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Estimating the evidence of selection and the reliability of inference in unigenic evolution

Andrew D Fernandes, Benjamin P Kleinstiver, David R Edgell, Lindi M Wahl, Gregory B Gloor
2010 Algorithms for Molecular Biology  
Conclusions: Our method is able to assess both the evidence of selection at individual amino acid sites and estimate the reliability of those inferences.  ...  An approximate power analysis is also developed to estimate the reliability of inference given the data.  ...  Acknowledgements This work was supported by the Natural Sciences and Engineering Research Council of Canada, the Government of Ontario, and the University of Western Ontario.  ... 
doi:10.1186/1748-7188-5-35 pmid:21059250 pmcid:PMC2994857 fatcat:gpviutcusngqznmpca7umyeu2y

Using Variable Rate Models to Identify Genes Under Selection in Sequence Pairs: Their Validity and Limitations for EST Sequences

Sheri A. Church, Kevin Livingstone, Zhao Lai, Alexander Kozik, Steven J. Knapp, Richard W. Michelmore, Loren H. Rieseberg
2007 Journal of Molecular Evolution  
Variable rate models are generally not used for comparisons of sequence pairs due to the limited information and the inaccuracy of estimates of specific substitution rates.  ...  Subsequent mapping studies in sunflower show four of five of the positively selected genes identified by these methods mapped to domestication QTLs.  ...  We thank Kent Bradford and Rick Kesseli for assisting in development of the EST database as well as the members of the Compositae Genome Group for valuable discussions concerning this project.  ... 
doi:10.1007/s00239-005-0299-5 pmid:17200807 fatcat:jrqdigups5fwbfsfltvqdv27em

Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles

Kai Wang, Wei Hong, Hengwu Jiao, Huabin Zhao
2017 Scientific Reports  
Together, this study is the first report of whole transcriptome sequencing data in Rhagophthalmidae and Lampyridae species, representing a valuable genomic resource for studying the origin and evolution  ...  Moreover, our transcriptome and mitogenome data provide useful phylogenetic information that could be of importance in future studies of phylogenetic inference.  ...  This work was supported in part by the National Natural Science Foundation of China (91331115) and a Specialized Research Fund for the Doctoral Program of Higher Education (20130141110066).  ... 
doi:10.1038/s41598-017-01835-9 pmid:28500331 pmcid:PMC5431921 fatcat:4vnmlijap5alhek7r4hvd7f3oq

Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the "Triploid Bridge" in Arundo (Poaceae)

Wuhe Jike, Mingai Li, Nicola Zadra, Enrico Barbaro, Gaurav Sablok, Giorgio Bertorelle, Omar Rota-Stabelli, Claudio Varotto
2020 International Journal of Molecular Sciences  
Our results clarify the complex nature of Arundo evolution and are valuable for future gene functional validation as well as reverse and comparative genomics efforts in the Arundo genus and other Arundinoideae  ...  Through the obtainment of 10 novel leaf transcriptomes for Arundo and outgroup species, our results prove that recurrent demiduplication has likely been a major driver of evolution in this species-poor  ...  Acknowledgments: The authors thank Jeng-I Tsai and Fong-Long Feng for providing A. formosana material. Conflicts of Interest: The authors declare no conflicts of interest.  ... 
doi:10.3390/ijms21155247 pmid:32722033 fatcat:dbis3ylzgfdlzj3iyfqn4fgl5q

Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes

Xiuhui Ma, Wei Dai, Jingliang Kang, Liandong Yang, Shunping He
2015 G3: Genes, Genomes, Genetics  
Analysis of the 1,656 orthologs among the six assembled catfish unigene sets provided consistent evidence for genome-wide accelerated evolution in the three glyptosternoid lineages living at high altitudes  ...  Genes showing signatures of rapid evolution and positive selection in the glyptosternoid lineages were also enriched in functions associated with energy metabolism and hypoxia.  ...  Substitution rate estimation and selection analyses To estimate the lineage-specific evolutionary rates for each branch of the six species, the Codeml program in the PAML package (Yang 2007) was run  ... 
doi:10.1534/g3.115.024448 pmid:26564948 pmcid:PMC4704712 fatcat:tazxh3qttfgclff4yapb7hgayy

Combined EST and Proteomic Analysis Identifies Rapidly Evolving Seminal Fluid Proteins in Heliconius Butterflies

J. R. Walters, R. G. Harrison
2010 Molecular biology and evolution  
At least one of these SFPs is evolving adaptively (dN/dS . 1), implicating a role for positive selection in this rapid evolution.  ...  This work establishes a strong precedent for future research on the causes and consequences of reproductive protein evolution in the Lepidoptera.  ...  McMillan and members of his laboratory, C. Jiggins and members of his laboratory, to M. Kronforst, to L. Gilbert and C. Estrada, and to Cheryl Tyndall and the Niagara Parks Butterfly Conservatory.  ... 
doi:10.1093/molbev/msq092 pmid:20375075 fatcat:jssjtdut3nav3a5kenhgjspbpm

Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus

Liandong Yang, Ying Wang, Zhaolei Zhang, Shunping He
2014 Genome Biology and Evolution  
Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia.  ...  An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G.  ...  We further deleted all gaps and "N" from the alignments to lower the effect of ambiguous bases on the inference of positive selection.  ... 
doi:10.1093/gbe/evu279 pmid:25543049 pmcid:PMC4316632 fatcat:sqel4cdrmbe2laypci5caeqglm

Sequence diversity in three tomato species: SNPs, markers, and molecular evolution

José M Jiménez-Gómez, Julin N Maloof
2009 BMC Plant Biology  
Using the available meta-information we classified genes into functional categories and obtained estimations of single nucleotide polymorphisms (SNP) quality, position in the gene, and effect on the encoded  ...  Evolutionary analyses on these polymorphism uncovered sets of genes potentially important for the evolution and domestication of tomato; interestingly these sets were enriched for genes involved in response  ...  Acknowledgements We thank Lukas Mueller for his very helpful information on the SGN datasets and for generating the list relating unigene and ESTs names. We thank Katherine S.  ... 
doi:10.1186/1471-2229-9-85 pmid:19575805 pmcid:PMC3224693 fatcat:dlme3ikrr5eqnfkebazzfbeoqq

Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes

G. Blanc
2004 The Plant Cell  
Using EST contigs (unigenes), we identified pairs of paralogous genes in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication.  ...  For nine of the investigated species (wheat and Arabidopsis thaliana), the age distributions of duplicated genes contain peaks corresponding to short evolutionary periods during which large numbers of  ...  Estimation of the level of synonymous substitutions is statistically reliable only when Ks < 1 (Li, 1997) , which suggests that the parts of the distributions where Ks > 1 in Figure 2 could be merely  ... 
doi:10.1105/tpc.021345 pmid:15208399 pmcid:PMC514152 fatcat:kooe36lejndopcuwpo46yx4dlm

EuroPineDB: a high-coverage web database for maritime pine transcriptome

Noé Fernández-Pozo, Javier Canales, Darío Guerrero-Fernández, David P Villalobos, Sara M Díaz-Moreno, Rocío Bautista, Arantxa Flores-Monterroso, M Ángeles Guevara, Pedro Perdiguero, Carmen Collada, M Teresa Cervera, Álvaro Soto (+5 others)
2011 BMC Genomics  
Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases.  ...  As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes.  ...  Acknowledgements The authors gratefully acknowledge the computer resources and technical support provided by the Plataforma Andaluza  ... 
doi:10.1186/1471-2164-12-366 pmid:21762488 pmcid:PMC3152544 fatcat:zi4tnn2xcncn5hvw6dfbixde7a

Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments

Wuxia Guo, Haidan Wu, Zhang Zhang, Chao Yang, Ling Hu, Xianggang Shi, Shuguang Jian, Suhua Shi, Yelin Huang
2017 Frontiers in Plant Science  
Comparative Transcriptomic Analysis in Rhizophoraceae genes may be crucial for increasing the capability of stress tolerance (i.e., defense against salt and oxidative stress) and development of adaptive  ...  traits (i.e., vivipary) of Rhizophoraceae mangroves, and thus plays an important role in their adaptation to the stressful intertidal environments.  ...  Positive Selection of Genes Involved in Stress Response and Embryo Development were also Important for Mangroves' Adaptation Natural selection may be the major force that drives species evolution and divergence  ... 
doi:10.3389/fpls.2017.00795 pmid:28559911 pmcid:PMC5432612 fatcat:ovxegmp42re3jmy2d3d7kz7jfu

Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life

Chao Tong, Tian Fei, Cunfang Zhang, Kai Zhao
2017 BMC Evolutionary Biology  
Through comprehensive molecular evolution analyses, we found that sets of genes controlling mitochondrion, ion homoeostasis, acid-base balance and innate immunity show significant signals of positive selection  ...  Understanding the genetic basis of adaptation to high altitude life is of paramount importance for preserving and managing genetic diversity in highland animals.  ...  Availability of data and materials Illumina sequenced read data were deposited in the NCBI Sequence Read Archive (accession # SRR1542352, SRR1542353, SRR5019657, SRR5019658 and SRR5019659).  ... 
doi:10.1186/s12862-017-0925-z pmid:28274203 pmcid:PMC5343388 fatcat:he3jutlwobchvdmhm3krmpohdi

Molecular evidence for recent divergence of X- and Y-linked gene pairs in Spinacia oleracea L

Yosuke Okazaki, Satoshi Takahata, Hideki Hirakawa, Yutaka Suzuki, Yasuyuki Onodera, Hidenori Sassa
2019 PLoS ONE  
be related to the evolution of dioecy in the species.  ...  significantly later than the evolution of dioecy in Spinacia.  ...  Acknowledgments The authors thank Tohoku Seed Co. Ltd. (Utsunomiya, Tochigi, Japan) for providing the spinach breeding lines used in this study.  ... 
doi:10.1371/journal.pone.0214949 pmid:30964889 pmcid:PMC6456208 fatcat:n4qnic26hnewhp2ccz32nsrl5u

Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

Ruisen Lu, Wuqin Xu, Qixiang Lu, Pan Li, Jocelyn Losh, Faiza Hina, Enxiang Li, Yingxiong Qiu
2018 Plant Diversity  
The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA)-Eastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy  ...  to investigate the transcriptome evolution of the two closely related species.  ...  Acknowledgements This research was supported by the National Natural Science Foundation of China (Grant Nos. 31370241, 31570214), the International Cooperation and Exchange of the National Natural Science  ... 
doi:10.1016/j.pld.2018.11.006 pmid:30740572 pmcid:PMC6317509 fatcat:jut7kzd7brgefd4vebyifcdp7e

Genome-wide detection of alternative splicing in expressed sequences of human genes

B. Modrek
2001 Nucleic Acids Research  
This method effectively copes with many of the problems inherent in making inferences about splicing and alternative splicing on the basis of EST sequences, which in addition to being fragmentary and full  ...  for the real complexity of expressed sequence data by building and analyzing a single multiple sequence alignment containing all of the expressed sequences in a particular cluster aligned to genomic sequence  ...  the evolution of novel functions in alternatively spliced exons, which are less subject to the effects of natural selection. 3 Alternative splicing appears increasingly to make an important contribution  ... 
doi:10.1093/nar/29.13.2850 pmid:11433032 pmcid:PMC55780 fatcat:xlmy2izienhczbvlxv7absqmdy
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