scholarly journals Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10014 ◽  
Author(s):  
Youmei Huang ◽  
Yanhui Liu ◽  
Man Zhang ◽  
Mengnan Chai ◽  
Qing He ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Developmental Process ◽  
Economic Value ◽  
Ananas Comosus ◽  
Functional Verification ◽  
Tropical Fruit ◽  
Genome Wide ◽  
Erf Family ◽  
Gene Structures ◽  
And Function

Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.

scholarly journals Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 275 ◽  
Author(s):  
Cao ◽  
Cheng ◽  
Zhang ◽  
Aslam ◽  
Yan ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Gene Families ◽  
Cellulose Synthase ◽  
Ananas Comosus ◽  
Tropical Fruit ◽  
Genome Wide ◽  
Gene Structures

The cellulose synthase (Ces) and cellulose synthase-like (Csl) gene families belonging to the cellulose synthase gene superfamily, are responsible for the biosynthesis of cellulose and hemicellulose of the plant cell wall, and play critical roles in plant development, growth and evolution. However, the Ces/Csl gene family remains to be characterized in pineapple, a highly valued and delicious tropical fruit. Here, we carried out genome-wide study and identified a total of seven Ces genes and 25 Csl genes in pineapple. Genomic features and phylogeny analysis of Ces/Csl genes were carried out, including phylogenetic tree, chromosomal locations, gene structures, and conserved motifs identification. In addition, we identified 32 pineapple AcoCes/Csl genes with 31 Arabidopsis AtCes/Csl genes as orthologs by the syntenic and phylogenetic approaches. Furthermore, a RNA-seq investigation exhibited the expression profile of several AcoCes/Csl genes in various tissues and multiple developmental stages. Collectively, we provided comprehensive information of the evolution and function of pineapple Ces/Csl gene superfamily, which would be useful for screening out and characterization of the putative genes responsible for tissue development in pineapple. The present study laid the foundation for future functional characterization of Ces/Csl genes in pineapple.

Identification and expression analysis of E2 ubiquitin-conjugating enzymes in cucumber

2021 ◽  
Author(s):  
Wei Lai ◽  
Zhaoyang Hu ◽  
Chuxia Zhu ◽  
Yingui Yang ◽  
Shiqiang Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Biological Processes ◽  
Protein Ubiquitination ◽  
Genome Wide ◽  
Conjugating Enzymes ◽  
Gene Structures ◽  
Ubiquitin Conjugating Enzymes ◽  
Genome Wide Survey

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

scholarly journals Genome-Wide identification and Analysis of the AP2/ERF Gene Family in Fragaria vesca

2019 ◽  
Author(s):  
Zekun Li ◽  
Yanhong Hong ◽  
Changmei Chen ◽  
Zhennan Wang ◽  
Aiying Zheng ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Expression Profiles ◽  
Critical Role ◽  
Evolutionary Relationship ◽  
Evolutionary Process ◽  
Promoter Sequence ◽  
Good Opportunity ◽  
Genome Wide ◽  
Duplication Events ◽  
Erf Family

Abstract Background: The AP2/ERF superfamily consists of primary transcription factors in plants that play a critical role in numerous aspects of various physiological stages and responses to stress stimuli. Nevertheless, there is little information related to AP2/ERF in strawberry, an important perennial fruit and model plant for horticulture. Results: In this study, 117 AP2/ERF genes were identified in strawberry and were grouped into four types of genes, AP2 (17), ERF (94), RAV (5) as well as soloist (1), according to the gene structure, phylogenetic tree and conserved domains. The duplication events and synteny analysis combination of genes offered a good opportunity to understand the evolutionary process of the FvAP2/ERF family. Moreover, identified orthologous genes and expression profiles of genes across various tissue, developmental stages and different treatments predicted potential functions of some AP2/ERF genes in strawberry. Conclusions: In this study, 117 genes were identified in the AP2/ERF family of strawberry, and their structure, chromosomes location, evolutionary relationship, promoter sequence and expression profile were investigated. Our findings provide valuable clues to gain better insights into each FvAP2/ERF gene under different types of biological developments and in response to stressors.

scholarly journals Comparative transcriptome analysis identifies genes associated with chlorophyll levels and reveals photosynthesis in green flesh of radish taproot

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0252031
Author(s):  
Yuan-yuan Li ◽  
Min Han ◽  
Rui-hua Wang ◽  
Ming-gang Gao
Keyword(s):  
Carbon Fixation ◽  
Developmental Stages ◽  
Developmental Process ◽  
Calvin Cycle ◽  
Comparative Transcriptome ◽  
Chl A ◽  
New Information ◽  
Green Tissue ◽  
And Function ◽  
Chl Fluorescence

The flesh of the taproot of Raphanus sativus L. is rich in chlorophyll (Chl) throughout the developmental process, which is why the flesh is green. However, little is known about which genes are associated with Chl accumulation in this non-foliar, internal green tissue and whether the green flesh can perform photosynthesis. To determine these aspects, we measured the Chl content, examined Chl fluorescence, and carried out comparative transcriptome analyses of taproot flesh between green-fleshed “Cuishuai” and white-fleshed “Zhedachang” across five developmental stages. Numerous genes involved in the Chl metabolic pathway were identified. It was found that Chl accumulation in radish green flesh may be due to the low expression of Chl degradation genes and high expression of Chl biosynthesis genes, especially those associated with Part Ⅳ (from Protoporphyrin Ⅸ to Chl a). Bioinformatics analysis revealed that differentially expressed genes between “Cuishuai” and “Zhedachang” were significantly enriched in photosynthesis-related pathways, such as photosynthesis, antenna proteins, porphyrin and Chl metabolism, carbon fixation, and photorespiration. Twenty-five genes involved in the Calvin cycle were highly expressed in “Cuishuai”. These findings suggested that photosynthesis occurred in the radish green flesh, which was also supported by the results of Chl fluorescence. Our study provides transcriptome data on radish taproots and provides new information on the formation and function of radish green flesh.

scholarly journals A Chromosome-Scale Assembly of the En ormous (32 Gb) Axolotl Genome

2018 ◽  
Author(s):  
Jeramiah J. Smith ◽  
Nataliya Timoshevskaya ◽  
Vladimir A. Timoshevskiy ◽  
Melissa C. Keinath ◽  
Drew Hardy ◽  
...  
Keyword(s):  
Large Scale ◽  
Genome Structure ◽  
Large Deletion ◽  
Ambystoma Mexicanum ◽  
Biological Research ◽  
Genome Wide ◽  
Genetic Stocks ◽  
Gene Structures ◽  
And Function ◽  
Genome Assemblies

ABSTRACTThe axolotl (Ambystoma mexicanum) provides critical models for studying regeneration, evolution and development. However, its large genome (~32 gigabases) presents a formidable barrier to genetic analyses. Recent efforts have yielded genome assemblies consisting of thousands of unordered scaffolds that resolve gene structures, but do not yet permit large scale analyses of genome structure and function. We adapted an established mapping approach to leverage dense SNP typing information and for the first time assemble the axolotl genome into 14 chromosomes. Moreover, we used fluorescence in situ hybridization to verify the structure of these 14 scaffolds and assign each to its corresponding physical chromosome. This new assembly covers 27.3 gigabases and encompasses 94% of annotated gene models on chromosomal scaffolds. We show the assembly’s utility by resolving genome-wide orthologies between the axolotl and other vertebrates, identifying the footprints of historical introgression events that occurred during the development of axolotl genetic stocks, and precisely mapping several phenotypes including a large deletion underlying the cardiac mutant. This chromosome-scale assembly will greatly facilitate studies of the axolotl in biological research.

scholarly journals Genome-wide survey and identification of AP2/ERF genes involved in shoot and leaf development in Liriodendron chinense

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yaxian Zong ◽  
Ziyuan Hao ◽  
Zhonghua Tu ◽  
Yufang Shen ◽  
Chengge Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Leaf Development ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Leaf Primordia ◽  
Response Factors ◽  
Anatomic Structure ◽  
Genome Wide ◽  
Liriodendron Chinense ◽  
Erf Family

Abstract Background Liriodendron chinense is a distinctive ornamental tree species due to its unique leaves and tulip-like flowers. The discovery of genes involved in leaf development and morphogenesis is critical for uncovering the underlying genetic basis of these traits. Genes in the AP2/ERF family are recognized as plant-specific transcription factors that contribute to plant growth, hormone-induced development, ethylene response factors, and stress responses. Results In this study, we identified 104 putative AP2/ERF genes in the recently released L. chinense genome and transcriptome database. In addition, all 104 genes were grouped into four subfamilies, the AP2, ERF, RAV, and Soloist subfamilies. This classification was further supported by the results of gene structure and conserved motif analyses. Intriguingly, after application of a series test of cluster analysis, three AP2 genes, LcERF 94, LcERF 96, and LcERF 98, were identified as tissue-specific in buds based on the expression profiles of various tissues. These results were further validated via RT-qPCR assays and were highly consistent with the STC analysis. We further investigated the dynamic changes of immature leaves by dissecting fresh shoots into seven discontinuous periods, which were empirically identified as shoot apical meristem (SAM), leaf primordia and tender leaf developmental stages according to the anatomic structure. Subsequently, these three candidates were highly expressed in SAM and leaf primordia but rarely in tender leaves, indicating that they were mainly involved in early leaf development and morphogenesis. Moreover, these three genes displayed nuclear subcellular localizations through the transient transformation of tobacco epidermal cells. Conclusions Overall, we identified 104 AP2/ERF family members at the genome-wide level and discerned three candidate genes that might participate in the development and morphogenesis of the leaf primordium in L. chinense.

scholarly journals Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola

PeerJ ◽  
2022 ◽  
Vol 9 ◽  
pp. e12558
Author(s):  
Chengru Li ◽  
Na Dong ◽  
Liming Shen ◽  
Meng Lu ◽  
Junwen Zhai ◽  
...  
Keyword(s):  
Fruit Development ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Fruit Size ◽  
Fleshy Fruit ◽  
Averrhoa Carambola ◽  
Star Fruit ◽  
Genome Wide ◽  
Yabby Gene ◽  
Gene Structures

Background Members of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available. Methods In the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed. Results Eight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.

scholarly journals Evolutionary and Expression Analysis of CAMTA Gene Family in Three Species (Arabidopsis, Maize and Tomato), and Gene Expression in Response to Developmental Stages

2021 ◽  
Author(s):  
Abbas Saidi ◽  
Zohreh Hajibarat
Keyword(s):  
Stress Proteins ◽  
Developmental Stages ◽  
Plant Tissues ◽  
Expression Data ◽  
Calmodulin Binding ◽  
Percent Identity ◽  
Genome Wide ◽  
Mrna Analysis ◽  
Gene Structures ◽  
First Time

Abstract The calmodulin-binding transcriptional activator (CAMTA) family has been known to be one of the fast responsive stress proteins. In this study, 17 CAMTA genes were selected in Arabidopsis, tomato and maize. The chromosomal distributions, gene structures, duplication patterns, phylogenetic tree, and developmental stage of the 17 CAMTA genes in the three species were analyzed to further investigate their functions. According to the synteny analysis, CAMTA genes of maize and tomato revealed higher similarity with each other as compared with Arabidopsis. A higher than 90 percent identity was observed between maize CAMTA genes (ZmCAMTA2 and ZmCAMTA3) and tomato CAMTA genes (SlCAMTA4, SlCAMTA4.1). To detect expression levels in different plant tissues, mRNA analysis of CAMTA genes were performed using publicly available expression data in the genvestigator. The aim of study was to identify and characterize CAMTA genes in three species, for the first time, via insilico genome-wide analysis approach. AtCAMTA1 and AtCAMTA2 and SlCAMTA2 and ZmCAMTA1 and ZmCAMTA2 genes were up-regulated during all developmental stages. The conserved motifs and gene structure in most proteins in each group were similar, validating the CAMTA phylogenetic classification. This study could be considered as a useful source for future CAMTA comparative studies in different plant species.

scholarly journals Mutation induction in the pineapple (Ananas comosus L. Merr) using colchicine

2021 ◽  
Vol 905 (1) ◽  
pp. 012082
Author(s):  
Rosmaina ◽  
R Elfianis ◽  
F Mursanto ◽  
A Janna ◽  
T Erawati ◽  
...  
Keyword(s):  
Plant Height ◽  
Leaf Shape ◽  
Economic Value ◽  
Colchicine Treatment ◽  
Ananas Comosus ◽  
Mutation Induction ◽  
Tropical Fruit ◽  
Randomized Design ◽  
Number Of Leaves ◽  
And Control

Abstract Pineapple is a tropical fruit that has high economic value. Mutation is a method to increase plant diversity which plays an essential role in plant improvement. This study aimed to induce mutations in pineapple using colchicine. This study was arranged in a factorial completely randomized design. The first factor was pineapple genotypes (i.e., Gemilang, Bangka, Queen, and Suska Kualu) and the second factor was colchicine concentration (i.e., 0.03%, 0.04%, 0.05%, and control). There were 16 treatments with five repetitions so the total was 80 experimental units. Observations were made for three months after treatment in the vegetative phase. Observation parameters included leaf shape, leaf color, plant height, number of leaves, leaf width, and length of stomata. This study indicated that the interaction between genotype and colchicine significantly differed in plant height and the number of leaves. Colchicine significantly increased the length of stomata, and genotype significantly affected all observed parameters. This study concluded that 0.05% colchicine significantly increased plant height (26.67%) and the number of leaves (48.98%) in the Gemilang genotype but decreased plant height and leaf number in other genotypes. This study suggests the need for observation of the flowering phase and fruit quality due to colchicine treatment.

scholarly journals Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7877 ◽  
Author(s):  
Yanhua Cao ◽  
Xiongwei Zhao ◽  
Yajuan Liu ◽  
Yalong Wang ◽  
Wenmei Wu ◽  
...  
Keyword(s):  
Natural Variation ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Cadmium Accumulation ◽  
Functional Verification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cd Accumulation ◽  
Genome Wide ◽  
Selection Of

P1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 ZmHMA genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and motif compositions. Furthermore, the expression patterns of different ZmHMA genes varied with developmental stages, and were tissue specific under normal conditions. ZmHMA2 and ZmHMA3 genes exhibited significant up-regulation under Cd treatment. Eventually, the association analysis between 103 inbred lines and alleles in ZmHMA2 and ZmHMA3 revealed that one insertion–deletion (InDel) in the intron from ZmHMA2 was associated with leaf Cd concentration under low Cd condition at the seedling stage. Twenty polymorphisms in ZmHMA3 were significantly associated with leaf Cd concentration under various Cd levels at seedling and maturing stages. Five single nucleotide polymorphisms (SNPs) and two InDels of these significantly associated polymorphic loci from ZmHMA3 caused the amino acid substitutions and insertion or deletion events. Importantly, the proteins encoded by ZmHMA2 and ZmHMA3 genes were located in the plasma membrane. This comprehensive analysis will provide an important theoretical basis for future functional verification of ZmHMA genes to unravel the mechanisms of Cd accumulation in leaves of maize. Additionally, the favorable alleles in ZmHMA3 will lay a foundation for the marker-assisted selection of low Cd accumulation in maize.

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