scholarly journals Low-Copy Genes in Terpenoid Metabolism: The Evolution and Expression of MVK and DXR Genes in Angiosperms

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 525
Author(s):  
Natacha Silva ◽  
Suzana Tiemi Ivamoto-Suzuki ◽  
Paula Oliveira Camargo ◽  
Raíssa Scalzoni Rosa ◽  
Luiz Filipe Protasio Pereira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Profile Analysis ◽  
Selection Effect ◽  
Digital Gene Expression ◽  
Purifying Selection ◽  
Gene Families ◽  
Single Copy ◽  
Environmental Cues ◽  
Evolutionary Analysis ◽  
Mva Pathway

Terpenoids are a diverse class of metabolites that impact plant metabolism in response to environmental cues. They are synthesized either via a predominantly cytosolic (MVA) pathway or a plastidic pathway (MEP). In Arabidopsis, several enzymes from the MVA and MEP pathways are encoded by gene families, excluding MVK and DXR, which are single-copy genes. In this study, we assess the diversity, evolution and expression of DXR and MVK genes in selected angiosperms and Coffea arabica in particular. Evolutionary analysis revealed that DXR and MVK underwent purifying selection, but the selection effect for DXR was stronger than it was for MVK. Digital gene expression (DGE) profile analysis of six species revealed that expression levels of MVK in flowers and roots were high, whereas for DXR peak values were observed in leaves. In C. arabica, both genes were highly expressed in flowers, and CaDXR was upregulated in response to methyl jasmonate. C. arabica DGE data were validated by assessing gene expression in selected organs, and by plants treated with hexanoic acid (Hx) using RT-qPCR. MVK expression was upregulated in roots treated with Hx. CaDXR was downregulated in leaves by Hx treatment in a genotype-specific manner, indicating a differential response to priming.

scholarly journals Digital Gene Expression Profiling of the Phytophthora sojae Transcriptome

2011 ◽  
Vol 24 (12) ◽  
pp. 1530-1539 ◽  
Author(s):  
Wenwu Ye ◽  
Xiaoli Wang ◽  
Kai Tao ◽  
Yuping Lu ◽  
Tingting Dai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Protein Localization ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Digital Gene Expression ◽  
Gene Families ◽  
Phytophthora Sojae ◽  
Web Based ◽  
Average Expression Level

The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at ten different developmental and infection stages based on a 3′-tag digital gene-expression protocol. More than 90 million clean sequence tags were generated and compared with the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes' expression patterns suggested four groups: i) mycelia and zoosporangia, ii) zoospores and cysts, iii) germinating cysts, and iv) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression–pattern clusters were obtained and the top 16 clusters, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and noncoding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis-related gene families revealed that most were infection induced but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database has been established.

scholarly journals Male mice with large inversions or deletions of X-palindrome arms are fertile and express their associated genes post-meiosis

2018 ◽  
Author(s):  
Alyssa N. Kruger ◽  
Quinn Ellison ◽  
Michele A. Brogley ◽  
Emma R. Gerlinger ◽  
Jacob L. Mueller
Keyword(s):  
Gene Expression ◽  
Sex Chromosomes ◽  
Transcriptional Repression ◽  
Sex Chromosome ◽  
Gene Families ◽  
Single Copy ◽  
Male Mice ◽  
Expression Levels ◽  
Gene Copies ◽  
Palindromic Structure

AbstractLarge (>10 kb) palindromic sequences are enriched on mammalian sex chromosomes. In mice, these palindromes harbor gene families (≥2 gene copies) expressed exclusively in post-meiotic testicular germ cells, at a time when most single-copy sex-linked genes are transcriptionally repressed. This distinct expression pattern led to the hypothesis that containment within palindrome structures or having ≥2 gene enables post-meiotic gene expression. We tested these two hypotheses by using CRISPR to precisely engineer large (10’s of kb) inversions and deletions of X chromosome palindrome arms for two regions carrying the mouse 4930567H17Rik and Mageb5 gene families. We found that 4930567H17Rik and Mageb5 gene expression is unaffected in mice carrying palindrome arm inversions, suggesting that palindromic structure is not important for mediating palindrome-associated gene expression. We also found that 4930567H17Rik and Mageb5 gene expression is reduced by half in mice carrying palindrome arm deletions, allowing us to test whether palindrome-associated genes are sensitive to reduced expression levels resulting in spermatogenic defects. Male mice carrying palindrome arm deletions of 4930567H17Rik or Mageb5, however, are fertile, have normal testis histology, and show no aberrations in spermatogenic cell population frequencies via FACS quantification. Together, these findings suggest that large palindromic structures on the sex chromosomes are not necessary for their associated genes to evade post-meiotic transcriptional repression and that these genes are not sensitive to reduced expression levels. Large sex chromosome palindromes may thus be important for other reasons, such as the long-term evolutionary stability of their associated gene families.

scholarly journals Identification and Evolution Analysis of the JAZ Gene Family in Maize

2021 ◽  
Author(s):  
Yang Han ◽  
Dawn Luthe
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Gene Families ◽  
Defense Responses ◽  
Maize Genome ◽  
Synteny Analysis ◽  
Genetic Redundancy ◽  
Duplication Events

Abstract Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results: In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds.Conclusions: Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

scholarly journals Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

PLoS Biology ◽  
2021 ◽  
Vol 19 (7) ◽  
pp. e3001309
Author(s):  
Diamantis Sellis ◽  
Frédéric Guérin ◽  
Olivier Arnaiz ◽  
Walker Pett ◽  
Emmanuelle Lerat ◽  
...  
Keyword(s):  
Gene Expression ◽  
Purifying Selection ◽  
Single Copy ◽  
Paramecium Tetraurelia ◽  
Protein Coding ◽  
Sexually Transmitted ◽  
Genetic Elements ◽  
Selfish Genetic Elements ◽  
Cellular Genes ◽  
Sexual Generation

Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences called internal eliminated sequences (IESs), which have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of 9 Paramecium species (from approximately 100 Mb in Paramecium aurelia species to >1.5 Gb in Paramecium caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single copy in present-day genomes, we identified several families of mobile IESs, including nonautonomous elements acquired via horizontal transfer, which generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.

scholarly journals New insights on the function of plant acyl carrier proteins from comparative and evolutionary analysis

2019 ◽  
Author(s):  
Xuezhen Yang ◽  
Xiaoxue Liu ◽  
Yanchen Zhou ◽  
Fan Zhang ◽  
Lan Huang ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Purifying Selection ◽  
Gene Families ◽  
Acid Synthesis ◽  
Evolutionary Analysis ◽  
Sequence Motifs ◽  
Carrier Proteins ◽  
Acyl Carrier Proteins

Abstract BackgroundAcyl carrier proteins (ACPs) play a central role in both plastidial and mitochondrial Type II fatty acid synthesis in plant cells. However, a large proportion of plant ACPs remain functionally uncharacterized, and their evolutionary history remains elusive. ResultsIn present study, 97 putative ACPs were identified from ten angiosperm species examined. Based on phylogenetic analysis, ACP genes were grouped into plastidial (cpACP: ACP1/2/3/4/5) and mitochondrial (mtACP: mtACP1/mtACP2/mtACP3) ACPs. Protein sequence (motifs and length), tertiary structure, and gene structure (exon number, average intron length, and intron phase) were highly conserved in different ACP subclades. The differentiation of ACPs into distinct types occurred 85–98 and 45–57 million years ago. A limited proportion of ACP genes experience tandem or segmental duplication, corresponding to two rounds of whole genome duplication. Ka/Ks ratios revealed that duplicated ACP genes underwent a purifying selection. Regarding expression patterns, most ACPs were expressed constitutively and tissue-specifically. Notably, the average expression levels of ACP1, mtACP3, and mtACP1 were positively correlated with those of ACP3, ACP4, and mtACP2, respectively. Analysis of cis-elements showed that seven motifs (CACTFTPPCA1, DOFCOREZM, GT1CONSENSUS, CAATBOX1, ARR1AT, POLLEN1LELAT52, and GATABOX) related to tissue-specific, ABA, and light-mediated gene regulation were ubiquitous in all ACPs investigated, which shed new light on the regulation patterns of these central enzymatic partners of the FAS system. ConclusionsThis study presents a thorough overview of angiosperm ACP gene families and provides informative clues for the functional characterization of plant ACPs in the future.

scholarly journals Identification and evolution analysis of the JAZ gene family in maize

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yang Han ◽  
Dawn Luthe
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Gene Families ◽  
Defense Responses ◽  
Maize Genome ◽  
Synteny Analysis ◽  
Genetic Redundancy ◽  
Duplication Events

Abstract Background Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds. Conclusions Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

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 identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Al Stress ◽  
Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

scholarly journals Digital Gene Expression Analysis of Epithelioid and Sarcomatoid Mesothelioma Reveals Differences in Immunogenicity

Cancers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1761
Author(s):  
Luka Brcic ◽  
Alexander Mathilakathu ◽  
Robert F. H. Walter ◽  
Michael Wessolly ◽  
Elena Mairinger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Antigen Processing ◽  
Checkpoint Inhibitors ◽  
Cytotoxic T Cells ◽  
Asbestos Exposure ◽  
Gene Expression Pattern ◽  
Digital Gene Expression ◽  
Cell Interaction ◽  
Time To Death ◽  
Sarcomatoid Mesothelioma

Malignant pleural mesothelioma (MPM) is an aggressive malignancy associated with asbestos exposure. Median survival ranges from 14 to 20 months after initial diagnosis. As of November 2020, the FDA approved a combination of immune checkpoint inhibitors after promising intermediate results. Nonetheless, responses remain unsatisfying. Adequate patient stratification to improve response rates is still lacking. This retrospective study analyzed formalin fixed paraffin embedded specimens from a cohort of 22 MPM. Twelve of those samples showed sarcomatoid, ten epithelioid differentiation. Complete follow-up, including radiological assessment of response by modRECIST and time to death, was available with reported deaths of all patients. RNA of all samples was isolated and subjected to digital gene expression pattern analysis. Our study revealed a notable difference between epithelioid and sarcomatoid mesothelioma, showing differential gene expression for 304/698 expressed genes. Whereas antigen processing and presentation to resident cytotoxic T cells as well as phagocytosis is highly affected in sarcomatoid mesothelioma, cell–cell interaction via cytokines seems to be of greater importance in epithelioid cases. Our work reveals the specific role of the immune system within the different histologic subtypes of MPM, providing a more detailed background of their immunogenic potential. This is of great interest regarding therapeutic strategies including immunotherapy in mesothelioma.

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