Evolutionary contribution of duplicated genes to genome evolution in the ginseng species complex

Abstract Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains under-investigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome and proteome datasets. Our genome-wide comparative analyses revealed that while the ginseng species complex were recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypo-methylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hyper-methylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.

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Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus

BMC Genomics ◽

10.1186/s12864-020-07274-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Jing Wen ◽

Peng-Feng Li ◽

Feng Ran ◽

Peng-Cheng Guo ◽

Jia-Tian Zhu ◽

...

Keyword(s):

Brassica Napus ◽

Expression Profiles ◽

Expression Patterns ◽

Protein Structures ◽

Small Scale ◽

Preferential Expression ◽

Qrt Pcr ◽

Genome Wide ◽

Duplication Events ◽

Small Scale Duplication

Abstract Background NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we report the global characterization of NPF in the important oil crop Brassica napus, including that for phylogeny, gene/protein structures, duplications, and expression patterns. Results A total of 199 B. napus (BnaNPFs) NPF-coding genes were identified. Phylogenetic analyses categorized these genes into 11 subfamilies, including three new ones. Sequence feature analysis revealed that members of each subfamily contain conserved gene and protein structures. Many hormone−/abiotic stress-responsive cis-acting elements and transcription factor binding sites were identified in BnaNPF promoter regions. Chromosome distribution analysis indicated that BnaNPFs within a subfamily tend to cluster on one chromosome. Syntenic relationship analysis showed that allotetraploid creation by its ancestors (Brassica rapa and Brassica oleracea) (57.89%) and small-scale duplication events (39.85%) contributed to rapid BnaNPF expansion in B. napus. A genome-wide spatiotemporal expression survey showed that NPF genes of each Arabidopsis and B. napus subfamily have preferential expression patterns across developmental stages, most of them are expressed in a few organs. RNA-seq analysis showed that many BnaNPFs (32.66%) have wide exogenous hormone-inductive profiles, suggesting important hormone-mediated patterns in diverse bioprocesses. Homologs in a clade or branch within a given subfamily have conserved organ/spatiotemporal and hormone-inductive profiles, indicating functional conservation during evolution. qRT-PCR-based comparative expression analysis of the 12 BnaNPFs in the NPF2–1 subfamily between high- and low-glucosinolate (GLS) content B. napus varieties revealed that homologs of AtNPF2.9 (BnaNPF2.12, BnaNPF2.13, and BnaNPF2.14), AtNPF2.10 (BnaNPF2.19 and BnaNPF2.20), and AtNPF2.11 (BnaNPF2.26 and BnaNPF2.28) might be involved in GLS transport. qRT-PCR further confirmed the hormone-responsive expression profiles of these putative GLS transporter genes. Conclusion We identified 199 B. napus BnaNPFs; these were divided into 11 subfamilies. Allopolyploidy and small-scale duplication events contributed to the immense expansion of BnaNPFs in B. napus. The BnaNPFs had preferential expression patterns in different tissues/organs and wide hormone-induced expression profiles. Four BnaNPFs in the NPF2–1 subfamily may be involved in GLS transport. Our results provide an abundant gene resource for further functional analysis of BnaNPFs.

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Genome-wide identification, evolution, and expression analysis of the KT/HAK/KUP family in pear

Genome ◽

10.1139/gen-2017-0254 ◽

2018 ◽

Vol 61 (10) ◽

pp. 755-765 ◽

Cited By ~ 4

Author(s):

Yingzhen Wang ◽

Jiahong Lü ◽

Dan Chen ◽

Jun Zhang ◽

Kaijie Qi ◽

...

Keyword(s):

Higher Plants ◽

Expression Patterns ◽

Purifying Selection ◽

Duplicated Genes ◽

Salt Stress Tolerance ◽

Chromosomal Distribution ◽

Qrt Pcr ◽

Physiological Processes ◽

Genome Wide ◽

Duplication Events

The K+ transporter/high-affinity K+/K+ uptake (KT/HAK/KUP) family, as one of the largest K+ transporter families in higher plants, plays an essential role in plant growth, mineral element absorption, salt stress tolerance, and other physiological processes. However, little is known about this family in pear (Pyrus). Here, we identified 20 K+ transporter genes in pear (P. bretschneideri) using genome-wide analysis. Their gene structure, chromosomal distribution, conserved motifs, phylogenetics, duplication events, and expression patterns were also examined. The results of phylogenetic analysis showed that PbrKT/HAK/KUP genes were clustered into three major groups (Groups I–III). Among the 20 PbrKT/HAK/KUP genes, 18 were mapped to nine chromosomes and two to scaffolds. Four WGD/segmental gene pairs were identified, indicating that WGD/segmental duplication may have contributed to the expansion of the KT/HAK/KUP family in pear. Among the four pairs of WGD/segmentally duplicated genes, both members of three pairs had been subjected to purifying selection, whereas the fourth pair had been subjected to positive selection. Furthermore, phenotypic experiments showed that the growth of pear seedlings was affected by potassium deficiency treatment. Expression patterns of 20 PbrKT/HAK/KUP genes in roots were further assayed with qRT-PCR. PbrHAK1 and PbrHAK12/16 were significantly expressed in response to K+ deficiency, suggesting that these genes are crucial for K+ uptake in pear, especially under the condition of K+ starvation. Our results provide a foundation for further study on the function of KT/HAK/KUP genes in pear.

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Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

Jurnal AgroBiogen ◽

10.21082/jbio.v12n2.2016.p119-130 ◽

2018 ◽

Vol 12 (2) ◽

pp. 119

Author(s):

Puji Lestari ◽

Suk-Ha Lee ◽

I Made Tasma ◽

Asadi Asadi

Keyword(s):

Gene Duplication ◽

Environmental Stress ◽

Biotic Stress ◽

Genome Duplication ◽

Environmental Changes ◽

Plant Genome ◽

Small Scale ◽

Duplicated Genes ◽

Duplication Events

Gene duplication to reveal adaptation clue of plant to environmental stress: A case study of NBS-LRR genes in soybean. Puji Lestari, Suk-Ha Lee, I Made Tasma, and Asadi. Adaptive strategies of plant to stress are fine-tuned by adjusting several activities including molecular mechanism which involve duplicated genes responsive to environmental changes. Genes responsive to the environmental stresses which are retained after small scale duplication are part of plant genome duplication. However, less information of duplicated genes could be adaptive to environmental changes in plant. This review presents an overview of duplication events in plant genomes which impact to gene duplication in relation to environmental changes, gene duplication as an adaptation mechanism, a case of duplicated nucleotide binding site-leucine-rich repeat (NBS-LRR) genes in soybean, and the gene duplication implementation for plant breeding in Indonesia. Notably, genome duplication events generate gene duplication and contribute to adaptive evolution against environmental changes. Generalization of plants to adapt the stressful conditions also probably improves our understanding of gene duplication as a mechanism of adaptation. Several recently duplicated NBS-LRR genes in soybean retain disease resistance QTL and the differential expression convince their contribution to biotic stress resistance in soybean. Proposed models of NBS-LRR genes duplication process may help to understand these genes response to the environmental changes. The duplication of genes resistant to pest/disease particularly NBS-LRR provides important information to select breeding parents and develop molecular markers related to desease resistance to genetically improve soybean in Indonesia. Overall, it may therefore be possible to enhance breeding which targets on genes tolerance/resistance to abiotic/biotic stress, and provide a molecular basis for crop-stress protection strategy and more improved soybean varieties specified for harsh environment.

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Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

Journal of Cotton Research ◽

10.1186/s42397-021-00079-3 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Lingling DOU ◽

Limin LV ◽

Yangyang KANG ◽

Ruijie TIAN ◽

Deqing HUANG ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Gene Family ◽

Segmental Duplication ◽

Gene Expression Pattern ◽

Cell Development ◽

Fiber Cell ◽

Fiber Cells ◽

Genome Wide ◽

Duplication Events ◽

Signaling Receptors

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

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The genetic architecture of structural left–right asymmetry of the human brain

Nature Human Behaviour ◽

10.1038/s41562-021-01069-w ◽

2021 ◽

Cited By ~ 1

Author(s):

Zhiqiang Sha ◽

Dick Schijven ◽

Amaia Carrion-Castillo ◽

Marc Joliot ◽

Bernard Mazoyer ◽

...

Keyword(s):

Brain Asymmetry ◽

Functional Enrichment ◽

Brain Organization ◽

Genome Wide ◽

Brain Expression ◽

Using Data ◽

Left Right Asymmetry ◽

The Uk ◽

Subcortical Volume

AbstractLeft–right hemispheric asymmetry is an important aspect of healthy brain organization for many functions including language, and it can be altered in cognitive and psychiatric disorders. No mechanism has yet been identified for establishing the human brain’s left–right axis. We performed multivariate genome-wide association scanning of cortical regional surface area and thickness asymmetries, and subcortical volume asymmetries, using data from 32,256 participants from the UK Biobank. There were 21 significant loci associated with different aspects of brain asymmetry, with functional enrichment involving microtubule-related genes and embryonic brain expression. These findings are consistent with a known role of the cytoskeleton in left–right axis determination in other organs of invertebrates and frogs. Genetic variants associated with brain asymmetry overlapped with those associated with autism, educational attainment and schizophrenia. Comparably large datasets will likely be required in future studies, to replicate and further clarify the associations of microtubule-related genes with variation in brain asymmetry, behavioural and psychiatric traits.

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Genome-wide genetic links between amyotrophic lateral sclerosis and autoimmune diseases

BMC Medicine ◽

10.1186/s12916-021-01903-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Chun Yu Li ◽

Tian Mi Yang ◽

Ru Wei Ou ◽

Qian Qian Wei ◽

Hui Fang Shang

Keyword(s):

Amyotrophic Lateral Sclerosis ◽

Autoimmune Diseases ◽

Genetic Correlation ◽

Functional Enrichment ◽

Genome Wide Association Studies ◽

Risk Genes ◽

Genome Wide ◽

Shared Risk ◽

Lateral Sclerosis ◽

Shared Genetic

Abstract Background Epidemiological and clinical studies have suggested comorbidity between amyotrophic lateral sclerosis (ALS) and autoimmune disorders. However, little is known about their shared genetic architecture. Methods To examine the relation between ALS and 10 autoimmune diseases, including asthma, celiac disease (CeD), Crohn’s disease (CD), inflammatory bowel disease (IBD), multiple sclerosis (MS), psoriasis, rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), and ulcerative colitis (UC), and identify shared risk loci, we first estimated the genetic correlation using summary statistics from genome-wide association studies, and then analyzed the genetic enrichment leveraging the conditional false discovery rate statistical method. Results We identified a significant positive genetic correlation between ALS and CeD, MS, RA, and SLE, as well as a significant negative genetic correlation between ALS and IBD, UC, and CD. Robust genetic enrichment was observed between ALS and CeD and MS, and moderate enrichment was found between ALS and UC and T1D. Thirteen shared genetic loci were identified, among which five were suggestively significant in another ALS GWAS, namely rs3828599 (GPX3), rs3849943 (C9orf72), rs7154847 (G2E3), rs6571361 (SCFD1), and rs9903355 (GGNBP2). By integrating cis-expression quantitative trait loci analyses in Braineac and GTEx, we further identified GGNBP2, ATXN3, and SLC9A8 as novel ALS risk genes. Functional enrichment analysis indicated that the shared risk genes were involved in four pathways including membrane trafficking, vesicle-mediated transport, ER to Golgi anterograde transport, and transport to the Golgi and subsequent modification. Conclusions Our findings demonstrate a specific genetic correlation between ALS and autoimmune diseases and identify shared risk loci, including three novel ALS risk genes. These results provide a better understanding for the pleiotropy of ALS and have implications for future therapeutic trials.

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Developmental cannabidiol exposure increases anxiety and modifies genome-wide brain DNA methylation in adult female mice

Clinical Epigenetics ◽

10.1186/s13148-020-00993-4 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Nicole M. Wanner ◽

Mathia Colwell ◽

Chelsea Drown ◽

Christopher Faulk

Keyword(s):

Dna Methylation ◽

Molecular Mechanisms ◽

Coat Color ◽

Brain Regions ◽

Functional Enrichment ◽

Positive Effects ◽

Genome Wide ◽

Nulliparous Female ◽

The Impact ◽

The Brain

Abstract Background Use of cannabidiol (CBD), the primary non-psychoactive compound found in cannabis, has recently risen dramatically, while relatively little is known about the underlying molecular mechanisms of its effects. Previous work indicates that direct CBD exposure strongly impacts the brain, with anxiolytic, antidepressant, antipsychotic, and other effects being observed in animal and human studies. The epigenome, particularly DNA methylation, is responsive to environmental input and can direct persistent patterns of gene regulation impacting phenotype. Epigenetic perturbation is particularly impactful during embryogenesis, when exogenous exposures can disrupt critical resetting of epigenetic marks and impart phenotypic effects lasting into adulthood. The impact of prenatal CBD exposure has not been evaluated; however, studies using the psychomimetic cannabinoid Δ9-tetrahydrocannabinol (THC) have identified detrimental effects on psychological outcomes in developmentally exposed adult offspring. We hypothesized that developmental CBD exposure would have similar negative effects on behavior mediated in part by the epigenome. Nulliparous female wild-type Agouti viable yellow (Avy) mice were exposed to 20 mg/kg CBD or vehicle daily from two weeks prior to mating through gestation and lactation. Coat color shifts, a readout of DNA methylation at the Agouti locus in this strain, were measured in F1 Avy/a offspring. Young adult F1 a/a offspring were then subjected to tests of working spatial memory and anxiety/compulsive behavior. Reduced-representation bisulfite sequencing was performed on both F0 and F1 cerebral cortex and F1 hippocampus to identify genome-wide changes in DNA methylation for direct and developmental exposure, respectively. Results F1 offspring exposed to CBD during development exhibited increased anxiety and improved memory behavior in a sex-specific manner. Further, while no significant coat color shift was observed in Avy/a offspring, thousands of differentially methylated loci (DMLs) were identified in both brain regions with functional enrichment for neurogenesis, substance use phenotypes, and other psychologically relevant terms. Conclusions These findings demonstrate for the first time that despite positive effects of direct exposure, developmental CBD is associated with mixed behavioral outcomes and perturbation of the brain epigenome.

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Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽

10.3390/insects11060326 ◽

2020 ◽

Vol 11 (6) ◽

pp. 326

Author(s):

Yu-Jun Wang ◽

Hua-Ling Wang ◽

Xiao-Wei Wang ◽

Shu-Sheng Liu

Keyword(s):

Gene Expression ◽

Slow Rate ◽

Species Complex ◽

Evolutionary Patterns ◽

Protein Coding ◽

Coding Sequences ◽

Species Comparisons ◽

Differential Gene ◽

Males And Females ◽

And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

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