scholarly journals Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Chinese Perch, Siniperca chuatsi

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 178 ◽  
Author(s):  
Li-Yuan Lv ◽  
Xu-Fang Liang ◽  
Shan He
Keyword(s):  
Olfactory Receptor ◽  
Evolutionary Dynamics ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Whole Genome Analysis ◽  
Siniperca Chuatsi ◽  
Piscivorous Fish ◽  
Chinese Perch ◽  
Or Genes

Olfaction, which is mediated by olfactory receptor (OR) genes, is essential in the daily life of fish, especially in foraging. However, Chinese perch (Siniperca chuatsi) is believed to prey with reliance on vision and lateral sensation, but not on olfaction. Therefore, understanding the evolutionary dynamics of the Chinese perch OR repertoire could provide insights into genetic evidence for adapting to a decreasing reliance on olfaction. Here, we reported a whole-genome analysis of the Chinese perch OR repertoire. Our analysis identified a total of 152 OR genes, including 123 functional genes and 29 pseudogenes, and showed their genomic organization. A phylogenetic tree was constructed, and the phylogenetic relationships of teleosts ORs was illustrated. The dN/dS (global ratios of non-synonymous to synonymous) analysis demonstrated that OR groups all appeared to be under purifying selection. Among the five Percomorpha fishes, Chinese perch only had 22 subfamilies, suggesting a decrease in OR diversities. The species-specific loss of subfamily 56 and 66 in Chinese perch, of which the genes belonged to subfamily 66, were orthologs of OR51E2, which recognized the plant odorant β-ionone, indicating that extremely piscivorous fish which might lose those receptors responded to plant-related odors. Finally, the expression profiles of OR genes in the olfactory epithelium at different developmental stages were investigated using RNA-seq data. From the aforementioned results, the evolution of the OR repertoire may be shaped by the adaption of vision-dependent specializations for foraging in Chinese perch. The first systematic study of OR genes in Chinese perch could provide valuable genomic resources for the further investigation of olfactory function in teleosts.

scholarly journals Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

2021 ◽  
Vol 22 (12) ◽  
pp. 6556
Author(s):  
Junjun Huang ◽  
Xiaoyu Li ◽  
Xin Chen ◽  
Yaru Guo ◽  
Weihong Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abc Transporters ◽  
Developmental Stages ◽  
Aluminum Toxicity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Purifying Selection ◽  
Biotic Stresses ◽  
Genome Wide ◽  
New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

scholarly journals Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

2020 ◽  
Vol 21 (6) ◽  
pp. 2209 ◽  
Author(s):  
Yuanyuan Wan ◽  
Zhen Wang ◽  
Jichun Xia ◽  
Shulin Shen ◽  
Mingwei Guan ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Brassica Species ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Plant Tolerance ◽  
Genome Wide Analysis ◽  
Genome Wide

Phosphorus transporter (PHT) genes encode H2PO4−/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1–PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.

scholarly journals Convergent degeneration of olfactory receptor gene repertoires in marine mammals

2019 ◽  
Author(s):  
Ake Liu ◽  
Funan He ◽  
Libing Shen ◽  
Ruixiang Liu ◽  
Zhijun Wang ◽  
...  
Keyword(s):  
Olfactory Receptor ◽  
Marine Mammals ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Gene Families ◽  
Average Gain ◽  
Mammalian Gene ◽  
Terrestrial Mammals ◽  
Gain And Loss ◽  
Or Genes

Abstract Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified and the factors that might underlie these variations are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had less OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous gene in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR genes compared with their related terrestrial lineages, which may be related to the weaker purifying selection. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

scholarly journals Genome-wide systematic characterization of HAK/KUP/KT gene family and their expression profiles during plant growth and in response to low K+ stress in Saccharum

2019 ◽  
Author(s):  
Xiaomin Feng ◽  
Yongjun Wang ◽  
Nannan Zhang ◽  
Zilin Wu ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Divergence Time ◽  
Constitutive Expression ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Gain Loss ◽  
Low K

Abstract Background: Plant genomes contain large number of HAK/KUP/KT transporters, and they play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant development. Potassium deficiency in soil of sugarcane main planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum). Results: In this study, 30 HAK/KUP/KT genes were identified from Saccharum spontaneum. Phylogenetics, duplication events, gene structure and expression pattern were analyzed. Phylogenetic analysis of HAK/KUP/KT genes from 15 representative plants showed that this gene family were divided into four groups (clade I-IV). Both ancient whole-genome duplication (WGD) and recent gene duplication contributed to the expansion of HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force to drive the evolution of HAK/KUP/KT genes. The divergence time of HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that HAK/KUP/KT genes was accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that HAK/KUP/KT genes from clade II and III mainly displayed constitutive expression in various tissues, while most genes from clade I and IV had no or very low expression in the tested tissues at different developmental stages. SsHAK1 and SsHAK21 displayed upregulated expression in response to low K+ stress. Yeast functional complementation analysis suggested that SsHAK1 and SsHAK21 could rescue K+ uptake ability in the yeast mutant. Conclusions: This study provided insight into the gene evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the high photosynthetic zone and mature zone of stem. Moreover HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important role in mediating potassium acquisition under limited K+ supply. Our results provide valuable information and key candidate genes for further study on the function of HAK/KUP/KT genes in Saccharum. Keywords: Saccharum, HAK/KUP/KT, evolution, gene expression, low K+ stress

scholarly journals A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1072 ◽  
Author(s):  
Cailin Qiao ◽  
Jing Yang ◽  
Yuanyuan Wan ◽  
Sirou Xiang ◽  
Mingwei Guan ◽  
...  
Keyword(s):  
Differential Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Purifying Selection ◽  
High Similarity ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events ◽  
Group 2 ◽  
Genome Wide Survey

The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.

scholarly journals Deciphering Evolutionary Dynamics of WRKY I Genes in Rosaceae Species

2021 ◽  
Vol 9 ◽  
Author(s):  
Lan Jiang ◽  
Yu Chen ◽  
De Bi ◽  
Yunpeng Cao ◽  
Jiucui Tong
Keyword(s):  
Evolutionary Dynamics ◽  
Developmental Stages ◽  
Higher Plants ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Functional Studies ◽  
Environmental Selection ◽  
Rosaceae Species ◽  
The Stability ◽  
And Function

WRKY transcription factors participate in various regulation processes at different developmental stages in higher plants. Here, 98 WRKY I genes were identified in seven Rosaceae species. The WRKY I genes are highly enriched in some subgroups and are selectively expanded in Chinese pear [Pyrus bretschneideri (P. bretschneideri)] and apple [Malus domestica (M. domestica)]. By searching for intra-species gene microsynteny, we found the majority of chromosomal segments for WRKY I-containing segments in both P. bretschneideri and M. domestica genomes, while paired segments were hardly identified in the other five genomes. Furthermore, we analyzed the environmental selection pressure of duplicated WRKY I gene pairs, which indicated that the strong purifying selection for WRKY domains may contribute to the stability of its structure and function. The expression patterns of duplication PbWRKY genes revealed that functional redundancy for some of these genes was derived from common ancestry and neo-functionalization or sub-functionalization for some of them. This study traces the evolution of WRKY I genes in Rosaceae genomes and lays the foundation for functional studies of these genes in the future. Our results also show that the rates of gene loss and gain in different Rosaceae genomes are far from equilibrium.

scholarly journals Genome-wide systematic characterization of HAK/KUP/KT gene family and their expression profiles during plant growth and in response to low K+ stress in Saccharum

2019 ◽  
Author(s):  
Xiaomin Feng ◽  
Yongjun Wang ◽  
Nannan Zhang ◽  
Zilin Wu ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Divergence Time ◽  
Constitutive Expression ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Gain Loss ◽  
Low K

Abstract Background Plant genomes contain large number of HAK/KUP/KT transporters, and they play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance as well as root morphogenesis and plant development. Potassium deficiency in soil of main sugarcane planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum). Results In this study, 30 HAK/KUP/KT genes were identified from Saccharum spontaneum. Phylogenetics, duplication events, gene structure and expression pattern were analyzed. Phylogenetic analysis of HAK/KUP/KT genes from 15 representative plants showed that this gene family were divided into four groups (clade I-IV). Both ancient whole-genome duplication (WGD) and recent gene duplication contributed to the expansion of HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force to drive the evolution of HAK/KUP/KT genes. The divergence time of HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that HAK/KUP/KT genes was accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that HAK/KUP/KT genes from clade II and III mainly displayed constitutive expression in various tissues, while most genes from clade I and IV had no or very low expression in the tested tissues at different developmental stages. SsHAK1 and SsHAK21 displayed upregulated expression in response to low K+ stress. Conclusions This study provided insight into the gene evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the high photosynthetic zone and mature zone of stem. Moreover HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important role in mediating potassium acquisition under limited K+ supply. Our results provide valuable information and key candidate genes for further study on the function of HAK/KUP/KT genes in Saccharum.

scholarly journals Convergent degeneration of olfactory receptor gene repertories in marine mammals

2019 ◽  
Author(s):  
Ake Liu ◽  
Funan He ◽  
Libing Shen ◽  
Jingqi Zhou
Keyword(s):  
Olfactory Receptor ◽  
Marine Mammals ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Gene Families ◽  
Average Gain ◽  
Mammalian Gene ◽  
Terrestrial Mammals ◽  
Gain And Loss ◽  
Or Genes

Abstract Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, it is still unclear whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals, and the factors that might underlie this variation are unknown. Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs). There were significant differences in the numbers of both OR repertoires and OGGs among different species. We found that all marine mammals had less OR genes than their related terrestrial lineages, with the least OR genes in cetaceans; this result may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher, respectively, than those of mammalian gene families. Additionally, we failed to detect any one-to-one orthologous gene in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions: Marine mammals have experienced large numbers of OR genes compared with their related terrestrial lineages, which may result from the weaker purifying selection. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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