scholarly journals New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mahnaz Nezamivand-Chegini ◽  
Esmaeil Ebrahimie ◽  
Ahmad Tahmasebi ◽  
Ali Moghadam ◽  
Saeid Eshghi ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Family Evolution ◽  
Individual Species ◽  
Phosphate Binding ◽  
Long Distance ◽  
Phosphate Sensing ◽  
Key Species ◽  
Almost All ◽  
Selaginella Moellendorffii ◽  
Functional Orthologs

Abstract Background SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. Results We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs. Conclusion This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

scholarly journals New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

2021 ◽  
Author(s):  
Mahnaz Nezamivand Chegini ◽  
Esmaeil Ebrahimie ◽  
Ahmad Tahmasebi ◽  
Ali Moghadam ◽  
Saied Eshghi ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Family Evolution ◽  
Individual Species ◽  
Phosphate Binding ◽  
Long Distance ◽  
Phosphate Sensing ◽  
Key Species ◽  
Almost All ◽  
Selaginella Moellendorffii ◽  
Functional Orthologs

AbstractBackgroundSPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes.ResultsWe analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs.ConclusionThis comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1 and AtPHO1;H1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

scholarly journals Expansion and accelerated evolution of 9-exon odorant receptors in Polistes paper wasps

2021 ◽  
Author(s):  
Andrew W Legan ◽  
Christopher M Jernigan ◽  
Sara E Miller ◽  
Matthieu F Fuchs ◽  
Michael J Sheehan
Keyword(s):  
Gene Family ◽  
Odorant Receptor ◽  
Receptor Gene ◽  
Gene Tree ◽  
Gene Family Evolution ◽  
Paper Wasp ◽  
Gene Copy ◽  
Evolutionary Divergence ◽  
Wasp Species ◽  
Or Gene

Abstract Independent origins of sociality in bees and ants are associated with independent expansions of particular odorant receptor (OR) gene subfamilies. In ants, one clade within the OR gene family, the 9-exon subfamily, has dramatically expanded. These receptors detect cuticular hydrocarbons (CHCs), key social signaling molecules in insects. It is unclear to what extent 9-exon OR subfamily expansion is associated with the independent evolution of sociality across Hymenoptera, warranting studies of taxa with independently derived social behavior. Here we describe odorant receptor gene family evolution in the northern paper wasp, Polistes fuscatus, and compare it to four additional paper wasp species spanning ∼40 million years of evolutionary divergence. We find 200 putatively functional OR genes in P. fuscatus, matching predictions from neuroanatomy, and more than half of these are in the 9-exon subfamily. Most OR gene expansions are tandemly arrayed at orthologous loci in Polistes genomes, and microsynteny analysis shows species-specific gain and loss of 9-exon ORs within tandem arrays. There is evidence of episodic positive diversifying selection shaping ORs in expanded subfamilies. Values of omega (d  N/dS) are higher among 9-exon ORs compared to other OR subfamilies. Within the Polistes OR gene tree, branches in the 9-exon OR clade experience relaxed negative (purifying) selection relative to other branches in the tree. Patterns of OR evolution within Polistes are consistent with 9-exon OR function in CHC perception by combinatorial coding, with both natural selection and neutral drift contributing to interspecies differences in gene copy number and sequence.

scholarly journals Genome-Wide Identification and Expression Analysis of the Histone Deacetylase Gene Family in Wheat (Triticum aestivum L.)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 19
Author(s):  
Peng Jin ◽  
Shiqi Gao ◽  
Long He ◽  
Miaoze Xu ◽  
Tianye Zhang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Mosaic Virus ◽  
Stress Responses ◽  
Viral Infections ◽  
Phylogenetic Analyses ◽  
Plant Viruses ◽  
Gene Family Evolution ◽  
Yellow Mosaic Virus ◽  
Wheat Yellow Mosaic Virus

Histone acetylation is a dynamic modification process co-regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Although HDACs play vital roles in abiotic or biotic stress responses, their members in Triticumaestivum and their response to plant viruses remain unknown. Here, we identified and characterized 49 T. aestivumHDACs (TaHDACs) at the whole-genome level. Based on phylogenetic analyses, TaHDACs could be divided into 5 clades, and their protein spatial structure was integral and conserved. Chromosomal location and synteny analyses showed that TaHDACs were widely distributed on wheat chromosomes, and gene duplication has accelerated the TaHDAC gene family evolution. The cis-acting element analysis indicated that TaHDACs were involved in hormone response, light response, abiotic stress, growth, and development. Heatmaps analysis of RNA-sequencing data showed that TaHDAC genes were involved in biotic or abiotic stress response. Selected TaHDACs were differentially expressed in diverse tissues or under varying temperature conditions. All selected TaHDACs were significantly upregulated following infection with the barley stripe mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV), and wheat yellow mosaic virus (WYMV), suggesting their involvement in response to viral infections. Furthermore, TaSRT1-silenced contributed to increasing wheat resistance against CWMV infection. In summary, these findings could help deepen the understanding of the structure and characteristics of the HDAC gene family in wheat and lay the foundation for exploring the function of TaHDACs in plants resistant to viral infections.

Comparison of colonial volvocine algae based on phylotranscriptomic analysis of gene family evolution and natural selection

2019 ◽  
Vol 55 (1) ◽  
pp. 100-112 ◽  
Author(s):  
Yuxin Hu ◽  
Weiyue Xing ◽  
Huiyin Song ◽  
Zhengyu Hu ◽  
Guoxiang Liu
Keyword(s):  
Natural Selection ◽  
Gene Family ◽  
Gene Family Evolution ◽  
Volvocine Algae

scholarly journals Snow is Not an Enemy, But another Road in Winter

2020 ◽  
pp. 1-2
Author(s):  
Oleg Khalidullin ◽  
Keyword(s):  
Road Surface ◽  
Long Distance ◽  
Surface Formation ◽  
Different Temperatures ◽  
Almost All

Snowfalls and blizzards block roads and create massive congestion on city streets and long-distance routes. Considering the processes of road surface formation during snowfall, it can be noted that snow during the fall is light fluffs, which, at an indefinite time, with different intensities, at different temperatures, stacked in layers, gradually by the wheels of cars, are compacted into a slippery tuberous canvas. The rubber tread, rolling through the freshly deposited layers, compresses the snow, forming a rut. The resulting trail adheres firmly to the asphalt. Almost all cars go on the trail, therefore the wheels of the following cars condense mainly the same track. On inactive roads, leaving the track during overtaking or detour leads to smoothing and compaction of the freezing walls of the track

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 Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family in Dasypyrum villosum L. Reveals That DvGELP53 Is Related to BSMV Infection

2021 ◽  
Vol 22 (22) ◽  
pp. 12317
Author(s):  
Heng Zhang ◽  
Xu Zhang ◽  
Jia Zhao ◽  
Li Sun ◽  
Haiyan Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Dasypyrum Villosum ◽  
Promoter Regions ◽  
Lipase Gene ◽  
Long Distance ◽  
Enzyme Superfamily ◽  
Genome Wide ◽  
A Genome ◽  
Long Distance Movement

GDSL-type esterase/lipase proteins (GELPs) characterized by a conserved GDSL motif at their N-terminus belong to the lipid hydrolysis enzyme superfamily. In plants, GELPs play an important role in plant growth, development and stress response. The studies of the identification and characterization of the GELP gene family in Triticeae have not been reported. In this study, 193 DvGELPs were identified in Dasypyrum villosum and classified into 11 groups (clade A–K) by means of phylogenetic analysis. Most DvGELPs contain only one GDSL domain, only four DvGELPs contain other domains besides the GDSL domain. Gene structure analysis indicated 35.2% DvGELP genes have four introns and five exons. In the promoter regions of the identified DvGELPs, we detected 4502 putative cis-elements, which were associated with plant hormones, plant growth, environmental stress and light responsiveness. Expression profiling revealed 36, 44 and 17 DvGELPs were highly expressed in the spike, the root and the grain, respectively. Further investigation of a root-specific expressing GELP, DvGELP53, indicated it was induced by a variety of biotic and abiotic stresses. The knockdown of DvGELP53 inhibited long-distance movement of BSMV in the tissue of D. villosum. This research provides a genome-wide glimpse of the D. villosum GELP genes and hints at the participation of DvGELP53 in the interaction between virus and plants.

Colonization of depopulated crinoids by symbionts: who comes from the bottom and who from the water column?

2015 ◽  
Vol 95 (8) ◽  
pp. 1607-1612 ◽  
Author(s):  
E.S. Mekhova ◽  
P.Y. Dgebuadze ◽  
V.N. Mikheev ◽  
T.A. Britayev
Keyword(s):  
Water Column ◽  
Field Experiments ◽  
Dispersal Ability ◽  
Long Distance ◽  
Sandy Substrate ◽  
Limited Dispersal ◽  
Set Up ◽  
Almost All ◽  
High Degree

Previous experiments with the comatulid Himerometra robustipinna (Carpenter, 1881) demonstrated intensive host-to-host migration processes for almost all symbiotic species both within host aggregations and among hosts separated by several metres. The aim of this study was to check the ability of symbionts to complete long-distance migrations, by means of two in situ experiments which depopulated the crinoid host. Two different sets of field experiments were set up: exposure of depopulated crinoids (set 1) on stony ‘islands’ isolated from native crinoid assemblages by sandy substrate, and (set 2) in cages suspended in the water column. Hosts from set 1 were exposed for 1, 2, 3 and 4 weeks to assess whether substrate has an influence on the symbionts' long-distance migrations. In set 2 cages were exposed for 10–11 days, aiming to check whether symbionts were able to disperse through the water column with currents. These experiments allow the conclusion that post-settled symbionts can actively migrate among their hosts. Symbionts are able to reach their hosts by employing two different ‘transport corridors’, by drifting or swimming in water column, and by moving on the bottom. Comparison of experimental results allows the division of symbionts into two conventional groups according to the dispersal ability of their post-settled stages: (1) species able to complete long-distance migrations, (2) species unable to migrate or having limited dispersal ability. The finding of the free-living shrimp Periclimenes diversipes Kemp, 1922 in set 2 raises the question about the factors that affect such a high degree of specialization of crinoid assemblages.

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