scholarly journals Genome-Wide Analysis of Chemosensory Protein Genes (CSPs) Family in Fig Wasps (Hymenoptera, Chalcidoidea)

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1149
Author(s):  
Zhaozhe Xin ◽  
Dawei Huang ◽  
Dan Zhao ◽  
Jiaxing Li ◽  
Xianqin Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Tandem Duplication ◽  
Fig Wasps ◽  
Chemosensory Protein ◽  
Index Analysis ◽  
Genome Wide ◽  
History Of ◽  
Genome Level ◽  
Species Specific ◽  
Adaptation Index

Chemosensory proteins (CSP) are a class of acidic soluble proteins which have various functions in chemoreception, resistance and immunity, but we still have very little knowledge on this gene family in fig wasps, a peculiar insects group (Hymenoptera, Chalcidoidea) that shelter in the fig syconia of Ficus trees. Here, we made the first comprehensive analysis of CSP gene family in the 11 fig wasps at whole-genome level. We manually annotated 104 CSP genes in the genomes of the 11 fig wasps, comprehensively analyzed them in gene characteristics, conserved cysteine patterns, motif orders, phylogeny, genome distribution, gene tandem duplication, and expansion and contraction patterns of the gene family. We also approximately predicted the gene expression by codon adaptation index analysis. Our study shows that the CSP gene family is conserved in the 11 fig wasps; the CSP gene numbers in pollinating fig wasps are less than in non-pollinating fig wasps, which may be due to their longer history of adaptation to fig syconia; the expansion of CSP gene in two non-pollinating fig wasps, Philotrypesis tridentata and Sycophaga agraensis, may be a species-specific phenomenon. These results provide us with useful information for understanding the evolution of the CSP gene family of insects in diverse living environments.

scholarly journals The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hao Song ◽  
Ximing Guo ◽  
Lina Sun ◽  
Qianghui Wang ◽  
Fengming Han ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Hard Clam ◽  
Gene Repertoire ◽  
Single Chromosome ◽  
Inhibitors Of Apoptosis ◽  
History Of ◽  
Evolutionary Success

Abstract Background Inhibitors of apoptosis (IAPs) are critical regulators of programmed cell death that are essential for development, oncogenesis, and immune and stress responses. However, available knowledge regarding IAP is largely biased toward humans and model species, while the distribution, function, and evolutionary novelties of this gene family remain poorly understood in many taxa, including Mollusca, the second most speciose phylum of Metazoa. Results Here, we present a chromosome-level genome assembly of an economically significant bivalve, the hard clam Mercenaria mercenaria, which reveals an unexpected and dramatic expansion of the IAP gene family to 159 members, the largest IAP gene repertoire observed in any metazoan. Comparative genome analysis reveals that this massive expansion is characteristic of bivalves more generally. Reconstruction of the evolutionary history of molluscan IAP genes indicates that most originated in early metazoans and greatly expanded in Bivalvia through both lineage-specific tandem duplication and retroposition, with 37.1% of hard clam IAPs located on a single chromosome. The expanded IAPs have been subjected to frequent domain shuffling, which has in turn shaped their architectural diversity. Further, we observed that extant IAPs exhibit dynamic and orchestrated expression patterns among tissues and in response to different environmental stressors. Conclusions Our results suggest that sophisticated regulation of apoptosis enabled by the massive expansion and diversification of IAPs has been crucial for the evolutionary success of hard clam and other molluscan lineages, allowing them to cope with local environmental stresses. This study broadens our understanding of IAP proteins and expression diversity and provides novel resources for studying molluscan biology and IAP function and evolution.

scholarly journals Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12617
Author(s):  
Yarui Wei ◽  
Shuliang Zhao ◽  
Na Liu ◽  
Yuxing Zhang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Systemic Acquired Resistance ◽  
Acquired Resistance ◽  
Signal Transduction Pathway ◽  
Promoter Regions ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Genome Level

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

scholarly journals Genome-Wide Identification, Evolutionary And Expression Analyses of LEA Gene Family In Peanut (Arachis Hypogaea L.)

2021 ◽  
Author(s):  
RuoLan Huang ◽  
Dong Xiao ◽  
Xin Wang ◽  
Yi Shen ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Segmental Duplication ◽  
Abiotic Stresses ◽  
Tandem Duplication ◽  
Critical Role ◽  
Recognition Sites ◽  
Genome Wide

Abstract Background: Late embryogenesis abundant (LEA) proteins are a group of highly hydrophilic glycine-rich proteins, which accumulate in the late stage of seed maturation and are associated with many abiotic stresses. However, few peanut LEA genes had been reported, and the research on the number, location, structure, molecular phylogeny and expression of AhLEAs was very limited. Results: In this study, 126 LEA genes were identified in the peanut genome through genome-wide analysis and were further divided into eight groups. Sequence analysis showed that most of the AhLEAs (85.7 %) had no or only one intron. LEA genes were randomly distributed on 20 chromosomes. Compared with tandem duplication, segmental duplication played a more critical role in AhLEAs amplication, and 93 segmental duplication AhLEAs and 5 pairs of tandem duplication genes were identified. Synteny analysis showed that some AhLEAs genes come from a common ancestor, and genome rearrangement and translocation occurred among these genomes. Almost all promoters of LEAs contain ABRE, MYB recognition sites, MYC recognition sites, and ERE cis-acting elements, suggesting that the LEA genes were involved in stress response. Gene expression analyses revealed that most of the LEAs were expressed in the late stages of peanut embryonic development. LEA3 (AH16G06810.1, AH06G03960.1), and Dehydrin (AH07G18700.1, AH17G19710.1) were highly expressed in roots, stems, leaves and flowers. Moreover, 100 AhLEAs were involved in response to drought, low-temperature, or Al stresses. Some LEAs that were regulated by different abiotic stresses were also regulated by hormones including ABA, brassinolide, ethylene and salicylic acid. Interestingly, AhLEAs that were up-regulated by ethylene and salicylic acid showed obvious subfamily preferences.Conclusions: AhLEAs are involved in abiotic stress response, and segmental duplication plays an important role in the evolution and amplification of AhLEAs. The genome-wide identification, classification, evolutionary and expression analyses of the AhLEA gene family provide a foundation for further exploring the LEA genes’ function in response to abiotic stress in peanuts.

scholarly journals Genome-wide identification and expression analysis of the JAZ gene family in turnip

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kai Jia ◽  
Cunyao Yan ◽  
Jing Zhang ◽  
Yunxia Cheng ◽  
Wenwen Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Specific Protein ◽  
Gene Pairs ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structure And Expression

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

scholarly journals Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (Citrullus lanatus)

Agriculture ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 447
Author(s):  
Huaiguo Shang ◽  
Na Zhang ◽  
Zhouli Xie ◽  
Siyu Deng ◽  
Licong Yi ◽  
...  
Keyword(s):  
Shoot Regeneration ◽  
Citrullus Lanatus ◽  
Expression Patterns ◽  
Genome Wide ◽  
Long Reads ◽  
Genome Wide Search ◽  
Fast Development ◽  
History Of ◽  
Pin Genes ◽  
Species Specific

As one of the world’s most popular fruits, watermelon (Citrus lanatus) is cultivated in more than 3 million hectares across the globe, with a yearly yield of more than 100 million tons. According to ‘97103’ genome version 1, a previous study has shown that the watermelon genome consists of 11 PIN genes. However, the higher quality ‘97103’ genome version 2 was recently assembled by using PacBio long reads with the benefit of fast development sequencing technology. Using this new assembly, we conducted a new genome-wide search for PIN genes in watermelon and compared it with cucumber and melon genomes. We identified nine, nine, and eight PINs in watermelon, cucumber, and melon, respectively. Phylogenetic analysis revealed a distinct evolutionary history of PIN proteins in watermelon, which is shown by the orphan PIN6 in watermelon. We further conducted an expression analysis of the watermelon PIN genes in silico and by qRT-PCR. ClaPIN6 might not play an essential role during shoot regeneration, which is closely related to species-specific evolution. However, the up-regulated expression patterns of ClaPIN1-1 and ClaPIN1-3 indicated their important roles during shoot regeneration. The result of this research will benefit future studies to understand the regulating mechanisms of auxin in watermelon shoot regeneration.

Genome-wide analysis of the MADS-box gene family in cucumber

Genome ◽  
2012 ◽  
Vol 55 (3) ◽  
pp. 245-256 ◽  
Author(s):  
Lifang Hu ◽  
Shiqiang Liu
Keyword(s):  
Gene Family ◽  
Tandem Duplication ◽  
Tissue Expression ◽  
Mads Box ◽  
Mads Box Genes ◽  
Motif Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Cucumber Genome ◽  
Mads Box Gene

MADS-box transcription factors are known to be involved in many important processes during plant growth and development. To date, few cucumber MADS-box genes and little tissue expression profiling have been reported. Recent completion of the cucumber whole-genome sequencing has allowed genome-wide analysis of the MADS-box gene family in cucumber as well as its comparison with other species. Here, we performed comprehensive analyses of the 43 cucumber MADS-box genes and compared them with those in Arabidopsis, poplar, and grapevine. The phylogenetic analysis showed that most cucumber members were comparable with those in other species, with the exception of AG members. At the same time, the three subfamilies FLC, AGL12, and Bs were absent in the cucumber genome. The conserved motif analysis revealed that most motifs outside the MADS domain were distributed only in specific groups. The analysis of chromosomal localization suggested that tandem duplication might contribute to the MADS-box gene expansion. Expression analysis revealed that 42 of 43 cucumber MADS-box members were expressed in multiple plant tissues, thereby implying their various roles in plants.

scholarly journals Genome-Wide Investigation of the ZF-HD Gene Family in Two Varieties of Alfalfa (Medicago sativa L.) and Its Expression Pattern Under Alkaline Stress

2021 ◽  
Author(s):  
Kai He ◽  
Chunxin Li ◽  
ZhenYue Zhang ◽  
Lifeng Zhan ◽  
Chunlong Cong ◽  
...  
Keyword(s):  
Stress Response ◽  
Gene Family ◽  
Stress Responses ◽  
Growth Regulation ◽  
Biological Information ◽  
Functional Study ◽  
Alkaline Stress ◽  
Genome Wide ◽  
The Difference ◽  
Genome Level

Abstract Background:Zinc finger homeodomain (ZHD) protein is a plant-specific transcription factor and a potential regulator of phosphoenolpyruvate carboxylase (PEPCase)-coding genes, and it also participates in plant growth regulation and abiotic stress responses. To study the function of MsZF-HD genes in the alkaline stress response, this paper assessed biological information and performed transcriptome analyses of the MsZF-HD gene family by using the genomes of two different varieties of alfalfa (XinJiangDa Ye and Zhongmu No. 1). Results:In total, 49 and 11 MsZF-HD genes were identified in these varieties, respectively, including the alleles of XinJiangDa Ye. According to their phylogenetic relationships, the 60 MsZF-HD genes were divided into 5 ZHD subfamilies and 1 MIF subfamily. A total of 88.3% of MsZF-HD genes do not contain introns and are unevenly distributed among the 6 chromosomes of alfalfa. A collinearity analysis indicated that 26 genes of XinJiangDa Ye have no orthologous genes in Zhongmu No. 1, although these genes (such as ZHD-X1–2, ZHD-X3–2 and ZHD-X4–2) have homologous genes in Arabidopsis thaliana, Medicago truncatula and Glycine max. Through RNA-seq and qRT–PCR verification, it was found that MsZF-HD genes are downregulated to participate in the alkaline stress response. Conclusion:The results of this study may lay the foundation for the cloning and functional study of MsZF-HD genes and provide a theoretical basis for revealing the difference between XinJiangDa Ye and Zhongmu No. 1 at the genome level.

Genome-wide identification and analysis of maize PAL gene family and its expression profile in response to high-temperature stress

2020 ◽  
Vol 52 (5) ◽  
Author(s):  
De-Gong Wu ◽  
Qiu-Wen Zhan ◽  
Hai-Bing Yu ◽  
Bao-Hong Huang ◽  
Xin-Xin Cheng ◽  
...  
Keyword(s):  
High Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Expression Profile ◽  
High Temperature Stress ◽  
Genome Wide

Genome-wide Analysis and Expression Profiling of SPS Gene Family in Brassica nupus L.

2018 ◽  
Vol 44 (2) ◽  
pp. 197
Author(s):  
Li ZHANG ◽  
Hong-Ju JIAN ◽  
Bo YANG ◽  
Ao-Xiang ZHANG ◽  
Chao ZHANG ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiling ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-Wide Identification, Classification, and Expression of NF-YB Gene Family in Soybean

2013 ◽  
Vol 38 (9) ◽  
pp. 1570-1582
Author(s):  
Wei-Jun ZHENG ◽  
Zhao-Shi XU ◽  
Zhi-Juan FENG ◽  
Lian-Cheng LI ◽  
Ming CHEN ◽  
...  
Keyword(s):  
Gene Family ◽  
Genome Wide
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