scholarly journals Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

2010 ◽  
Vol 27 (8) ◽  
pp. 1822-1832 ◽  
Author(s):  
T. I. Gossmann ◽  
B.-H. Song ◽  
A. J. Windsor ◽  
T. Mitchell-Olds ◽  
C. J. Dixon ◽  
...  
Keyword(s):  
Plant Species ◽  
Adaptive Evolution ◽  
Genome Wide

Genome-wide understanding of evolutionary and functional relationships of rice Yellow Stripe-Like (YSL) transporter family in comparison with other plant species

Biologia ◽  
2021 ◽  
Author(s):  
Rajen Chowdhury ◽  
Saranya Nallusamy ◽  
Varanavasiappan Shanmugam ◽  
Arul Loganathan ◽  
Raveendran Muthurajan ◽  
...  
Keyword(s):  
Plant Species ◽  
Functional Relationships ◽  
Transporter Family ◽  
Genome Wide ◽  
Yellow Stripe

scholarly journals Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume)

2020 ◽  
Author(s):  
Koji Numaguchi ◽  
Takashi Akagi ◽  
Yuto Kitamura ◽  
Ryo Ishikawa ◽  
Takashige Ishii
Keyword(s):  
Adaptive Evolution ◽  
Artificial Selection ◽  
Population Differentiation ◽  
List Type ◽  
Nucleotide Polymorphisms ◽  
Prunus Mume ◽  
Japanese Apricot ◽  
Interspecific Introgression ◽  
Genome Wide ◽  
Evolutionary Paths

SummaryDomestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity.We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (P. armeniaca), plum (P. salicina), and peach (P. persica). Based on their genome-wide single nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume.Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution.These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selection.

scholarly journals Genome‐wide adaptive evolution to underground stresses in subterranean mammals: Hypoxia adaption, immunity promotion, and sensory specialization

2020 ◽  
Vol 10 (14) ◽  
pp. 7377-7388
Author(s):  
Mengwan Jiang ◽  
Luye Shi ◽  
Xiujuan Li ◽  
Qianqian Dong ◽  
Hong Sun ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Genome Wide ◽  
Subterranean Mammals

scholarly journals Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shulin Zhang ◽  
Zailong Tian ◽  
Haipeng Li ◽  
Yutao Guo ◽  
Yanqi Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Plant Species ◽  
26S Proteasome ◽  
Genome Wide Analysis ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome ◽  
F Box Protein

Abstract Background F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects. Results In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction. Conclusion The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.

Identification and analysis of copine/BONZAI proteins among evolutionarily diverse plant species

Genome ◽  
2016 ◽  
Vol 59 (8) ◽  
pp. 565-573 ◽  
Author(s):  
Baohong Zou ◽  
Xuexue Hong ◽  
Yuan Ding ◽  
Xiang Wang ◽  
He Liu ◽  
...  
Keyword(s):  
Plant Species ◽  
Protein Localization ◽  
Calcium Dependent ◽  
Functional Studies ◽  
Phylogeny Analysis ◽  
Genome Wide ◽  
Evolutionarily Conserved ◽  
Von Willebrand ◽  
Diverse Plant Species ◽  
Willebrand Factor

Copines are evolutionarily conserved calcium-dependent membrane-binding proteins with potentially critical biological functions. In plants, the function of these proteins has not been analyzed except for in Arabidopsis thaliana where they play critical roles in development and disease resistance. To facilitate functional studies of copine proteins in crop plants, genome-wide identification, curation, and phylogeny analysis of copines in 16 selected plant species were conducted. All the identified 32 plant copines have conserved features of the two C2 domains (C2A and C2B) and the von Willebrand factor A (vWA) domain. Different from animal and protozoa copines, plant copines have glycine at the second residue potentially acquiring a unique protein myristoylation modification. Phylogenetic analysis suggests that copine was present as one copy when evolving from green algae to basal flowering plants, and duplicated before the divergence of monocots and dicots. In addition, gene expression and protein localization study of rice copines suggests both conserved and different properties of copines in dicots and monocots. This study will contribute to uncovering the role of copine genes in different plant species.

scholarly journals Genome-wide Identification ofWRKYGenes in the Desert PoplarPopulus euphraticaand Adaptive Evolution of the Genes in Response to Salt Stress

2015 ◽  
Vol 11s1 ◽  
pp. EBO.S22067 ◽  
Author(s):  
Jianchao Ma ◽  
Jing Lu ◽  
Jianmei Xu ◽  
Bingbing Duan ◽  
Xiaodong He ◽  
...  
Keyword(s):  
Salt Stress ◽  
Adaptive Evolution ◽  
Genome Wide

scholarly journals Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions

2017 ◽  
Author(s):  
Han Chen ◽  
Haidong Shu ◽  
Liyuan Wang ◽  
Fan Zhang ◽  
Xi Li ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Plant Pathogens ◽  
Phytophthora Sojae ◽  
Genome Architecture ◽  
Epigenetic Mark ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Methylated Dna ◽  
Genome Wide

AbstractFilamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this “two-speed” genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6- methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.

scholarly journals Does Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level?

2018 ◽  
Author(s):  
Juraj Bergman ◽  
Adam Eyre-Walker
Keyword(s):  
Amino Acids ◽  
Adaptive Evolution ◽  
Evolutionary Biology ◽  
Amino Acid Level ◽  
Neutral Evolution ◽  
Relative Contribution ◽  
Mutational Step ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Evolution Of Proteins

AbstractA longstanding question in evolutionary biology is the relative contribution of large and small effect mutations to the adaptive process. We have investigated this question in proteins by estimating the rate of adaptive evolution between all pairs of amino acids separated by one mutational step using a McDonald-Kreitman type approach and genome-wide data from several Drosophila species. We find that the rate of adaptive evolution is higher amongst amino acids that are more similar. This is partly due to the fact that the proportion of mutations that are adaptive is higher amongst more similar amino acids. We also find that the rate of neutral evolution between amino acids is higher amongst similar amino acids. Overall our results suggest that both the adaptive and non-adaptive evolution of proteins is dominated by substitutions between amino acids that are more similar.

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