Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene familiesThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

The completion of the Populus trichocarpa (Torr. & A. Gray) (poplar) genome sequence offers an opportunity to study complete genome families in a third fully sequenced angiosperm (after Arabidopsis and rice) and to conduct comparative genomics studies of angiosperm gene family evolution. We focussed on gene families encoding phenylpropanoid and phenylpropanoid-like enzymes, and identified and annotated the full set of genes encoding these and related enzymes in the poplar genome. We used a similar approach to identify an analogous set of genes from the rice genome and generated phylogenetic trees for nine phenylpropanoid gene families from aligned poplar, Arabidopsis, and rice predicted protein sequences. This enabled us to identify the likely full set of bona fide poplar lignin-related phenylpropanoid genes (poplar “lignification toolbox”) apparent within well-defined clades in all phylogenetic trees. Analysis of expression data for poplar genes confirmed and refined annotations of lignin-related genes, which generally showed high expression in wood-forming tissues. Expression data from both poplar and Arabidopsis were used to make inferences regarding biochemical and biological functions of phenylpropanoid-like genes with unknown functions. The comparative approach also provided insights into the evolution of angiosperm phenylpropanoid-like gene families, illustrating lineage-specific clades as well as ancient clades containing genes with apparent conserved function.

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Gene families and evolution of trehalose metabolism in plants

Functional Plant Biology ◽

10.1071/fp06315 ◽

2007 ◽

Vol 34 (6) ◽

pp. 550 ◽

Cited By ~ 82

Author(s):

John E. Lunn

Keyword(s):

Physcomitrella Patens ◽

Oryza Sativa L ◽

Populus Trichocarpa ◽

Gene Families ◽

Class I ◽

Trehalose Metabolism ◽

Genes Encoding ◽

Catalytically Active ◽

Large Families ◽

Selaginella Moellendorffii

The genomes of Arabidopsis thaliana L., rice (Oryza sativa L.) and poplar (Populus trichocarpa Torr. & A.Gray) contain large families of genes encoding trehalose-phosphate synthase (TPS) and trehalose-phosphatase (TPP). The class I subfamily of TPS genes encodes catalytically active TPS enzymes, and is represented by only one or two genes in most species. A. thaliana is atypical in having four class I TPS genes, three of which (AtTPS2–4) encode unusual short isoforms of TPS that appear to be found only in members of the Brassicaceae family. The class II TPS genes encode TPS-like proteins with a C-terminal TPP-like domain, but there is no experimental evidence that they have any enzymatic activity and their function is unknown. Both classes of TPS gene are represented in the genomes of chlorophyte algae (Ostreococcus species) and non-flowering plants [Physcomitrella patens (Hedw.) Bruch & Schimp.(B.S.G.) and Selaginella moellendorffii (Hieron. in Engl. & Prantl.)]. This survey shows that the gene families encoding the enzymes of trehalose metabolism are very ancient, pre-dating the divergence of the streptophyte and chlorophyte lineages. It also provides a frame of reference for future studies to elucidate the function of trehalose metabolism in plants.

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Identification of RING-H2 Gene Candidates Related to Wood Formation in Poplar

Forests ◽

10.3390/f10080698 ◽

2019 ◽

Vol 10 (8) ◽

pp. 698

Author(s):

Guimin Tong ◽

Hongmei Shen ◽

Shenquan Cao ◽

Wenjing Xu ◽

Xujun Ma ◽

...

Keyword(s):

Tandem Duplication ◽

Populus Trichocarpa ◽

Microarray Dataset ◽

Wood Formation ◽

Multiple Gene ◽

Poplar Genome ◽

Gene Expression Analyses ◽

Genes Encoding ◽

Duplication Events ◽

Ubiquitin Ligase E3

RING-H2 genes, the most abundant RING-type genes encoding putative ubiquitin ligase E3, are involved in diverse biological processes. Whether RING-H2 genes are related to wood formation remains to be identified in trees. In this study, we identified 288 RING-H2 genes in Populus trichocarpa, and found that the segmental and tandem duplication events contributed to RING-H2 gene expansion. Microarray dataset (from Affymetrix poplar genome arrays) showed that 64 of the 249 RING-H2 genes were highly or preferentially expressed in stem xylem. According to the AspWood RNAseq dataset, the transcription levels of genes PtrRHH21, 33, 48, 69, 88, 93, 94, 121, 141, 166, 175, 192, 208, 214, 250 and 257 were significantly increased in the xylem ranging from the expanding xylem to the lignifying xylem, suggesting their association with wood formation. Promoter analyses revealed that most of the preferentially xylem-expressed RING-H2 genes possessed SNBE, TERE, M46RE, AC and SMRE cis-elements, which are involved in secondary cell wall biosynthesis and programmed cell death. Based on the promoter GUS-based analysis result, PtrRHH94 was indicated to be associated with wood formation in transgenic P. trichocarpa. Taken together, dozens of Populus RING-H2 gene candidates associated with wood formation have been identified based on multiple gene expression analyses.

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The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics

Journal of Pathogens ◽

10.4061/2011/716041 ◽

2011 ◽

Vol 2011 ◽

pp. 1-11 ◽

Cited By ~ 33

Author(s):

Stéphane Hacquard ◽

Benjamin Petre ◽

Pascal Frey ◽

Arnaud Hecker ◽

Nicolas Rouhier ◽

...

Keyword(s):

Populus Trichocarpa ◽

Rust Fungus ◽

Gene Families ◽

Genetic Determinants ◽

Plant Host ◽

Recombinant Protein Purification ◽

Functional Studies ◽

Regulated Expression ◽

Genes Encoding ◽

Host Tissues

Poplars are extensively cultivated worldwide, and their susceptibility to the leaf rust fungusMelampsora larici-populinaleads to considerable damages in plantations. Despite a good knowledge of the poplar rust life cycle, and particularly the epidemics on poplar, the perennial status of the plant host and the obligate biotrophic lifestyle of the rust fungus are bottlenecks for molecular investigations. Following the completion of bothM. larici-populinaandPopulus trichocarpagenome sequences, gene families involved in poplar resistance or in rust fungus virulence were investigated, allowing the identification of key genetic determinants likely controlling the outcome of the interaction. Specific expansions of resistance and defense-related genes in poplar indicate probable innovations in perennial species in relation with host-pathogen interactions. The genome ofM. Larici-populinacontains a strikingly high number of genes encoding small secreted proteins (SSPs) representing hundreds of candidate effectors. Transcriptome analyses of interacting partners in compatible and incompatible interactions revealed conserved set of genes involved in poplar defense reactions as well as timely regulated expression of SSP transcripts during host tissues colonisation. Ongoing functional studies of selected candidate effectors will be achieved mainly on the basis of recombinant protein purification and subsequent characterisation.

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A peroxisomal β-oxidative pathway contributes to the formation of C6–C1 aromatic volatiles in poplar

Plant Physiology ◽

10.1093/plphys/kiab111 ◽

2021 ◽

Author(s):

Nathalie D Lackus ◽

Axel Schmidt ◽

Jonathan Gershenzon ◽

Tobias G Köllner

Keyword(s):

Cinnamic Acid ◽

Aromatic Compounds ◽

Populus Trichocarpa ◽

Alternative Pathway ◽

Gene Families ◽

Defense Responses ◽

In Planta ◽

Black Cottonwood ◽

Oxidative Pathway

AbstractBenzenoids (C6–C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6–C3). The biosynthesis of C6–C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6–C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

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Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽

10.1093/genetics/159.4.1765 ◽

2001 ◽

Vol 159 (4) ◽

pp. 1765-1778

Author(s):

Gregory J Budziszewski ◽

Sharon Potter Lewis ◽

Lyn Wegrich Glover ◽

Jennifer Reineke ◽

Gary Jones ◽

...

Keyword(s):

Large Scale ◽

Protein Translocation ◽

Gene Families ◽

Mutant Phenotype ◽

Lethal Mutant ◽

A Genome ◽

Genes Encoding ◽

High Level ◽

Mutant Lines ◽

Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

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Amynthas corticis genome reveals molecular mechanisms behind global distribution

Communications Biology ◽

10.1038/s42003-021-01659-4 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Xing Wang ◽

Yi Zhang ◽

Yufeng Zhang ◽

Mingming Kang ◽

Yuanbo Li ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Mechanisms ◽

Gene Families ◽

The Body ◽

Gene Family Evolution ◽

Complex Environments ◽

Protein Coding ◽

Itraq Analysis ◽

Rdna Sequencing ◽

Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

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New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update

10.21203/rs.3.rs-1201297/v1 ◽

2021 ◽

Author(s):

Fangfang Huang ◽

Yingru Jiang ◽

Tiantian Chen ◽

Haoran Li ◽

Mengjia Fu ◽

...

Keyword(s):

Functional Genomics ◽

Rice Genome ◽

Model Organism ◽

Gene Families ◽

Food Crop ◽

Protein Coding ◽

Protein Coding Genes ◽

Major Food

Abstract As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ∼2800 functionally characterized rice genes and ∼5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 49,000 users with over 490,000 page views. The funRiceGenes database has been continuously updated with newly cloned rice genes and newly published literature, based on the progress of rice functional genomics studies. Up to Nov 2021, ≥4100 functionally characterized rice genes and ∼6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new features in the last five years.

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Characterization of Epidemic IncI1-Iγ Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella enterica from Animals and Humans

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05006-14 ◽

2015 ◽

Vol 59 (9) ◽

pp. 5357-5365 ◽

Cited By ~ 36

Author(s):

Hilde Smith ◽

Alex Bossers ◽

Frank Harders ◽

Guanghui Wu ◽

Neil Woodford ◽

...

Keyword(s):

Escherichia Coli ◽

Salmonella Enterica ◽

Phylogenetic Trees ◽

Functional Study ◽

Content Type ◽

Gene Associations ◽

Genes Encoding ◽

Marked Resistance

ABSTRACTThe aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-Iγ plasmids obtained fromEscherichia coliandSalmonella entericaisolates from animal and human reservoirs. For this, 251 IncI1-Iγ plasmids carrying various extended-spectrum β-lactamase (ESBL) or AmpC β-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-Iγ plasmids could be assigned to various dominant clades, whereas rarely detected plasmids clustered together as a distinct clade. Similar phylogenetic trees were obtained using only the plasmid backbone sequences, showing that the differences observed between the plasmids belonging to distinct clades resulted mainly from differences between their backbone sequences. Plasmids belonging to the various clades differed particularly in the presence/absence of genes encoding partitioning and addiction systems, which contribute to stable inheritance during cell division and plasmid maintenance. Despite this, plasmids belonging to the various phylogenetic clades also showed marked resistance gene associations, indicating the circulation of successful plasmid-gene combinations. The variation intraYandexcAgenes found in IncI1-Iγ plasmids is conserved within pMLST sequence types and plays a role in incompatibility, although functional study is needed to elucidate the role of these genes in plasmid epidemiology.

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Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0009665 ◽

2021 ◽

Vol 15 (8) ◽

pp. e0009665

Author(s):

Shuai Xu ◽

Zhenpeng Li ◽

Yuanming Huang ◽

Lichao Han ◽

Yanlin Che ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Gene Families ◽

Single Copy ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Evolutionary Relationships ◽

Taxonomic Structure ◽

Pan Genome ◽

Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

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Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei

10.1101/2021.03.14.435331 ◽

2021 ◽

Author(s):

Kim Vertacnik ◽

Danielle Herrig ◽

R Keating Godfrey ◽

Tom Hill ◽

Scott Geib ◽

...

Keyword(s):

Gene Family ◽

Family Size ◽

Draft Genome ◽

Gene Families ◽

Gene Family Evolution ◽

Gene Gain ◽

Ecological Specialization ◽

Dietary Specialization ◽

Pine Sawfly ◽

Neodiprion Lecontei

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions and characterized their genomic distributions and evolutionary history. Our results suggest that expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), and antimicrobial peptide (AMP) subfamilies may have contributed to pine adaptation. By contrast, there was no evidence of recent gene family contraction via pseudogenization. Next, we compared the number of genes in these same families across insect taxa that vary in diet, dietary specialization, and social behavior. In Hymenoptera, herbivory was associated with large GR and small olfactory receptor (OR) families, eusociality was associated with large OR and small AMP families, and--unlike investigations among more closely related taxa--ecological specialization was not related to gene family size. Overall, our results suggest that gene families that mediate ecological interactions may expand and contract predictably in response to particular selection pressures, however, the ecological drivers and temporal pace of gene gain and loss likely varies considerably across gene families.

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