scholarly journals The Arabidopsis thaliana pan-NLRome

2019 ◽  
Author(s):  
Anna-Lena Van de Weyer ◽  
Freddy Monteiro ◽  
Oliver J. Furzer ◽  
Marc T. Nishimura ◽  
Volkan Cevik ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Yield Loss ◽  
Gene Families ◽  
Leucine Rich Repeat ◽  
Dynamic Interactions ◽  
Long Read ◽  
Selective Forces ◽  
Variable Gene ◽  
High Diversity

AbstractDisease is both among the most important selection pressures in nature and among the main causes of yield loss in agriculture. In plants, resistance to disease is often conferred by Nucleotide-binding Leucine-rich Repeat (NLR) proteins. These proteins function as intracellular immune receptors that recognize pathogen proteins and their effects on the plant. Consistent with evolutionarily dynamic interactions between plants and pathogens, NLRs are known to be encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define the majority of the Arabidopsis thaliana species-wide “NLRome”. From NLR sequence enrichment and long-read sequencing of 65 diverse A. thaliana accessions, we infer that the pan-NLRome saturates with approximately 40 accessions. Despite the high diversity of NLRs, half of the pan-NLRome is present in most accessions. We chart the architectural diversity of NLR proteins, identify novel architectures, and quantify the selective forces that act on specific NLRs, domains, and positions. Our study provides a blueprint for defining the pan-NLRome of plant species.

scholarly journals Organ-specific NLR resistance gene expression varies with plant symbiotic status

2017 ◽  
Author(s):  
David Munch ◽  
Vikas Gupta ◽  
Asger Bachmann ◽  
Wolfgang Busch ◽  
Simon Kelly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Expression Data ◽  
Leucine Rich Repeat ◽  
Root Infection ◽  
Organ Specific ◽  
Specific Receptors

AbstractNucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns would reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from 9 plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae species, including oilseed rape and the model plant Arabidopsis thaliana, were unique in showing NLR expression skewed towards the shoot across multiple phylogenetically distinct groups of NLRs. The Brassicaceae NLR expression shift coincides with loss of the endomycorrhization pathway, which enables intracellular root infection by symbionts. We propose that its loss offer two likely explanations for the unusual Brassicaceae NLR expression pattern: loss of NLR-guarded symbiotic components and elimination of constraints on general root defences associated with exempting symbionts from targeting. This hypothesis is consistent with the existence of Brassicaceae-specific receptors for conserved microbial molecules and suggests that Brassicaceae species are rich sources of unique antimicrobial root defences.

scholarly journals Effects of Climate Change on Grassland Biodiversity and Productivity

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1047
Author(s):  
Gianni Bellocchi ◽  
Catherine Picon-Cochard
Keyword(s):  
Climate Change ◽  
Plant Species ◽  
Livestock Farming ◽  
Low Input ◽  
The Core ◽  
Fodder Production ◽  
Grassland Biodiversity ◽  
High Diversity

Associated with livestock farming, grasslands with a high diversity of plant species are at the core of low-input fodder production worldwide [...]

scholarly journals Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
PingHsun Hsieh ◽  
Vy Dang ◽  
Mitchell R. Vollger ◽  
Yafei Mao ◽  
Tzu-Hsueh Huang ◽  
...  
Keyword(s):  
Copy Number ◽  
Homo Sapiens ◽  
Segmental Duplications ◽  
Sensor Protein ◽  
Long Read ◽  
Number Variation ◽  
Selective Forces ◽  
Structural Mutations ◽  
Cold Sensor ◽  
Human Specific

AbstractTRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. Here, our results of TCAF copy number expansion, selection signals in hominins, and differential TCAF2 expression between haplogroups and high TCAF2 and TRPM8 expression in liver and prostate in modern-day humans imply TCAF diversification among hominins potentially in response to cold or dietary adaptations.

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

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.

scholarly journals Dynamic Interactions and the Evolutionary Genetics of Dental Patterning

1998 ◽  
Vol 9 (4) ◽  
pp. 369-398 ◽  
Author(s):  
K.M. Weiss ◽  
D.W. Stock ◽  
Z. Zhao
Keyword(s):  
Morphological Structure ◽  
Homeobox Gene ◽  
Evolutionary Genetics ◽  
Gene Families ◽  
Developmental Genetics ◽  
Dynamic Interactions ◽  
Extracellular Signaling ◽  
Combinatorial Codes ◽  
Tooth Type ◽  
Mammalian Teeth

The mammalian dentition is a segmental, or periodically arranged, organ system whose components are arrayed in specific number and in regionally differentiated locations along the linear axes of the jaws. This arrangement evolved from simpler dentitions comprised of many single-cusp teeth of relatively indeterminate number. The different types of mammalian teeth have subsequently evolved as largely independent units. The experimentally documented developmental autonomy of dental primordia shows that the basic dental pattern is established early in embryogenesis. An understanding of how genetic patterning processes may work must be consistent with the different modes of development, and partially independent evolution, of the upper and lower dentition in mammals. The periodic nature of the location, number, and morphological structure of teeth suggests that processes involving the quantitative interaction of diffusible signaling factors may be involved. Several extracellular signaling molecules and their interactions have been identified that may be responsible for locating teeth along the jaws and for the formation of the incisor field. Similarly, the wavelike expression of signaling factors within developing teeth suggests that dynamic interactions among those factors may be responsible for crown patterns. These factors seem to be similar among different tooth types, but the extent to which crown differences can be explained strictly in terms of variation in the parameters of interactions among the same genes, as opposed to tooth-type-specific combinatorial codes of gene expression, is not yet known. There is evidence that combinatorial expression of intracellular transcription factors, including homeobox gene families, may establish domains within the jaws in which different tooth types are able to develop. An evolutionary perspective can be important for our understanding of dental patterning and the designing of appropriate experimental approaches, but dental patterns also raise basic unresolved questions about the nature of the evolutionary assumptions made in developmental genetics.

scholarly journals INVENTARISASI TUMBUHAN BAWAH BERKHASIAT OBAT DI TAMAN NASIONAL GUNUNG GEDE PANGRANGO PROVINSI JAWA BARAT BERBASISKAN ANALISIS SPASIAL

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Yanieta Arbiastutie ◽  
Djoko Marsono ◽  
Wahyuningsih MSH ◽  
Rishadi Purwanto
Keyword(s):  
Plant Species ◽  
Land Management ◽  
National Park ◽  
Woody Plant ◽  
Management Unit ◽  
Primary Forest ◽  
Diverse Species ◽  
Multi Stage ◽  
The Family ◽  
High Diversity

Diversity of biological resources in primary forest is not only limited to the woody plant species, but also covered by underground plant which has diverse species high diversity. This underground plant as one part of the forest ecosystem is a plant that has potential as a medicine. The study aims to conduct an inventory of underground plant species in Gunung Gede Pangrango National Park West Java Province. The method for inventory used spasial analysis with land management unit and multi stage sampling. The spasial analysis used three categories, first the zonation map, second the soil characterization map and the third altitude map. The LMU consist of 6 areas with total plot number 60. The results showed there are 83 species underground plant consist of 45 family. The family consist of Acanthaceae, Annonaceae, Apiaceae, Apocynaceae, Araceae, Araliaceae, Aspleniaceae, Asteraceae, Balsaminaceae, Begoniaceae, Compositae, Convolvulaceae, Cucurbitaceae, Cyperaceae, Elaeagnaceae, Equisetaceae, Fabaceae, Gesneriaceae, Gramineae, Hypoxidaceae, Lamiaceae, Malvaceae, Marattiaceae, Melastomataceae, Menispermaceae, Moraceae, Musaceae, Myrsinaceae, Oxalidaceae, Passifloraceae, Piperaceae, Plantaginaceae, Polygalaceae, Primulaceae, Rosaceae, Rubiaceae, Sellagineaeeae, Smilaceae, Solanaceae, Symplocaceae, Urticaceae, Verbenaceae, Woodsiaceae, Zingiberaceae. The underground plant has a potential as medicinal plant.Keywords: Gunung Gede Pangrango National Park, inventory, land management unit, medicinal plant, underground plant

scholarly journals Functional Reconstitution of Thymopoiesis after Human Immunodeficiency Virus Infection

2000 ◽  
Vol 74 (6) ◽  
pp. 2943-2948 ◽  
Author(s):  
Scott G. Kitchen ◽  
Scott Killian ◽  
Janis V. Giorgi ◽  
Jerome A. Zack
Keyword(s):  
Human Immunodeficiency Virus ◽  
Antiretroviral Treatment ◽  
Gene Families ◽  
Cell Receptor ◽  
Combination Antiretroviral Therapy ◽  
Thymic Function ◽  
Immunodeficiency Virus ◽  
Variable Gene ◽  
Costimulatory Signals

ABSTRACT We have utilized combination antiretroviral therapy following human immunodeficiency virus type 1-induced human CD4+ thymocyte depletion in the SCID-hu mouse to examine the immune competence of reconstituting thymocytes which appear following administration of combination therapy. These cells express a normal distribution of T-cell receptor variable gene families and are responsive to costimulatory signals. These results suggest that normal thymic function may be restored following antiretroviral treatment.

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