scholarly journals Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution

2018 ◽  
Author(s):  
Shu-Miaw Chaw ◽  
Yu-Ching Liu ◽  
Han-Yu Wang ◽  
Yu-Wei Wu ◽  
Chan-Yi Ivy Lin ◽  
...  
Keyword(s):  
Gene Family Evolution ◽  
Plant Genome ◽  
Flowering Plant ◽  
Small Scale ◽  
Phylogenomic Analysis ◽  
Segmental Duplications ◽  
Duplication Events ◽  
Reference Quality ◽  
Terpenoid Synthase ◽  
Camphor Tree

AbstractWe present reference-quality genome assembly and annotation for the stout camphor tree (SCT; Cinnamomum kanehirae [Laurales, Lauraceae]), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales, and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry relative to monocots. Two whole genome duplication events were inferred within the magnoliid lineage, one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of terpenoid synthase subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.

scholarly journals Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution

Nature Plants ◽  
2019 ◽  
Vol 5 (1) ◽  
pp. 63-73 ◽  
Author(s):  
Shu-Miaw Chaw ◽  
Yu-Ching Liu ◽  
Yu-Wei Wu ◽  
Han-Yu Wang ◽  
Chan-Yi Ivy Lin ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Plant Genome ◽  
Flowering Plant ◽  
Plant Genome Evolution ◽  
Camphor Tree

scholarly journals Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean

2018 ◽  
Vol 12 (2) ◽  
pp. 119
Author(s):  
Puji Lestari ◽  
Suk-Ha Lee ◽  
I Made Tasma ◽  
Asadi Asadi
Keyword(s):  
Gene Duplication ◽  
Environmental Stress ◽  
Biotic Stress ◽  
Genome Duplication ◽  
Environmental Changes ◽  
Plant Genome ◽  
Small Scale ◽  
Duplicated Genes ◽  
Duplication Events

<p><strong>Gene duplication to reveal adaptation </strong><strong>clue</strong><strong> of plant to environmental stress: A case study of NBS-LRR genes in soybean. <em>Puji Lestari, Suk-Ha Lee</em></strong><strong><em>, I Made Tasma</em></strong><strong><em>, </em></strong><strong><em>and </em></strong><strong><em>Asadi</em></strong><strong>. </strong>Adaptive strategies of plant to stress are fine-tuned by adjusting several activities including molecular mechanism which involve duplicated genes responsive to environmental changes. Genes responsive to the environmental stresses which are retained after small scale duplication are part of plant genome duplication. However, less information of duplicated genes could be adaptive to environmental changes in plant. This review presents an overview of duplication events in plant genomes which impact to gene duplication in relation to environmental changes, gene duplication as an adaptation mechanism, a case of duplicated nucleotide binding site-<em>leucine</em>-<em>rich</em> repeat (NBS-LRR) genes in soybean, and the gene duplication implementation for plant breeding in Indonesia. Notably, genome duplication events generate gene duplication and contribute to adaptive evolution against environmental changes. Generalization of plants to adapt the stressful conditions also probably improves our understanding of gene duplication as a mechanism of adaptation. Several recently duplicated NBS-LRR genes in soybean retain disease resistance QTL and the differential expression convince their contribution to biotic stress resistance in soybean. Proposed models of NBS-LRR genes duplication process may help to understand these genes response to the environmental changes. The duplication of genes resistant to pest/disease particularly NBS-LRR provides important information to select breeding parents and develop molecular markers related to desease resistance to genetically improve soybean in Indonesia. Overall, it may therefore be possible to enhance breeding which targets on genes tolerance/resistance to abiotic/biotic stress, and provide a molecular basis for crop-stress protection strategy and more improved soybean varieties specified for harsh environment.</p>

scholarly journals The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
D. Blaine Marchant ◽  
Emily B. Sessa ◽  
Paul G. Wolf ◽  
Kweon Heo ◽  
W. Brad Barbazuk ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Green Plant ◽  
Land Plant ◽  
Plant Genome ◽  
Flowering Plant ◽  
Ceratopteris Richardii ◽  
Repeat Elements ◽  
Homosporous Fern ◽  
Homosporous Ferns ◽  
Large Genomes

AbstractFerns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.

scholarly journals Genome-Wide Analysis of WRKY Gene Family and the Dynamic Responses of Key WRKY Genes Involved in Ostrinia furnacalis Attack in Zea mays

2021 ◽  
Vol 22 (23) ◽  
pp. 13045
Author(s):  
Yin Tang ◽  
Jingfei Guo ◽  
Tiantao Zhang ◽  
Shuxiong Bai ◽  
Kanglai He ◽  
...  
Keyword(s):  
Gene Family ◽  
Target Genes ◽  
Gene Families ◽  
Dynamic Responses ◽  
Phylogenomic Analysis ◽  
Maize Genome ◽  
Wrky Gene ◽  
Ostrinia Furnacalis ◽  
Corn Borer ◽  
Duplication Events

WRKY transcription factors comprise one of the largest gene families and serve as key regulators of plant defenses against herbivore attack. However, studies related to the roles of WRKY genes in response to herbivory are limited in maize. In this study, a total of 128 putative maize WRKY genes (ZmWRKYs) were identified from the new maize genome (v4). These genes were divided into seven subgroups (groups I, IIa–e, and III) based on phylogenomic analysis, with distinct motif compositions in each subgroup. Syntenic analysis revealed that 72 (56.3%) of the genes were derived from either segmental or tandem duplication events (69 and 3, respectively), suggesting a pivotal role of segmental duplication in the expansion of the ZmWRKY family. Importantly, transcriptional regulation prediction showed that six key WRKY genes contribute to four major defense-related pathways: L-phenylalanine biosynthesis II and flavonoid, benzoxazinoid, and jasmonic acid (JA) biosynthesis. These key WRKY genes were strongly induced in commercial maize (Jingke968) infested with the Asian corn borer, Ostrinia furnacalis, for 0, 2, 4, 12 and 24 h in the field, and their expression levels were highly correlated with predicted target genes, suggesting that these genes have important functions in the response to O. furnacalis. Our results provide a comprehensive understanding of the WRKY gene family based on the new assembly of the maize genome and lay the foundation for further studies into functional characteristics of ZmWRKY genes in commercial maize defenses against O. furnacalis in the field.

scholarly journals Mechanistic insights into the evolution of DUF26-containing proteins in land plants

2018 ◽  
Author(s):  
Aleksia Vaattovaara ◽  
Benjamin Brandt ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
Andres Veidenberg ◽  
...  
Keyword(s):  
Size Variation ◽  
Gene Families ◽  
Land Plants ◽  
Small Scale ◽  
Carbohydrate Binding ◽  
Whole Genome ◽  
Domain Of Unknown Function ◽  
Duplication Events ◽  
New Gene ◽  
Dosage Balance

AbstractLarge protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation in plants. Here we infer the evolutionary history of a representative protein family, the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 first appeared in secreted proteins. Domain duplications and rearrangements led to the emergence of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). While the DUF26 itself is specific to land plants, structural analyses of Arabidopsis PDLP5 and PDLP8 ectodomains revealed strong similarity to fungal lectins. Therefore, we propose that DUF26-containing proteins constitute a novel group of plant carbohydrate-binding proteins. Following their appearance, CRKs expanded both through tandem duplications and preferential retention of duplicates in whole genome duplication events, whereas PDLPs evolved according to the dosage balance hypothesis. Based on our findings, we suggest that the main mechanism of expansion in new gene families is small-scale duplication, whereas genome fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.

scholarly journals Pangenomic analysis reveals pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

2017 ◽  
Author(s):  
Andrew D. Armitage ◽  
Andrew Taylor ◽  
Maria K. Sobczyk ◽  
Laura Baxter ◽  
Bethany P.J. Greenfield ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Fold Increase ◽  
Rna Seq ◽  
In Planta ◽  
Basal Rot ◽  
Expression Studies ◽  
Duplication Events ◽  
Reference Quality ◽  
Syntenic Conservation ◽  
Onion Basal Rot

AbstractA reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage.Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core.RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta.

Phylogenomic analysis reveals ancient segmental duplications in the human genome

2016 ◽  
Vol 94 ◽  
pp. 95-100 ◽  
Author(s):  
Madiha Hafeez ◽  
Madiha Shabbir ◽  
Fouzia Altaf ◽  
Amir Ali Abbasi
Keyword(s):  
Human Genome ◽  
Phylogenomic Analysis ◽  
Segmental Duplications

scholarly journals Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Wen ◽  
Peng-Feng Li ◽  
Feng Ran ◽  
Peng-Cheng Guo ◽  
Jia-Tian Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Small Scale ◽  
Preferential Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Duplication Events ◽  
Small Scale Duplication

Abstract Background NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we report the global characterization of NPF in the important oil crop Brassica napus, including that for phylogeny, gene/protein structures, duplications, and expression patterns. Results A total of 199 B. napus (BnaNPFs) NPF-coding genes were identified. Phylogenetic analyses categorized these genes into 11 subfamilies, including three new ones. Sequence feature analysis revealed that members of each subfamily contain conserved gene and protein structures. Many hormone−/abiotic stress-responsive cis-acting elements and transcription factor binding sites were identified in BnaNPF promoter regions. Chromosome distribution analysis indicated that BnaNPFs within a subfamily tend to cluster on one chromosome. Syntenic relationship analysis showed that allotetraploid creation by its ancestors (Brassica rapa and Brassica oleracea) (57.89%) and small-scale duplication events (39.85%) contributed to rapid BnaNPF expansion in B. napus. A genome-wide spatiotemporal expression survey showed that NPF genes of each Arabidopsis and B. napus subfamily have preferential expression patterns across developmental stages, most of them are expressed in a few organs. RNA-seq analysis showed that many BnaNPFs (32.66%) have wide exogenous hormone-inductive profiles, suggesting important hormone-mediated patterns in diverse bioprocesses. Homologs in a clade or branch within a given subfamily have conserved organ/spatiotemporal and hormone-inductive profiles, indicating functional conservation during evolution. qRT-PCR-based comparative expression analysis of the 12 BnaNPFs in the NPF2–1 subfamily between high- and low-glucosinolate (GLS) content B. napus varieties revealed that homologs of AtNPF2.9 (BnaNPF2.12, BnaNPF2.13, and BnaNPF2.14), AtNPF2.10 (BnaNPF2.19 and BnaNPF2.20), and AtNPF2.11 (BnaNPF2.26 and BnaNPF2.28) might be involved in GLS transport. qRT-PCR further confirmed the hormone-responsive expression profiles of these putative GLS transporter genes. Conclusion We identified 199 B. napus BnaNPFs; these were divided into 11 subfamilies. Allopolyploidy and small-scale duplication events contributed to the immense expansion of BnaNPFs in B. napus. The BnaNPFs had preferential expression patterns in different tissues/organs and wide hormone-induced expression profiles. Four BnaNPFs in the NPF2–1 subfamily may be involved in GLS transport. Our results provide an abundant gene resource for further functional analysis of BnaNPFs.

scholarly journals Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

2017 ◽  
Vol 114 (22) ◽  
pp. E4435-E4441 ◽  
Author(s):  
Tianying Lan ◽  
Tanya Renner ◽  
Enrique Ibarra-Laclette ◽  
Kimberly M. Farr ◽  
Tien-Hao Chang ◽  
...  
Keyword(s):  
Genome Structure ◽  
Nuclear Genome ◽  
Carnivorous Plant ◽  
Plant Genome ◽  
Peptide Transport ◽  
Special Importance ◽  
Specific Expression ◽  
Gene Copies ◽  
Duplication Events ◽  
Syntenic Gene

Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

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