scholarly journals Genome-wide Identification and Functional Analysis of the H3 Gene Family in Cotton

2020 ◽  
Author(s):  
ZHANG Youping ◽  
ZHANG Jia ◽  
WANG Qiaolian ◽  
Li Simin ◽  
ZUO Dongyun ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Leaf Growth ◽  
Critical Role ◽  
Virus Induced Gene Silencing ◽  
Rapid Phase ◽  
Conserved Sequence ◽  
Nucleosome Structure ◽  
Stomatal Guard Cells ◽  
Pistil Development

Abstract Background: Histones are major components of chromatin, which is a nucleosome structure associated with chromosome segregation, DNA packaging and transcriptional regulation. Histone H3 is encoded by many genes in most eukaryotic species, but little information is known about the Histone H3 gene family in cotton.Results: In this study, we identified and analyzed the evolution and expression of histone H3 gene family in cotton. First, 34 G. hirsutum genes were identified belonging to the H3 gene family which were divided into four subclasses: CENH3, H3.1, H3.3 and H3-like. Among these H3.1 subclass contained the highest number of genes (22 members) followed by H3.3 subclass (9 members). In addition, there were18 and 16 H3 genes identified in G. arboretum and G. raimondii, respectively. Furthermore, we conducted conserved sequence analysis of H3 proteins, and found that the four amino acids signature including A31F41S87A90 for H3.1 and T31Y41H87L90 for H3.3 could be used to discriminate H3.1 from H3.3. The expression of H3 gene family varied in different tissues and developmental stages of G. hirsutum, where H3.1 subclass genes play a critical role in pistil development. By virus-induced gene silencing of GhCENH3 (Gh_D07G1382) gene, the size of leaf got smaller with pYL156-CENH3 than that with pYL156 in TM-1. Whereas, the number of the stomata in the leaf epidermis and number of chloroplasts in the leaf stomatal guard cells by pYL156-CENH3 was more than that by pYL156 and pYL156-PDS.Conclusions: Four sub-classes (CENH3, H3.1, H3.3 and H3-like) of H3 gene family were highly conserved in cotton during the rapid phase of evolution among which CENH3 is necessary for leaf growth. These findings are useful for providing further insights into cotton biology and breeding.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

scholarly journals Systematic CRISPR-Cas9-Mediated Modifications of Plasmodium yoelii ApiAP2 Genes Reveal Functional Insights into Parasite Development

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Cui Zhang ◽  
Zhenkui Li ◽  
Huiting Cui ◽  
Yuanyuan Jiang ◽  
Zhenke Yang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Protein Expression ◽  
Gene Family ◽  
Developmental Stages ◽  
Critical Role ◽  
Plasmodium Yoelii ◽  
Complex Life Cycle ◽  
Parasite Development ◽  
Malaria Parasites ◽  
Functional Roles

ABSTRACT Malaria parasites have a complex life cycle with multiple developmental stages in mosquito and vertebrate hosts, and different developmental stages express unique sets of genes. Unexpectedly, many transcription factors (TFs) commonly found in eukaryotic organisms are absent in malaria parasites; instead, a family of genes encoding proteins similar to the plant Apetala2 (ApiAP2) transcription factors is expanded in the parasites. Several malaria ApiAP2 genes have been shown to play a critical role in parasite development; however, the functions of the majority of the ApiAP2 genes remain to be elucidated. In particular, no study on the Plasmodium yoelii ApiAP2 (PyApiAP2) gene family has been reported so far. This study systematically investigated the functional roles of PyApiAP2 genes in parasite development. Twenty-four of the 26 PyApiAP2 genes were selected for disruption, and 12 were successfully knocked out using the clustered regularly interspaced short palindromic repeat–CRISPR-associated protein 9 (CRISPR-Cas9) method. The effects of gene knockout (KO) on parasite development in mouse and mosquito stages were evaluated. Ten of 12 successfully disrupted genes, including two genes that have not been functionally characterized in any Plasmodium species previously, were shown to be critical for P. yoelii development of sexual and mosquito stages. Additionally, seven of the genes were labeled for protein expression analysis, revealing important information supporting their functions. This study represents the first systematic functional characterization of the P. yoelii ApiAP2 gene family and discovers important insights on the roles of the ApiAP2 genes in parasite development. IMPORTANCE Malaria is a parasitic disease that infects hundreds of millions of people, leading to an estimated 0.35 million deaths in 2015. A better understanding of the mechanism of gene expression regulation during parasite development may provide important clues for disease control and prevention. In this study, systematic gene disruption experiments were performed to study the functional roles of members of the Plasmodium yoelii ApiAP2 (PyApiAP2) gene family in parasite development. Genes that are critical for the development of male and female gametocytes, oocysts, and sporozoites were characterized. The protein expression profiles for seven of the PyApiAP2 gene products were also analyzed, revealing important information on their functions. This study provides expression and functional information for many PyApiAP2 genes, which can be explored for disease management.

scholarly journals Genome-wide Identification and Function Analysis of HMAD Gene Family in Cotton (Gossypium Spp.)

2020 ◽  
Author(s):  
Qinqin Wang ◽  
Xuke Lu ◽  
Xiugui Chen ◽  
Lanjie Zhao ◽  
Mingge Han ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Gene Family ◽  
Metal Toxicity ◽  
Crop Production ◽  
Developmental Stages ◽  
Function Analysis ◽  
Heavy Metal Toxicity ◽  
Conserved Sequence ◽  
Genome Wide ◽  
And Function

Abstract Background: Soil salinized and heavy metal toxicity has become a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in different plants, little is known in Gossypium.Results: A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family and divided into five classes. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements and transcription factor binding sites (TFBS) for abiotic stress.Conclusions: Current study provides important information about HMAD genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.

scholarly journals Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cuili Pan ◽  
Zhaoxiong Lei ◽  
Shuzhe Wang ◽  
Xingping Wang ◽  
Dawei Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Adipocyte Differentiation ◽  
Bos Taurus ◽  
Adipogenic Differentiation ◽  
Critical Role ◽  
Bos Indicus ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

scholarly journals Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shujuan Tian ◽  
Jiao Jiang ◽  
Guo-qi Xu ◽  
Tan Wang ◽  
Qiyan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Fruit Development ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Citrullus Lanatus ◽  
Binding Motif ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Expression Profile Analysis

Abstract Background Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear. Results In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones. Conclusions Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

scholarly journals Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 315
Author(s):  
Hailin Liu ◽  
Xin Han ◽  
Jue Ruan ◽  
Lian Xu ◽  
Bing He
Keyword(s):  
Ginkgo Biloba ◽  
Leaf Development ◽  
Developmental Stages ◽  
Leaf Growth ◽  
Rna Seq ◽  
Final Size ◽  
Dioecious Species ◽  
Related Factors ◽  
New Genes ◽  
Gene Modules

The final size of plant leaves is strictly controlled by environmental and genetic factors, which coordinate cell expansion and cell cycle activity in space and time; however, the regulatory mechanisms of leaf growth are still poorly understood. Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics, and its fan-shaped leaves are unique in gymnosperms, while the mechanism of G. biloba leaf development remains unclear. In this study we studied the transcriptome of G. biloba leaves at three developmental stages using high-throughput RNA-seq technology. Approximately 4167 differentially expressed genes (DEGs) were obtained, and a total of 12,137 genes were structure optimized together with 732 new genes identified. More than 50 growth-related factors and gene modules were identified based on DEG and Weighted Gene Co-expression Network Analysis. These results could remarkably expand the existing transcriptome resources of G. biloba, and provide references for subsequent analysis of ginkgo leaf development.

scholarly journals Roles of the 14-3-3 gene family in cotton flowering

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Na Sang ◽  
Hui Liu ◽  
Bin Ma ◽  
Xianzhong Huang ◽  
Lu Zhuo ◽  
...  
Keyword(s):  
Gene Family ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Bimolecular Fluorescence Complementation ◽  
Structural Motif ◽  
Virus Induced Gene Silencing ◽  
Protein Protein Interactions ◽  
Basic Leucine Zipper ◽  
Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

Growth, development and allometry of Philophthalmus nocturnus in the eyes of domestic chicks

1992 ◽  
Vol 66 (2) ◽  
pp. 100-107 ◽  
Author(s):  
V. G. M. Swarnakumari ◽  
R. Madhavi
Keyword(s):  
Growth Rate ◽  
Developmental Stages ◽  
Adult Stage ◽  
The Body ◽  
Lag Phase ◽  
Allometric Growth ◽  
Body Width ◽  
Rapid Phase ◽  
Growth Development ◽  
Two Phases

ABSTRACTFifty day-old chicks were each infected with 10 excysted metaccreariae of Philophthalimus nocturnus Looss. 1907 around each orbit and growth, development and allometry were studied. The growth rate showed two phases over a period of 35 days, a limited lag phase lasting two days post-infection in which flukes did not exceed 440 μm in length, and a rapid phase during which growth was rapid and flukes reached a size of 3·008–3·504 mm on day 35. Five developmental stages were noticed during the course of development of the metacercaria to the egg-producing adult stage. Eggs appeared in the uterus on day 14 and oculate miracidia on day 25. The hindhody, testes and ovary showed positive allometric growth, the pharnyx less so, whereas negative allometric growth was shown by the forebody. Body width, oral sucker and ventral sucker were close to isometry, growing at the same rate as the body length.

scholarly journals Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation

2022 ◽  
Vol 23 (2) ◽  
pp. 746
Author(s):  
Bo Li ◽  
Xiangzhan Zhang ◽  
Ruiwei Duan ◽  
Chunhong Han ◽  
Jian Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Developmental Stages ◽  
Genomic Analysis ◽  
Pyrus Communis ◽  
Anthocyanin Content ◽  
Anthocyanin Accumulation ◽  
Rna Seq ◽  
Virus Induced Gene Silencing ◽  
Functional Identification ◽  
Glutathione S Transferase

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding.

scholarly journals Evolution of the codling moth pheromone via an ancient gene duplication

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jean-Marc Lassance ◽  
Bao-Jian Ding ◽  
Christer Löfstedt
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Cydia Pomonella ◽  
Fatty Acid Desaturase ◽  
Codling Moth ◽  
Fatty Acyl ◽  
Integrative Approach ◽  
Heterologous Expression Systems ◽  
Genetic Novelty ◽  
Ancient Gene

AbstractBackgroundDefining the origin of genetic novelty is central to our understanding of the evolution of novel traits. Diversification among fatty acid desaturase (FAD) genes has played a fundamental role in the introduction of structural variation in fatty acyl derivatives. Because of its central role in generating diversity in insect semiochemicals, the FAD gene family has become a model to study how gene family expansions can contribute to the evolution of lineage-specific innovations. Here we used the codling moth (Cydia pomonella) as a study system to decipher the proximate mechanism underlying the production of the ∆8∆10 signature structure of olethreutine moths. Biosynthesis of the codling moth sex pheromone, (E8,E10)-dodecadienol (codlemone), involves two consecutive desaturation steps, the first of which is unusual in that it generates anE9 unsaturation. The second step is also atypical: it generates a conjugated diene system from theE9 monoene C12intermediate via 1,4-desaturation.ResultsHere we describe the characterization of the FAD gene acting in codlemone biosynthesis. We identify 27 FAD genes corresponding to the various functional classes identified in insects and Lepidoptera. These genes are distributed across theC. pomonellagenome in tandem arrays or isolated genes, indicating that the FAD repertoire consists of both ancient and recent duplications and expansions. Using transcriptomics, we show large divergence in expression domains: some genes appear ubiquitously expressed across tissue and developmental stages; others appear more restricted in their expression pattern. Functional assays using heterologous expression systems reveal that one gene, Cpo_CPRQ, which is prominently and exclusively expressed in the female pheromone gland, encodes an FAD that possesses bothE9 and ∆8∆10 desaturation activities. Phylogenetically, Cpo_CPRQ clusters within the Lepidoptera-specific ∆10/∆11 clade of FADs, a classic reservoir of unusual desaturase activities in moths.ConclusionsOur integrative approach shows that the evolution of the signature pheromone structure of olethreutine moths relied on a gene belonging to an ancient gene expansion. Members of other expanded FAD subfamilies do not appear to play a role in chemical communication. This advises for caution when postulating the consequences of lineage-specific expansions based on genomics alone.

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