Phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate Hox clusters

Pathogens hitting the plant cell wall is the first impetus that triggers the phenylpropanoid pathway for plant defense. The phenylpropanoid pathway bifurcates into the production of an enormous array of compounds based on the few intermediates of the shikimate pathway in response to cell wall breaches by pathogens. The whole metabolomic pathway is a complex network regulated by multiple gene families and it exhibits refined regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. The pathway genes are involved in the production of anti-microbial compounds as well as signaling molecules. The engineering in the metabolic pathway has led to a new plant defense system of which various mechanisms have been proposed including salicylic acid and antimicrobial mediated compounds. In recent years, some key players like phenylalanine ammonia lyases (PALs) from the phenylpropanoid pathway are proposed to have broad spectrum disease resistance (BSR) without yield penalties. Now we have more evidence than ever, yet little understanding about the pathway-based genes that orchestrate rapid, coordinated induction of phenylpropanoid defenses in response to microbial attack. It is not astonishing that mutants of pathway regulator genes can show conflicting results. Therefore, precise engineering of the pathway is an interesting strategy to aim at profitably tailored plants. Here, this review portrays the current progress and challenges for phenylpropanoid pathway-based resistance from the current prospective to provide a deeper understanding.

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Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

Genome Biology and Evolution ◽

10.1093/gbe/evaa060 ◽

2020 ◽

Vol 12 (6) ◽

pp. 948-964

Author(s):

Melissa B DeBiasse ◽

William N Colgan ◽

Lincoln Harris ◽

Bradley Davidson ◽

Joseph F Ryan

Keyword(s):

Gene Loss ◽

Morphological Diversity ◽

Gene Families ◽

Model Species ◽

Hox Gene ◽

Hox Cluster ◽

Species Phylogeny ◽

Potential Impact ◽

Important Nodes ◽

Hox Clusters

Abstract Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, “inflated” atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.

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Development and Characterisation of Irap Markers From Expressed Retrotransposon-like sequences in Pinus sylvestris L.

Proceedings of the Latvian Academy of Sciences Section B Natural Exact and Applied Sciences ◽

10.2478/prolas-2013-0082 ◽

2014 ◽

Vol 67 (6) ◽

pp. 485-492 ◽

Cited By ~ 1

Author(s):

Angelika Voronova ◽

Dainis Ruņģis

Keyword(s):

Genetic Diversity ◽

Pinus Sylvestris ◽

Scots Pine ◽

Repetitive Sequences ◽

Gene Families ◽

Considerable Proportion ◽

Long Terminal Repeats ◽

Multiple Gene ◽

Plant Genomes

AbstractConifer genomes are large and stably diploid, in contrast to angiosperms, which are more variable both in genome size and ploidy. Conifer genomes are characterised by multiple gene families and pseudogenes, contain large inter-gene regions and a considerable proportion of repetitive sequences. All members of plant retrotransposon orders have been identified in gymnosperm genomes, however active elements have not been described. Investigation of transposable elements in Scots pine (Pinus sylvestris L.) could offer insights into transposon-mediated reorganisation under stress conditions in complex and ancient plant genomes. Nine Pinus sylvestris specific markers were developed to hypothetical long terminal repeats (LTRs) from differentially expressed retrotransposon-like fragments after heat stress and insect damage. Genetic diversity of 150 trees from a naturally regenerated pine stand was investigated using the IRAP method. The developed markers revealed high levels of genetic diversity and were able to distinguish subpopulations growing in long-term differential environmental conditions. Somaclonal variation was also investigated using these markers and polymorphic fragments were identified between ramets of Scots pine clones growing in two different plantations, possibly indicating evidence of recent transposition events. Sequencing of the polymorphic fragments identified two groups of sequences containing LTR sequences of an unknown retrotransposon with homology to the LTRs of the Copia-17-PAb-I element.

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Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress

The Plant Journal ◽

10.1046/j.1365-313x.2003.01839.x ◽

2003 ◽

Vol 35 (6) ◽

pp. 675-692 ◽

Cited By ~ 200

Author(s):

Frans J. M. Maathuis ◽

Victor Filatov ◽

Pawel Herzyk ◽

Gerard C. Krijger ◽

Kristian B. Axelsen ◽

...

Keyword(s):

Transcriptome Analysis ◽

Gene Families ◽

Multiple Gene

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Efficient marker free CRISPR/Cas9 genome editing for functional analysis of gene families in filamentous fungi

Fungal Biology and Biotechnology ◽

10.1186/s40694-019-0076-7 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 11

Author(s):

Tim M. van Leeuwe ◽

Mark Arentshorst ◽

Tim Ernst ◽

Ebru Alazi ◽

Peter J. Punt ◽

...

Keyword(s):

Genome Editing ◽

Filamentous Fungi ◽

Marker Gene ◽

Gene Families ◽

Selection Marker ◽

Dna Fragments ◽

Additional Advantage ◽

Multiple Gene ◽

Large Gene ◽

Marker Free

Abstract Background CRISPR/Cas9 mediated genome editing has expedited the way of constructing multiple gene alterations in filamentous fungi, whereas traditional methods are time-consuming and can be of mutagenic nature. These developments allow the study of large gene families that contain putatively redundant genes, such as the seven-membered family of crh-genes encoding putative glucan–chitin crosslinking enzymes involved in cell wall biosynthesis. Results Here, we present a CRISPR/Cas9 system for Aspergillus niger using a non-integrative plasmid, containing a selection marker, a Cas9 and a sgRNA expression cassette. Combined with selection marker free knockout repair DNA fragments, a set of the seven single knockout strains was obtained through homology directed repair (HDR) with an average efficiency of 90%. Cas9–sgRNA plasmids could effectively be cured by removing selection pressure, allowing the use of the same selection marker in successive transformations. Moreover, we show that either two or even three separate Cas9–sgRNA plasmids combined with marker-free knockout repair DNA fragments can be used in a single transformation to obtain double or triple knockouts with 89% and 38% efficiency, respectively. By employing this technique, a seven-membered crh-gene family knockout strain was acquired in a few rounds of transformation; three times faster than integrative selection marker (pyrG) recycling transformations. An additional advantage of the use of marker-free gene editing is that negative effects of selection marker gene expression are evaded, as we observed in the case of disrupting virtually silent crh family members. Conclusions Our findings advocate the use of CRISPR/Cas9 to create multiple gene deletions in both a fast and reliable way, while simultaneously omitting possible locus-dependent-side-effects of poor auxotrophic marker expression.

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Cloning and sequencing of tubulin cDNAs from Artemia franciscana: evidence for differential expression of α- and β-tubulin genes

Biochemistry and Cell Biology ◽

10.1139/o09-050 ◽

2009 ◽

Vol 87 (6) ◽

pp. 989-997 ◽

Cited By ~ 1

Author(s):

Katy A. Garant ◽

Thomas H. MacRae

Keyword(s):

Allelic Variation ◽

Gene Families ◽

Artemia Franciscana ◽

Multiple Gene ◽

Cdna Sequences ◽

Life History Stages ◽

Tubulin Genes ◽

Tubulin Mrna ◽

Developmental Phases ◽

Β Tubulin

Tubulin is a heterodimeric protein composed of α- and β-tubulin. In most organisms, they are encoded by multiple gene families whose members are subject to differential regulation. The objective of the work described herein was to better understand tubulin gene expression in the extremophile Artemia franciscana To this end tubulin cDNAs were cloned and sequenced. αAT2, an α-tubulin cDNA, differed by one nucleotide from αAT1, a previously cloned Artemia cDNA. This change, possibly generated by allelic variation, caused an M313V substitution in α-tubulin. The amino acid sequence of β-tubulin encoded by βAT1, one of only a very limited number of cloned crustacean β-tubulin cDNA sequences yet available, and the first from Artemia, was similar to other β-tubulins. However, βAT1 possessed four degenerate TATA boxes in the 5′ untranslated region, although authentic TATA and CCAAT boxes occurred in the 3′ non-coding sequence. Analyses by quantitative PCR demonstrated that the amount of tubulin mRNA declined relative to total mRNA in progressive life history stages of Artemia and also that the organism contained more αAT2- than βAT1-tubulin mRNA at all developmental phases examined.

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The recent escalation in strength of pyrethroid resistance in Anopheles coluzzi in West Africa is linked to increased expression of multiple gene families

BMC Genomics ◽

10.1186/s12864-015-1342-6 ◽

2015 ◽

Vol 16 (1) ◽

pp. 146 ◽

Cited By ~ 46

Author(s):

Kobié H Toé ◽

Sagnon N’Falé ◽

Roch K Dabiré ◽

Hilary Ranson ◽

Christopher M Jones

Keyword(s):

West Africa ◽

Pyrethroid Resistance ◽

Gene Families ◽

Multiple Gene

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Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer

Nature Communications ◽

10.1038/s41467-021-21093-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Eivind A. B. Undheim ◽

Ronald A. Jenner

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogenetic Analyses ◽

Gene Families ◽

Venom Gland ◽

Bacterial Gene ◽

Multiple Gene ◽

Genomic Analyses ◽

Endogenous Proteins ◽

Animal Venoms

AbstractVenoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show that centipede venoms have recruited at least five gene families from bacterial and fungal donors, involving at least eight horizontal gene transfer events. These results establish centipedes as currently the only known animals with venoms used in predation and defence that contain multiple gene families derived from horizontal gene transfer. The results also provide the first evidence for the implication of horizontal gene transfer in the evolutionary origin of venom in an animal lineage. Three of the bacterial gene families encode virulence factors, suggesting that horizontal gene transfer can provide a fast track channel for the evolution of novelty by the exaptation of bacterial weapons into animal venoms.

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Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.0803 ◽

2021 ◽

Vol 288 (1955) ◽

pp. 20210803

Author(s):

Xiuping Zhang ◽

David Blair ◽

Justyna Wolinska ◽

Xiaolin Ma ◽

Wenwu Yang ◽

...

Keyword(s):

Predation Risk ◽

Community Dynamics ◽

Transcriptional Profiling ◽

Gene Families ◽

Multiple Gene ◽

Fish Kairomone ◽

Apoptosis Pathways ◽

Genomic Regions ◽

Cycle Regulation ◽

Perceived Predation Risk

Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri , a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow Daphnia to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow Daphnia to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.

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New insights into heparan sulphate biosynthesis from the study of mutant mice

Biochemical Society Symposium ◽

10.1042/bss0690047 ◽

2002 ◽

Vol 69 ◽

pp. 47-57 ◽

Cited By ~ 8

Author(s):

Catherine L. R. Merry ◽

John T. Gallagher

Keyword(s):

Growth Factors ◽

Biosynthetic Pathway ◽

Heparan Sulphate ◽

Mutant Mice ◽

Gene Products ◽

Multiple Gene ◽

Adhesion Proteins ◽

Ligand Interactions

Heparan sulphate (HS) is an essential co-receptor for a number of growth factors, morphogens and adhesion proteins. The biosynthetic modifications involved in the generation of a mature HS chain may determine the strength and outcome of HS–ligand interactions. These modifications are catalysed by a complex family of enzymes, some of which occur as multiple gene products. Various mutant mice have now been generated, which lack the function of isolated components of the HS biosynthetic pathway. In this discussion, we outline the key findings of these studies, and use them to put into context our own work concerning the structure of the HS generated by the Hs2st-/- mice.

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