scholarly journals Mycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Families

2014 ◽  
Vol 6 (6) ◽  
pp. 1454-1465 ◽  
Author(s):  
Pablo Librado ◽  
Filipe G. Vieira ◽  
Alejandro Sánchez-Gracia ◽  
Sergios-Orestis Kolokotronis ◽  
Julio Rozas
Keyword(s):  
Gene Families ◽  
Gene Gain ◽  
Gain And Loss

scholarly journals Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes

2019 ◽  
Vol 11 (10) ◽  
pp. 2750-2766 ◽  
Author(s):  
Gavin M Douglas ◽  
Morgan G I Langille
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Gene Families ◽  
Gene Gain ◽  
Loss Of Function ◽  
Shotgun Metagenomics ◽  
Gain And Loss ◽  
Natural Communities

Abstract High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

Analysis of gene gain and loss in the evolution of predatory bacteria

Gene ◽  
2017 ◽  
Vol 598 ◽  
pp. 63-70 ◽  
Author(s):  
Nan Li ◽  
Kai Wang ◽  
Henry N Williams ◽  
Jun Sun ◽  
Changling Ding ◽  
...  
Keyword(s):  
Gene Gain ◽  
Predatory Bacteria ◽  
Gain And Loss

scholarly journals Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

PLoS Genetics ◽  
2005 ◽  
Vol preprint (2007) ◽  
pp. e231
Author(s):  
Gregory C Kettler ◽  
Adam C. Martiny ◽  
Katherine Huang ◽  
Jeremy Zucker ◽  
Maureen Coleman ◽  
...  
Keyword(s):  
Gene Gain ◽  
Gain And Loss

scholarly journals Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei

2021 ◽  
Author(s):  
Kim Vertacnik ◽  
Danielle Herrig ◽  
R Keating Godfrey ◽  
Tom Hill ◽  
Scott Geib ◽  
...  
Keyword(s):  
Gene Family ◽  
Family Size ◽  
Draft Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Gene Gain ◽  
Ecological Specialization ◽  
Dietary Specialization ◽  
Pine Sawfly ◽  
Neodiprion Lecontei

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions and characterized their genomic distributions and evolutionary history. Our results suggest that expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), and antimicrobial peptide (AMP) subfamilies may have contributed to pine adaptation. By contrast, there was no evidence of recent gene family contraction via pseudogenization. Next, we compared the number of genes in these same families across insect taxa that vary in diet, dietary specialization, and social behavior. In Hymenoptera, herbivory was associated with large GR and small olfactory receptor (OR) families, eusociality was associated with large OR and small AMP families, and--unlike investigations among more closely related taxa--ecological specialization was not related to gene family size. Overall, our results suggest that gene families that mediate ecological interactions may expand and contract predictably in response to particular selection pressures, however, the ecological drivers and temporal pace of gene gain and loss likely varies considerably across gene families.

scholarly journals Accelerated Rate of Gene Gain and Loss in Primates

Genetics ◽  
2007 ◽  
Vol 177 (3) ◽  
pp. 1941-1949 ◽  
Author(s):  
Matthew W. Hahn ◽  
Jeffery P. Demuth ◽  
Sang-Gook Han
Keyword(s):  
Gene Gain ◽  
Gain And Loss

CAFE 5 models variation in evolutionary rates among gene families

2020 ◽  
Author(s):  
Fábio K Mendes ◽  
Dan Vanderpool ◽  
Ben Fulton ◽  
Matthew W Hahn
Keyword(s):  
Software Package ◽  
Computational Analysis ◽  
Source Code ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Supplementary Information ◽  
Rate Variation ◽  
Gene Gain ◽  
Command Line ◽  
Gains And Losses

Abstract Motivation Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, Computational Analysis of gene Family Evolution (CAFE), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. Results Here, we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modeling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. Availability and implementation CAFE 5 source code, documentation, test data and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species

Antioxidants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 257
Author(s):  
Qiang Li ◽  
Hélène San Clemente ◽  
Yongrui He ◽  
Yongyao Fu ◽  
Christophe Dunand
Keyword(s):  
Reactive Oxygen Species ◽  
Comparative Analysis ◽  
Gene Network ◽  
Expression Patterns ◽  
Reactive Oxygen ◽  
Evolutionary Process ◽  
Gene Families ◽  
Eucalyptus Species ◽  
Gene Gain ◽  
Oxygen Species

Eucalyptus is a worldwide hard-wood species which increasingly focused on. To adapt to various biotic and abiotic stresses, Eucalyptus have evolved complex mechanisms, increasing the cellular concentration of reactive oxygen species (ROS) by numerous ROS controlling enzymes. To better analyse the ROS gene network and discuss the differences between four Eucalyptus species, ROS gene network including 11 proteins families (1CysPrx, 2CysPrx, APx, APx-R, CIII Prx, Diox, GPx, Kat, PrxII, PrxQ and Rboh) were annotated and compared in an expert and exhaustive manner from the genomic data available from E. camaldulensis, E. globulus, E. grandis, and E. gunnii. In addition, a specific sequencing strategy was performed in order to determine if the missed sequences in at least one organism are the results of gain/loss events or only sequencing gaps. We observed that the automatic annotation applied to multigenic families is the source of miss-annotation. Base on the family size, the 11 families can be categorized into duplicated gene families (CIII Prx, Kat, 1CysPrx, and GPx), which contain a lot of gene duplication events and non-duplicated families (APx, APx-R, Rboh, DiOx, 2CysPrx, PrxII, and PrxQ). The gene family sizes are much larger in Eucalyptus than most of other angiosperms due to recent gene duplications, which could give higher adaptability to environmental changes and stresses. The cross-species comparative analysis shows gene gain and loss events during the evolutionary process. The 11 families possess different expression patterns, while in the Eucalyptus genus, the ROS families present similar expression patterns. Overall, the comparative analysis might be a good criterion to evaluate the adaptation of different species with different characters, but only if data mining is as exhaustive as possible. It is also a good indicator to explore the evolutionary process.

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