The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with significant potential for expanded cultivation as a biodiesel feedstock. The remarkable stress resilience of B. carinata and desirable seed fatty acid profile addresses the ongoing food vs. fuel debate as the crop is productive on marginal lands otherwise not suitable for even closely related species. B. carinata is one of six key Brassica spp. that share three major genomes: three diploid species (AA, BB, CC) that spontaneously hybridized in a pairwise manner, forming three allotetraploid species (AABB, AACC, and BBCC). Each of these genomes has been researched extensively, except for that of B. carinata. In the present study, we report a high-quality, 1.31 Gbp genome with 156.9-fold sequencing coverage for B. carinata var. Gomenzer, completing and confirming the classic Triangle of U, a theory of the evolutionary relationships among these six species that arose almost a century ago. Our assembly provides insights into the genomic features that give rise to B. carinata's superior agronomic traits for developing more climate-resilient Brassica crops with excellent oil production. Notably, we identified an expansion of transcription factor networks and agronomically-important gene families. Completing the Triangle of U comparative genomics platform allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in domestication and agronomical improvement.

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Brassica carinata genome characterization clarifies U’s triangle model of evolution and polyploidy in Brassica

Plant Physiology ◽

10.1093/plphys/kiab048 ◽

2021 ◽

Author(s):

Xiaoming Song ◽

Yanping Wei ◽

Dong Xiao ◽

Ke Gong ◽

Pengchuan Sun ◽

...

Keyword(s):

Genome Sequencing ◽

Agronomic Traits ◽

Repetitive Sequences ◽

Genomic Analysis ◽

Brassica Species ◽

Brassica Carinata ◽

Comparative Genomic ◽

Ethiopian Mustard ◽

A Genome ◽

Genome Triplication

Abstract Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent agronomic traits. Here, the high-quality genome sequence of B. carinata is reported. Characterization revealed a genome anchored to 17 chromosomes with a total length of 1.087 Gb and an N50 scaffold length of 60 Mb. Repetitive sequences account for approximately 634 Mb or 58.34% of the B. carinata genome. Notably, 51.91% of 97,149 genes are confined to the terminal 20% of chromosomes as a result of the expansion of repeats in pericentromeric regions. Brassica carinata shares one whole-genome triplication event with the five other species in U’s triangle, a classic model of evolution and polyploidy in Brassica. Brassica carinata was deduced to have formed ∼0.047 Mya, which is slightly earlier than B. napus but later than B. juncea. Our analysis indicated that the relationship between the two subgenomes (BcaB and BcaC) is greater than that between other two tetraploid subgenomes (BjuB and BnaC) and their respective diploid parents. RNA-seq datasets and comparative genomic analysis were used to identify several key genes in pathways regulating disease resistance and glucosinolate metabolism. Further analyses revealed that genome triplication and tandem duplication played important roles in the expansion of those genes in Brassica species. With the genome sequencing of B. carinata completed, the genomes of all six Brassica species in U’s triangle are now resolved. The data obtained from genome sequencing, transcriptome analysis, and comparative genomic efforts in this study provide valuable insights into the genome evolution of the six Brassica species in U’s triangle.

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Analysis of Genetic Parameters for Some Agronomic Traits of Introduced Ethiopian Mustard (Brassica carinata A. Brun) Genotypes

International Journal of Agricultural Research ◽

10.3923/ijar.2012.160.165 ◽

2012 ◽

Vol 7 (3) ◽

pp. 160-165

Author(s):

Yared Semahegn Belete ◽

Misteru Tesfaye Wold Yohannes ◽

Tadesse Debele Wami

Keyword(s):

Genetic Parameters ◽

Agronomic Traits ◽

Brassica Carinata ◽

Ethiopian Mustard

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Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa042 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Qian-Hao Zhu ◽

Warwick Stiller ◽

Philippe Moncuquet ◽

Stuart Gordon ◽

Yuman Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Agronomic Traits ◽

Gene Families ◽

Mutant Phenotype ◽

Wild Type ◽

Calcium Dependent ◽

Dependent Protein ◽

Flanking Region ◽

Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

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Role of heterotrimeric Gα proteins in maize development and enhancement of agronomic traits

PLoS Genetics ◽

10.1371/journal.pgen.1007374 ◽

2018 ◽

Vol 14 (4) ◽

pp. e1007374 ◽

Cited By ~ 20

Author(s):

Qingyu Wu ◽

Michael Regan ◽

Hiro Furukawa ◽

David Jackson

Keyword(s):

Agronomic Traits

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Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

10.1101/2021.12.09.471732 ◽

2021 ◽

Author(s):

Laszlo G Nagy ◽

Peter Jan Vonk ◽

Markus Kunzler ◽

Csenge Foldi ◽

Mate Viragh ◽

...

Keyword(s):

Cell Wall ◽

Fruiting Body ◽

Expression Patterns ◽

Schizophyllum Commune ◽

Gene Families ◽

Second Phase ◽

Fruiting Bodies ◽

Body Development ◽

Fruiting Body Development

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Key words: functional annotation; comparative genomics; cell wall remodeling; development; fruiting body morphogenesis; mushroom; transcriptome

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A Model for Predicting Cation Selectivity and Permeability in AMPA and NMDA Receptors Based on Receptor Subunit Composition

Frontiers in Synaptic Neuroscience ◽

10.3389/fnsyn.2021.779759 ◽

2021 ◽

Vol 13 ◽

Author(s):

Sampath Kumar ◽

Sanjay S. Kumar

Keyword(s):

Experimental Data ◽

Divalent Cations ◽

Ion Selectivity ◽

Gene Families ◽

Subunit Composition ◽

Receptor Subunit ◽

Cation Selectivity ◽

Subunit Stoichiometry ◽

Ampa And Nmda Receptors

Glutamatergic AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) and NMDA (N-methyl-D-aspartate) receptors are implicated in diverse functions ranging from synaptic plasticity to cell death. They are heterotetrameric proteins whose subunits are derived from multiple distinct gene families. The subunit composition of these receptors determines their permeability to monovalent and/or divalent cations, but it is not entirely clear how this selectivity arises in native and recombinantly-expressed receptor populations. By analyzing the sequence of amino acids lining the selectivity filters within the pore forming membrane helices (M2) of these subunits and by correlating subunit stoichiometry of these receptors with their ability to permeate Na+ and/or Ca2+, we propose here a mathematical model for predicting cation selectivity and permeability in these receptors. The model proposed is based on principles of charge attractivity and charge neutralization within the pore forming region of these receptors; it accurately predicts and reconciles experimental data across various platforms including Ca2+ permeability of GluA2-lacking AMPARs and ion selectivity within GluN3-containing di- and tri-heteromeric NMDARs. Additionally, the model provides insights into biophysical mechanisms regulating cation selectivity and permeability of these receptors and the role of various subunits in these processes.

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The other face of MUC1 protein in cancer progression – the role of MUC1-C subunit

Postępy Higieny i Medycyny Doświadczalnej ◽

10.5604/01.3001.0012.8399 ◽

2019 ◽

Vol 73 ◽

pp. 20-32

Author(s):

Alicja M. Kmiecik ◽

Piotr Dzięgiel ◽

Maciej Ugorski

Keyword(s):

Cancer Progression ◽

Tyrosine Kinases ◽

Cancer Metabolism ◽

Noncovalent Complex ◽

Gene Families ◽

Mitochondrial Outer Membrane ◽

Apical Side ◽

C Subunit ◽

Induced Apoptosis

MUC1 is high-molecular-weight glycoprotein which is widely expressed on epithelial cell layers of various organs and is aberrantly overexpressed in most human carcinomas such as breast, ovarian or colon cancer. MUC1 contains three domains: short cytoplasmic and transmembrane domains, and a long extracellular domain. The protein is translated as a single polypeptide that undergoes auto-cleavage into two subunits: MUC1-N and MUC1-C, that form a stable noncovalent complex at the cell membrane. In normal epithelial cells, MUC1 expression is restricted to the apical side of the cells. During cancer transformation there is a loss of cell polarity and MUC1-C is found over the entire cell surface while MUC1-N is shed from the surface of carcinoma cells. As the result of depolarization, MUC1-C interacts with receptor tyrosine kinases (RTKs), such as EGFR and activates intracellular pathways which are important for cancer progression. Overexpression of MUC1 is also associated with the accumulation of MUC1-C in the cytoplasm and targeting of this subunit to the nucleus or mitochondria. Nuclear localization of MUC1-C is associated with activation of gene families involved in oncogenesis or cancer metabolism. Other results have shown that MUC1-C localizes to the mitochondrial outer membrane, where it blocks stress induced apoptosis. Recent studies have been directed at the MUC1-C subunit which reminds to be attractive target for the development of anti-cancer agents. In this review, the role of MUC1-C in cancer progression is discussed.

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Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica

International Journal of Molecular Sciences ◽

10.3390/ijms21103424 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3424 ◽

Cited By ~ 1

Author(s):

Weimiao Liu ◽

Tianqi Lyu ◽

Liai Xu ◽

Ziwei Hu ◽

Xingpeng Xiong ◽

...

Keyword(s):

Molecular Evolution ◽

Cell Walls ◽

Plant Cell Wall ◽

Diploid Species ◽

Brassica Species ◽

Gene Families ◽

Structural Proteins ◽

Development Processes ◽

Positive Correlations ◽

Complete Genomic

Expansins are a kind of structural proteins of the plant cell wall, and they enlarge cells by loosening the cell walls. Therefore, expansins are involved in many growth and development processes. The complete genomic sequences of Brassica rapa, Brassica oleracea and Brassica nigra provide effective platforms for researchers to study expansin genes, and can be compared with analogues in Arabidopsis thaliana. This study identified and characterized expansin families in B. rapa, B. oleracea, and B. nigra. Through the comparative analysis of phylogeny, gene structure, and physicochemical properties, the expansin families were divided into four subfamilies, and then their expansion patterns and evolution details were explored accordingly. Results showed that after the three species underwent independent evolution following their separation from A. thaliana, the expansin families in the three species had increased similarities but fewer divergences. By searching divergences of promoters and coding sequences, significant positive correlations were revealed among orthologs in A. thaliana and the three basic species. Subsequently, differential expressions indicated extensive functional divergences in the expansin families of the three species, especially in reproductive development. Hence, these results support the molecular evolution of basic Brassica species, potential functions of these genes, and genetic improvement of related crops.

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Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis

Scientific Reports ◽

10.1038/s41598-020-71701-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Joon-Yung Cha ◽

Sang-Ho Kang ◽

Imdad Ali ◽

Sang Cheol Lee ◽

Myung Geun Ji ◽

...

Keyword(s):

Heat Stress ◽

Humic Acid ◽

Heat Shock ◽

Stress Tolerance ◽

Transcriptional Activation ◽

Molecular Mechanisms ◽

Agronomic Traits ◽

Enrichment Analysis ◽

Gene Families ◽

Heat Stress Tolerance

Abstract Humic acid (HA) is composed of a complex supramolecular association and is produced by humification of organic matters in soil environments. HA not only improves soil fertility, but also stimulates plant growth. Although numerous bioactivities of HA have been reported, the molecular evidences have not yet been elucidated. Here, we performed transcriptomic analysis to identify the HA-prompted molecular mechanisms in Arabidopsis. Gene ontology enrichment analysis revealed that HA up-regulates diverse genes involved in the response to stress, especially to heat. Heat stress causes dramatic induction in unique gene families such as Heat-Shock Protein (HSP) coding genes including HSP101, HSP81.1, HSP26.5, HSP23.6, and HSP17.6A. HSPs mainly function as molecular chaperones to protect against thermal denaturation of substrates and facilitate refolding of denatured substrates. Interestingly, wild-type plants grown in HA were heat-tolerant compared to those grown in the absence of HA, whereas Arabidopsis HSP101 null mutant (hot1) was insensitive to HA. We also validated that HA accelerates the transcriptional expression of HSPs. Overall, these results suggest that HSP101 is a molecular target of HA promoting heat-stress tolerance in Arabidopsis. Our transcriptome information contributes to understanding the acquired genetic and agronomic traits by HA conferring tolerance to environmental stresses in plants.

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