge [J].
Bateman, Alex ;
Martin, Maria-Jesus ;
Orchard, Sandra ;
Magrane, Michele ;
Alpi, Emanuele ;
Bely, Benoit ;
Bingley, Mark ;
Britto, Ramona ;
Bursteinas, Borisas ;
Busiello, Gianluca ;
Bye-A-Jee, Hema ;
Da Silva, Alan ;
De Giorgi, Maurizio ;
Dogan, Tunca ;
Castro, Leyla Garcia ;
Garmiri, Penelope ;
Georghiou, George ;
Gonzales, Daniel ;
Gonzales, Leonardo ;
Hatton-Ellis, Emma ;
Ignatchenko, Alexandr ;
Ishtiaq, Rizwan ;
Jokinen, Petteri ;
Joshi, Vishal ;
Jyothi, Dushyanth ;
Lopez, Rodrigo ;
Luo, Jie ;
Lussi, Yvonne ;
MacDougall, Alistair ;
Madeira, Fabio ;
Mahmoudy, Mahdi ;
Menchi, Manuela ;
Nightingale, Andrew ;
Onwubiko, Joseph ;
Palka, Barbara ;
Pichler, Klemens ;
Pundir, Sangya ;
Qi, Guoying ;
Raj, Shriya ;
Renaux, Alexandre ;
Lopez, Milagros Rodriguez ;
Saidi, Rabie ;
Sawford, Tony ;
Shypitsyna, Aleksandra ;
Speretta, Elena ;
Turner, Edward ;
Tyagi, Nidhi ;
Vasudev, Preethi ;
Volynkin, Vladimir ;
Wardell, Tony .
NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D506-D515
[6]  
Beletsky AV, 2017, GENOM DATA, V11, P60, DOI 10.1016/j.gdata.2016.11.020
[7]   Nuclear DNA amounts in angiosperms: Progress, problems and prospects [J].
Bennett, MD ;
Leitch, IJ .
ANNALS OF BOTANY, 2005, 95 (01) :45-90
[8]   Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysis [J].
Butts, Carter T. ;
Bierma, Jan C. ;
Martin, Rachel W. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016, 84 (10) :1517-1533
[9]   BLAST plus : architecture and applications [J].
Camacho, Christiam ;
Coulouris, George ;
Avagyan, Vahram ;
Ma, Ning ;
Papadopoulos, Jason ;
Bealer, Kevin ;
Madden, Thomas L. .
BMC BIOINFORMATICS, 2009, 10
[10]   Cognitive Function: Is There More to Anticoagulation in Atrial Fibrillation Than Stroke? [J].
Cao, Lin ;
Pokorney, Sean D. ;
Hayden, Kathleen ;
Welsh-Bohmer, Kathleen ;
Newby, L. Kristin .
JOURNAL OF THE AMERICAN HEART ASSOCIATION, 2015, 4 (08) :e001573