scholarly journals Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants

2018 ◽  
Vol 10 (6) ◽  
pp. 1554-1572 ◽  
Author(s):  
Hélène Boulain ◽  
Fabrice Legeai ◽  
Endrick Guy ◽  
Stéphanie Morlière ◽  
Nadine E Douglas ◽  
...  
Keyword(s):  
Gene Family ◽  
Host Plants ◽  
Specific Gene ◽  
Fast Evolution ◽  
Lineage Specific Gene

scholarly journals The roles of LINEs, LTRs and SINEs in lineage-specific gene family expansions in the human and mouse genomes

2016 ◽  
Author(s):  
Václav Janoušek ◽  
Christina M Laukaitis ◽  
Alexey Yanchukov ◽  
Robert Karn
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Specific Gene ◽  
Second Phase ◽  
Open Chromatin ◽  
Gene Family Expansion ◽  
Family Expansion ◽  
Human And Mouse ◽  
Lineage Specific Gene ◽  
Runaway Process

We explored genome-wide patterns of RT content surrounding lineage-specific gene family expansions in the human and mouse genomes. Our results suggest that the size of a gene family is an important predictor of the RT distribution in close proximity to the family members. The distribution differs considerably between the three most common RT classes (LINEs, LTRs and SINEs). LINEs and LTRs tend to be more abundant around genes of multi-copy gene families, whereas SINEs tend to be depleted around such genes. Detailed analysis of the distribution and diversity of LINEs and LTRs with respect to gene family size suggests that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role, promoting gene duplication. This suggests that gene family expansions, especially in the mouse genome, might undergo two phases, the first is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Our observations also suggest that specific differences exist in this gene family expansion process between human and mouse genomes.

Lineage specific gene family enrichment at the microscale in marine systems

2013 ◽  
Vol 16 (5) ◽  
pp. 605-617 ◽  
Author(s):  
Andrew E Allen ◽  
Lisa Zeigler Allen ◽  
John P McCrow
Keyword(s):  
Gene Family ◽  
Specific Gene ◽  
Marine Systems ◽  
Lineage Specific Gene ◽  
Family Enrichment

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 Identification of lineage-specific gene family expansions in a database of gene families

2018 ◽  
Author(s):  
Avril Coghlan ◽  
Diogo Ribeiro ◽  
Avril Coghlan ◽  
Bhavana Harsha ◽  
Matthew Berriman
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Specific Gene ◽  
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.

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