Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)

Abstract Background In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. Results In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. Conclusions Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.

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The opium poppy genome and morphinan production

Science ◽

10.1126/science.aat4096 ◽

2018 ◽

Vol 362 (6412) ◽

pp. 343-347 ◽

Cited By ~ 51

Author(s):

Li Guo ◽

Thilo Winzer ◽

Xiaofei Yang ◽

Yi Li ◽

Zemin Ning ◽

...

Keyword(s):

Whole Genome Duplication ◽

Gene Fusion ◽

Genome Duplication ◽

Papaver Somniferum ◽

Opium Poppy ◽

Whole Genome ◽

Synteny Analysis ◽

Benzylisoquinoline Alkaloid ◽

Metabolic Products ◽

Insight Into

Morphinan-based painkillers are derived from opium poppy (Papaver somniferumL.). We report a draft of the opium poppy genome, with 2.72 gigabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 1.77 and 204 megabases, respectively. Synteny analysis suggests a whole-genome duplication at ~7.8 million years ago and ancient segmental or whole-genome duplication(s) that occurred before the Papaveraceae-Ranunculaceae divergence 110 million years ago. Syntenic blocks representative of phthalideisoquinoline and morphinan components of a benzylisoquinoline alkaloid cluster of 15 genes provide insight into how this cluster evolved. Paralog analysis identified P450 and oxidoreductase genes that combined to form theSTORRgene fusion essential for morphinan biosynthesis in opium poppy. Thus, gene duplication, rearrangement, and fusion events have led to evolution of specialized metabolic products in opium poppy.

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Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2009.1592 ◽

2009 ◽

Vol 277 (1683) ◽

pp. 869-876 ◽

Cited By ~ 17

Author(s):

Gavin C. Conant

Keyword(s):

Transcription Factors ◽

Regulatory Network ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Transcriptional Regulatory Network ◽

Whole Genome ◽

Functional Roles ◽

Transcriptional Regulatory ◽

Dosage Balance ◽

Tf Gene

I study the reorganization of the yeast transcriptional regulatory network after whole-genome duplication (WGD). Individual transcription factors (TFs) were computationally removed from the regulatory network, and the resulting networks were analysed. TF gene pairs that survive in duplicate from WGD show detectable redundancy as a result of that duplication. However, in most other respects, these duplicated TFs are indistinguishable from other TFs in the genome, suggesting that the duplicate TFs produced by WGD were rapidly diverted to distinct functional roles in the regulatory network. Separately, I find that genes targeted by many TFs appear to be preferentially retained in duplicate after WGD, an effect I attribute to selection to maintain dosage balance in the regulatory network after WGD.

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Faculty Opinions recommendation of Reciprocal gene loss following experimental whole-genome duplication causes reproductive isolation in yeast.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.10069956.10824063 ◽

2011 ◽

Author(s):

Santiago F Elena ◽

Stéphanie Bedhomme

Keyword(s):

Reproductive Isolation ◽

Whole Genome Duplication ◽

Gene Loss ◽

Genome Duplication ◽

Whole Genome

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Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽

10.1093/genetics/156.3.1249 ◽

2000 ◽

Vol 156 (3) ◽

pp. 1249-1257

Author(s):

Ilya Ruvinsky ◽

Lee M Silver ◽

Jeremy J Gibson-Brown

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Gene Families ◽

Vertebrate Evolution ◽

Whole Genome ◽

Vertebrate Genome ◽

T Box ◽

Genetic Complexity ◽

History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

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Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

G3 Genes|Genome|Genetics ◽

10.1534/g3.114.012294 ◽

2014 ◽

Vol 4 (9) ◽

pp. 1717-1730 ◽

Cited By ~ 37

Author(s):

M. Kodama ◽

M. S. O. Brieuc ◽

R. H. Devlin ◽

J. J. Hard ◽

K. A. Naish

Keyword(s):

Comparative Mapping ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Coho Salmon ◽

Chromosomal Rearrangements ◽

Oncorhynchus Kisutch ◽

Duplication Event ◽

Whole Genome ◽

Genome Duplication Event ◽

Whole Genome Duplication Event

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Whole-Genome DNA Methylation Analysis in Hydrogen Peroxide Overproducing Transgenic Tobacco Resistant to Biotic and Abiotic Stresses

Plants ◽

10.3390/plants10010178 ◽

2021 ◽

Vol 10 (1) ◽

pp. 178

Author(s):

Ana L. Villagómez-Aranda ◽

Luis F. García-Ortega ◽

Irineo Torres-Pacheco ◽

Ramón G. Guevara-González

Keyword(s):

Hydrogen Peroxide ◽

Dna Methylation ◽

Transgenic Tobacco ◽

Stress Responses ◽

Abiotic Stresses ◽

Methylation Status ◽

Physiological Adaptation ◽

Whole Genome ◽

Sequencing Analysis ◽

Biotic And Abiotic Stresses

Epigenetic regulation is a key component of stress responses, acclimatization and adaptation processes in plants. DNA methylation is a stable mark plausible for the inheritance of epigenetic traits, such that it is a potential scheme for plant breeding. However, the effect of modulators of stress responses, as hydrogen peroxide (H2O2), in the methylome status has not been elucidated. A transgenic tobacco model to the CchGLP gene displayed high H2O2 endogen levels correlated with biotic and abiotic stresses resistance. The present study aimed to determine the DNA methylation status changes in the transgenic model to obtain more information about the molecular mechanism involved in resistance phenotypes. The Whole-genome bisulfite sequencing analysis revealed a minimal impact of overall levels and distribution of methylation. A total of 9432 differential methylated sites were identified in distinct genome regions, most of them in CHG context, with a trend to hypomethylation. Of these, 1117 sites corresponded to genes, from which 83 were also differentially expressed in the plants. Several genes were associated with respiration, energy, and calcium signaling. The data obtained highlighted the relevance of the H2O2 in the homeostasis of the system in stress conditions, affecting at methylation level and suggesting an association of the H2O2 in the physiological adaptation to stress functional linkages may be regulated in part by DNA methylation.

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Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

Genome Biology ◽

10.1186/s13059-021-02323-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gareth B. Gillard ◽

Lars Grønvold ◽

Line L. Røsæg ◽

Matilde Mengkrog Holen ◽

Øystein Monsen ◽

...

Keyword(s):

Genome Evolution ◽

Whole Genome Duplication ◽

Genome Stability ◽

Genome Duplication ◽

Gene Dosage ◽

Whole Genome ◽

Specific Expression ◽

Tissue Specific ◽

Genome Doubling ◽

Expression Evolution

Abstract Background Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago. Results We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. Conclusions Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

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Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

Nature Communications ◽

10.1038/s41467-020-20508-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Amit Rai ◽

Hideki Hirakawa ◽

Ryo Nakabayashi ◽

Shinji Kikuchi ◽

Koki Hayashi ◽

...

Keyword(s):

Genome Assembly ◽

Whole Genome Duplication ◽

Experimental Validation ◽

Genome Duplication ◽

Indole Alkaloids ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Plant Genomes ◽

Genome Triplication ◽

Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

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