Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics

被引:8
作者
Wheeler, Gregory L. [1 ]
Carstens, Bryan C. [1 ]
机构
[1] Ohio State Univ, Dept Evolut Ecol & Organismal Biol, Columbus, OH 43210 USA
来源
PEERJ | 2018年 / 6卷
关键词
Carnivorous plants; Gene Ontology; Functional genomics; Convergent evolution; PROTEOME ANALYSIS; GENE DUPLICATION; POLYPLOIDY; DATABASE; ANNOTATION; ABSORPTION; SEQUENCES; TRANSPORT; PHYLOGENY; NUTRIENTS;
D O I
10.7717/peerj.4322
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines the convergence of functional overrepresentation of genes previously implicated in plant carnivory. Gene Ontology (GO) coding was used to quantitatively score functional representation in these taxa, in terms of proportion of carnivory-associated functions relative to all functional sequence. Statistical analysis revealed that, in carnivorous plants as a group, only two of the 24 functions tested showed a signal of substantial overrepresentation. However, when the four carnivorous taxa were analyzed individually, 11 functions were found to be significant in at least one taxon. Though carnivorous plants collectively may show overrepresentation. on functions from the predicted set, the specific functions that are overrepresented vary substantially from taxon to taxon. While it is possible that some functions serve a similar practical purpose such that one taxon does not need to utilize both to achieve the same result, it appears that. there are multiple approaches for the evolution of carnivorous function plant genomes. Our approach could be applied to tests of functional convergence in other systems provided on the availability of genomes and annotation data for a group,
引用
收藏
页数:28
相关论文
共 82 条
[1]   Leaf absorption of mineral nutrients in carnivorous plants stimulates root nutrient uptake [J].
Adamec, L .
NEW PHYTOLOGIST, 2002, 155 (01) :89-100
[2]   Polyploidy and genome evolution in plants [J].
Adams, KL ;
Wendel, JF .
CURRENT OPINION IN PLANT BIOLOGY, 2005, 8 (02) :135-141
[3]   Targeted cellular process profiling approach for uterine leiomyoma using cDNA microarray, proteomics and gene ontology analysis [J].
Ahn, WS ;
Kim, KW ;
Bae, SM ;
Yoon, JH ;
Lee, JM ;
Namkoong, SE ;
Kim, JH ;
Kim, CK ;
Lee, YJ ;
Kim, YW .
INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY, 2003, 84 (06) :267-279
[4]   Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs [J].
Altenhoff, Adrian M. ;
Studer, Romain A. ;
Robinson-Rechavi, Marc ;
Dessimoz, Christophe .
PLOS COMPUTATIONAL BIOLOGY, 2012, 8 (05)
[5]   Aspartic proteinases are expressed in pitchers of the carnivorous plant Nepenthes alata Blanco [J].
An, CI ;
Fukusaki, E ;
Kobayashi, A .
PLANTA, 2002, 214 (05) :661-667
[6]   Digestive mutualism, an alternate pathway in plant carnivory [J].
Anderson, B ;
Midgley, JJ .
OIKOS, 2003, 102 (01) :221-224
[7]  
[Anonymous], 2017, FIGTREE GRAPHICAL VI
[8]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[9]   AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology [J].
Balsa-Canto, Eva ;
Henriques, David ;
Gabor, Attila ;
Banga, Julio R. .
BIOINFORMATICS, 2016, 32 (21) :3357-3359
[10]   Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution [J].
Blanc, G ;
Wolfe, KH .
PLANT CELL, 2004, 16 (07) :1679-1691