scholarly journals Evolution of SHORT VEGETATIVE PHASE ( SVP ) genes in Rosaceae: Implications of lineage‐specific gene duplication events and function diversifications with respect to their roles in processes other than bud dormancy

2020 ◽  
Vol 13 (3) ◽  
Author(s):  
Jinyi Liu ◽  
Min Ren ◽  
Hui Chen ◽  
Silin Wu ◽  
Huijun Yan ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Bud Dormancy ◽  
Specific Gene ◽  
Vegetative Phase ◽  
Short Vegetative Phase ◽  
Duplication Events ◽  
And Function ◽  
Lineage Specific Gene

scholarly journals Deep Evaluation to the Evolution History of Heat Shock Factor (HSF) Gene Family and Its Expansion Pattern in Seed Plants

2020 ◽  
Author(s):  
Yiying Liao ◽  
Zhiming Liu ◽  
Andrew W. Gichira ◽  
Min Yang ◽  
Ruth Wambui Mbichi ◽  
...  
Keyword(s):  
Heat Shock ◽  
Gene Duplication ◽  
Gene Family ◽  
Phylogenetic Reconstruction ◽  
Heat Shock Factor ◽  
Specific Gene ◽  
Ancestral State ◽  
Duplication Events ◽  
History Of ◽  
Lineage Specific Gene

Abstract BackgroundHSF (Heat shock factor) genes are essential in the irreplaceable functions in some of the basic developmental pathways in plants. Despite the extensive studies on the structure, function diversification, and evolution of HSF, their divergent history and gene duplication pattern remain unsolved. To further illustrate the probable divergent patterns in these subfamilies, we visited the evolutionary history of the HSF via phylogenetic reconstruction and genomic syntenic analyses by taking advantage of the increased sampling of genomic data for pteridophyta, gymnosperms and basal angiosperms. ResultsWe identified a novel clade including HSFA2, HSFA6, HSFA7, HSFA9 with complex relationship, very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We suggested that HSFA9 was derived from HSFA2 through gene duplication in eudicots at ancestral state, and then expanded in a lineage-specific way. Our findings indicated that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in common ancestors of monocots. We also presumed that HSFC2 was derived from HSFC1 in ancestral monocots. ConclusionThis work proposes that in the era of early differentiation of angiosperms during the radiation of flowering plants, the member size of HSF gene family was also being adjusted, accompanied with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying evolution history of multigene family.

scholarly journals Extensive lineage-specific gene duplication and evolution of the spiggin multi-gene family in stickleback

2007 ◽  
Vol 7 (1) ◽  
pp. 209 ◽  
Author(s):  
Ryouka Kawahara ◽  
Mutsumi Nishida
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Specific Gene ◽  
Lineage Specific Gene

scholarly journals Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Juan Liu ◽  
Anupma Sharma ◽  
Marie Jamille Niewiara ◽  
Ratnesh Singh ◽  
Ray Ming ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Carica Papaya ◽  
Cysteine Proteases ◽  
Specific Gene ◽  
Lineage Specific Gene

scholarly journals Patterns of gene evolution following duplications and speciations in vertebrates

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8813 ◽  
Author(s):  
Kyle T. David ◽  
Jamie R. Oaks ◽  
Kenneth M. Halanych
Keyword(s):  
Gene Duplication ◽  
Gene Evolution ◽  
Strong Support ◽  
Duplication Event ◽  
Gene Trees ◽  
Loss Of Function ◽  
Eukaryotic Genes ◽  
Gene Copies ◽  
Duplication Events ◽  
And Function

Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

scholarly journals Rapid Rates of Lineage-Specific Gene Duplication and Deletion in the α-Globin Gene Family

2008 ◽  
Vol 25 (3) ◽  
pp. 591-602 ◽  
Author(s):  
Federico G. Hoffmann ◽  
Juan C. Opazo ◽  
Jay F. Storz
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Globin Gene ◽  
Specific Gene ◽  
Lineage Specific Gene

scholarly journals A Tree Ortholog of SHORT VEGETATIVE PHASE Floral Repressor Mediates Photoperiodic Control of Bud Dormancy

2019 ◽  
Vol 29 (1) ◽  
pp. 128-133.e2 ◽  
Author(s):  
Rajesh Kumar Singh ◽  
Pal Miskolczi ◽  
Jay P. Maurya ◽  
Rishikesh P. Bhalerao
Keyword(s):  
Bud Dormancy ◽  
Vegetative Phase ◽  
Photoperiodic Control ◽  
Short Vegetative Phase ◽  
Floral Repressor

scholarly journals Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution

PLoS Biology ◽  
2004 ◽  
Vol 2 (7) ◽  
pp. e207 ◽  
Author(s):  
Andrew Fortna ◽  
Young Kim ◽  
Erik MacLaren ◽  
Kriste Marshall ◽  
Gretchen Hahn ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Specific Gene ◽  
Great Ape ◽  
Gene Duplication And Loss ◽  
Ape Evolution ◽  
Lineage Specific Gene

scholarly journals Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes

2001 ◽  
Vol 11 (4) ◽  
pp. 555-565 ◽  
Author(s):  
I. King Jordan ◽  
Kira S. Makarova ◽  
John L. Spouge ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Gene Duplication ◽  
Average Score ◽  
Specific Gene ◽  
Tandem Gene Duplication ◽  
New Genes ◽  
A Genome ◽  
Prokaryotic Genomes ◽  
Bacterial Chromosomes ◽  
Large Clusters ◽  
Lineage Specific Gene

Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (∼5%–33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size ≥20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss.

Sign in / Sign up

Export Citation Format

Share Document