scholarly journals Evolutionary genomics of grape (Vitis viniferassp.vinifera) domestication

2017 ◽  
Vol 114 (44) ◽  
pp. 11715-11720 ◽  
Author(s):  
Yongfeng Zhou ◽  
Mélanie Massonnet ◽  
Jaleal S. Sanjak ◽  
Dario Cantu ◽  
Brandon S. Gaut
Keyword(s):  
Stress Responses ◽  
Sugar Metabolism ◽  
Genomic Region ◽  
Plant Domestication ◽  
Perennial Crop ◽  
Specific Expression ◽  
Annual Crops ◽  
In The Wild ◽  
The Cost ◽  
Wild Sample

We gathered genomic data from grapes (Vitis viniferassp.vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.

scholarly journals Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yao Chen ◽  
Panpan Zhu ◽  
Shaoyuan Wu ◽  
Yan Lu ◽  
Jian Sun ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Raw Material ◽  
Functional Study ◽  
Ipomoea Trifida ◽  
Specific Expression ◽  
Adverse Environmental Condition ◽  
In The Wild

Abstract Background GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China. However, the function of sweet potato GRAS genes remains unknown. Results In this study, we identified and characterised 70 GRAS members from Ipomoea trifida, which is the progenitor of sweet potato. The chromosome distribution, phylogenetic tree, exon-intron structure and expression profiles were analysed. The distribution map showed that GRAS genes were randomly located in 15 chromosomes. In combination with phylogenetic analysis and previous reports in Arabidopsis and rice, the GRAS proteins from I. trifida were divided into 11 subfamilies. Gene structure showed that most of the GRAS genes in I. trifida lacked introns. The tissue-specific expression patterns and the patterns under abiotic stresses of ItfGRAS genes were investigated via RNA-seq and further tested by RT-qPCR. Results indicated the potential functions of ItfGRAS during plant development and stress responses. Conclusions Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.

scholarly journals Genome-Wide Identification and Characterization of HSP90-RAR1-SGT1-Complex Members From Arachis Genomes and Their Responses to Biotic and Abiotic Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Cuiling Yuan ◽  
Chunjuan Li ◽  
Xiaobo Zhao ◽  
Caixia Yan ◽  
Juan Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Chromosomal Location ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Biotic And Abiotic Stress ◽  
Specific Expression ◽  
Systematic Analysis ◽  
In The Wild ◽  
Wild Peanut

The molecular chaperone complex HSP90-RAR1-SGT1 (HRS) plays important roles in both biotic and abiotic stress responses in plants. A previous study showed that wild peanut Arachis diogoi SGT1 (AdSGT1) could enhance disease resistance in transgenic tobacco and peanut. However, no systematic analysis of the HRS complex in Arachis has been conducted to date. In this study, a comprehensive analysis of the HRS complex were performed in Arachis. Nineteen HSP90, two RAR1 and six SGT1 genes were identified from the allotetraploid peanut Arachis hypogaea, a number close to the sum of those from the two wild diploid peanut species Arachis duranensis and Arachis ipaensis. According to phylogenetic and chromosomal location analyses, thirteen orthologous gene pairs from Arachis were identified, all of which except AhHSP90-A8, AhHSP90-B9, AdHSP90-9, and AiHSP90-9 were localized on the syntenic locus, and they shared similar exon-intron structures, conserved motifs and expression patterns. Phylogenetic analysis showed that HSP90 and RAR1 from dicot and monocot plants diverged into different clusters throughout their evolution. Chromosomal location analysis indicated that AdSGT1 (the orthologous gene of AhSGT1-B3 in this study) might provide resistance to leaf late spot disease dependent on the orthologous genes of AhHSP90-B10 and AhRAR1-B in the wild peanut A. diogoi. Several HRS genes exhibited tissue-specific expression patterns, which may reflect the sites where they perform functions. By exploring published RNA-seq data, we found that several HSP90 genes play major roles in both biotic and abiotic stress responses, especially salt and drought responses. Autoactivation assays showed that AhSGT1-B1 could not be used as bait for yeast two-hybrid (Y2H) library screening. AhRAR1 and AhSGT1 could strongly interact with each other and interact with AhHSP90-B8. The present study represents the first systematic analysis of HRS complex genes in Arachis and provides valuable information for functional analyses of HRS complex genes. This study also offers potential stress-resistant genes for peanut improvement.

scholarly journals The Evolutionary Genomics of Grape (Vitis viniferassp.vinifera) Domestication

2017 ◽  
Author(s):  
Yongfeng Zhou ◽  
Mélanie Massonnet ◽  
Jaleal Sanjak ◽  
Dario Cantu ◽  
Brandon S. Gaut
Keyword(s):  
Sex Determination ◽  
Stress Responses ◽  
Clonal Propagation ◽  
Population Decline ◽  
Genomic Data ◽  
Population History ◽  
Plant Domestication ◽  
Deleterious Mutations ◽  
Perennial Crop ◽  
Low Intensity

ABSTRACTWe gathered genomic data from grapes (Vitis viniferassp.vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ~22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne) thereafter. The long decline may reflect low intensity management by humans prior to domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development and stress responses. In contrast, candidate selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.Significance StatementWe generated genomic data to estimate the population history of grapes, the most economically important horticultural crop in the world. Domesticated grapes experienced a protracted, 22,000 year population decline prior to domestication; we hypothesize that this decline reflects low intensity cultivation by humans prior to domestication. Domestication altered the mating system of grapes. The sex determination region is detectable as a region of heightened genetic divergence between wild and cultivated accessions. Based on gene expression analyses, we propose new candidate genes that alter sex determination. Finally, grapes contain more deleterious mutations in heterozygous states than their wild ancestors. The accumulation of deleterious mutations is due in part to clonal propagation, which shelters deleterious, recessive mutations.

scholarly journals Genome-wide analysis of CrRLK1L genes and their expression profiling during fiber development in cotton

2020 ◽  
Author(s):  
Dongyun Zuo ◽  
Javaria Ashraf ◽  
Hailiang Cheng ◽  
Shang Liu ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Plant Immunity ◽  
Fiber Development ◽  
The Other ◽  
Element Analysis ◽  
Specific Expression ◽  
Group Iii ◽  
Group I ◽  
Genome Wide ◽  
Specific Expression Pattern

Abstract Background: Catharanthus roseus receptor-like kinase 1-like (CrRLK1Ls) proteins play important roles in cell growth, plant morphogenesis, reproduction, hormone signaling, plant immunity and stress responses in Arabidopsis. However, not much information is available about their functions during cotton fiber development.Results: We identified a total of 125, 73 and 71 full-length putative CrRLK1L genes in G. hirsutum, G. arboreum and G. raimondii, which are much greater than that of the other plants. The phylogenetic and gene structure analysis divided the cotton CrRLK1L genes into six major groups, among which only group I and II contained AtCrRLK1Ls of Arabidopsis, suggesting that other groups (group III-VI) were expanded by gene duplication during cotton evolution. Genome collinearity analysis revealed that half of the At02 genes in G. hirsutum derived from A02 of G. arboreum, while the other half (GhCrRLK1L6 and GhCrRLK1L7) originated from Dt03 and Dt02 of G. raimondii, indicating segmental duplication between noncorresponding chromosomes during polyploidization of G. hirsutum. In addition, expression and cis-element analysis revealed that only 22 GhCrRLK1Ls showed specific expression pattern during fiber development which are mainly due to the presence of binding sites for NAC, MYB and WRKY transcription factors.Conclusions: This study provides a strong foundation to further explore the molecular mechanism of CrRLK1L genes during fiber development in upland cotton.

scholarly journals Identification and molecular characterization of a Chlamydomonas reinhardtii mutant that shows a light intensity dependent progressive chlorophyll deficiency

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 142
Author(s):  
Phillip B Grovenstein ◽  
Darryel A Wilson ◽  
Kathryn D Lankford ◽  
Kelsey A Gaston ◽  
Surangi Perera ◽  
...  
Keyword(s):  
Light Intensity ◽  
Insertional Mutagenesis ◽  
Protoporphyrin Ix ◽  
Model Organism ◽  
Genomic Region ◽  
Oxygenic Photosynthesis ◽  
Autotrophic Growth ◽  
Wild Type ◽  
Light Intensities ◽  
In The Wild

The green micro-alga Chlamydomonas reinhardtii is an elegant model organism to study all aspects of oxygenic photosynthesis. Chlorophyll (Chl) and heme are major tetrapyrroles that play an essential role in energy metabolism in photosynthetic organisms. These tetrapyrroles are synthesized via a common branched pathway that involves mainly nuclear encoded enzymes. One of the enzymes in the pathway is Mg chelatase (MgChel) which inserts Mg2+ into protoporphyrin IX (PPIX, proto) to form Magnesium-protoporphyrin IX (MgPPIX, Mgproto), the first biosynthetic intermediate in the Chl branch. The GUN4 (genomes uncoupled 4) protein is not essential for the MgChel activity but has been shown to significantly stimulate its activity. We have isolated a light sensitive mutant, 6F14, by random DNA insertional mutagenesis. 6F14 cannot tolerate light intensities higher than 90-100 μmol photons m-2 s-1. It shows a light intensity dependent progressive photo-bleaching. 6F14 is incapable of photo-autotrophic growth under light intensity higher than 100 μmol photons m-2 s-1. PCR based analyses show that in 6F14 the insertion of the plasmid outside the GUN4 locus has resulted in a genetic rearrangement of the GUN4 gene and possible deletions in the genomic region flanking the GUN4 gene. Our gun4 mutant has a Chl content very similar to that in the wild type in the dark and is very sensitive to fluctuations in the light intensity in the environment unlike the earlier identified Chlamydomonas gun4 mutant. Complementation with a functional copy of the GUN4 gene restored light tolerance, Chl biosynthesis and photo-autotrophic growth under high light intensities in 6F14. 6F14 is the second gun4 mutant to be identified in C. reinhardtii. Additionally, we show that our two gun4 complements over-express the GUN4 protein and show a higher Chl content per cell compared to that in the wild type strain.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

Energetics: the costs of living and reproducing for an individual cephalopod

1996 ◽  
Vol 351 (1343) ◽  
pp. 1083-1104 ◽  
Keyword(s):  
Specific Dynamic Action ◽  
Energy Budgets ◽  
Food Conversion ◽  
Laboratory Studies ◽  
Feeding Rates ◽  
Historical Factors ◽  
In The Wild ◽  
Excretion Rates ◽  
The Cost ◽  
Conversion Efficiencies

Cephalopods, like all other animals, have to decide how to allocate resources; maintenance processes, growth of somatic and reproductive tissues, and locomotor activity all have costs. We should like to be able to identify these costs and discover how efficiently cephalopods make use of the prey that they capture and digest. Cephalopods generally grow fast and mature rapidly; a first task is to determine how accurately laboratory studies reflect growth in the wild, because much of the information we need (such as food conversion efficiencies, excretion rates or the costs of locomotion) can be collected only from animals kept in the laboratory. Comparison of laboratory feeding and growth rates for octopods, sepioids and teuthoids with fisheries data suggests that data collected from cephalopods fed ad libitum in the laboratory may be used validly to construct energy budgets representative of individuals in the wild. The immediate cost of feeding (the specific dynamic action) has been thoroughly documented in Octopus , as has the longer-term elevation or depression of metabolic rate by feeding or starvation; it is assumed that similar costs will be found in squid. The cost of locomotion has been studied in both octopods and squid, but we have only limited data on how much time the animals spend moving, and how rapidly, in the wild. Excretory and faecal losses are assessed from laboratory studies, and maintenance costs estimated from feeding rates that just maintain body mass in the laboratory. Comparison of gross and net food conversion efficiencies suggest that squid convert food into tissues less efficiently than octopods, owing primarily to their greater time spent in locomotion. We present a representative series of energy budgets for octopods (based on Octopus ) and squids (based on Illex and Loligo ), for starving, feeding, migrating and maturing individuals. A major contrast is provided by Nautilus, which lives for ten or twenty years and grows only slowly. Finally we speculate on the possible biochemical and historical factors that may have limited the adaptive radiation of cephalopods, resulting in a group lacking herbivores, detritivores or filter-feeders but extremely successful as carnivores.

Secondary sexual characters, energy use, senescence, and the cost of reproduction in sockeye salmon

1999 ◽  
Vol 77 (11) ◽  
pp. 1663-1675 ◽  
Author(s):  
Andrew P Hendry ◽  
Ole K Berg
Keyword(s):  
Egg Production ◽  
Sockeye Salmon ◽  
Energy Use ◽  
Relative Size ◽  
Cost Of Reproduction ◽  
Bristol Bay ◽  
Secondary Sexual Characters ◽  
In The Wild ◽  
The Cost ◽  
Secondary Sexual

Reproductive development and energy stores were characterized for sockeye salmon (Oncorhynchus nerka) maturing in the wild (Pick Creek, Bristol Bay, Alaska). Between freshwater entry and the start of spawning, ovaries increased in mass by 87.1% and secondary sexual characters increased in linear dimension by 13.0-47.4%. Between the start of spawning and death, secondary sexual characters decreased in relative size by 3.3-12.7%. Mass-specific somatic energy declined from freshwater entry (6.7% fat, 20.6% protein, 6.6 kJ·g-1) to the start of spawning (1.6% fat, 18.0% protein, 4.5 kJ·g-1) and finally to death (0.1% fat, 14.4% protein, 2.9 kJ·g-1). Stored fat appeared to be used primarily for upriver migration and egg production, whereas stored protein appeared to be used primarily for the development of secondary sexual characters and metabolism during spawning. Most development of secondary sexual characters occurred late in maturation, perhaps to forestall deterioration of muscle tissue. Relative to populations with long freshwater migrations, Bristol Bay sockeye salmon stored less fat before entering fresh water and used less fat before death. The total energy cost of reproduction (freshwater entry until death, including gonad investment) was 74.1% for females and 66.1% for males, higher than levels typically reported for iteroparous salmonids.

Genomic Organization, Chromatin Structure, and Transcriptional Regulation of the Murine Alpha Hemoglobin Stabilizing Protein (AHSP) Gene.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3633-3633
Author(s):  
Louis C. Dore ◽  
Christopher R. Vakoc ◽  
Gerd A. Blobel ◽  
Ross C. Hardison ◽  
David M. Bodine ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Gene Activation ◽  
Inverse Correlation ◽  
Regulatory Elements ◽  
Genomic Region ◽  
Beta Thalassemia ◽  
Syntenic Block ◽  
Coding Region ◽  
Specific Expression

Abstract Alpha Hemoglobin Stabilizing Protein (AHSP, Eraf) is an abundant erythroid protein that binds and stabilizes alpha globin and alpha hemoglobin (Hb). In mice, loss of AHSP causes hemolytic anemia, with elevated levels of reactive oxygen species and Hb precipitation in erythrocytes. Loss of AHSP exacerbates beta thalassemia phenotypes in mice, presumably by enhancing the toxicity of excessive free alpha Hb. Based on these findings, AHSP is a candidate modifier gene for beta thalassemia in humans. No mutations in the AHSP coding region have been identified in patients to date. However, several groups reported an inverse correlation between beta thalassemia severity and erythroid AHSP expression levels, raising the possibility that AHSP is a quantitative trait modifier of beta thalassemia. To address this possibility, it is important to define the mechanisms that control expression of the AHSP gene. Transcripts of murine Ahsp are inducible by GATA-1. The goals of the current studies are to investigate the mechanisms of this induction and to define the DNA domain that regulates the locus. Using phylogenetic comparisons, we identified a hotspot for mammalian chromosomal rearrangement just downstream of the Ahsp gene. This hotspot is located at the end of a syntenic block of approximately 350 kb that is conserved in mammals and likely marks the 3′ end of the gene regulatory domain. We focused our initial functional studies on a 7 kb genomic region bounded at the 5′ (centromeric) end of Ahsp by the nearest adjacent gene, an EST expressed in multiple tissues, and at the 3′ (telomeric) end by the rearrangement hotspot. In transient transfection assays, the Ahsp promoter region conferred erythroid-specific expression to a linked reporter gene. In heterologous cells, GATA-1 transactivated the Ahsp promoter in a dose-dependent fashion. To examine GATA-1 binding and its subsequent effects on the Ahsp gene in vivo, we used G1E-ER4 cells, a GATA-1 null erythroblast line that undergoes terminal erythroid maturation after activation of an estradiol-inducible form of GATA-1. We made several findings with regards to the role of GATA-1 in Ahsp gene regulation. First, GATA-1 and its cofactor, Friend of GATA-1 (FOG-1), bind directly to the Ahsp locus at regions that contain conserved GATA consensus motifs and are predicted to be important erythroid regulatory elements by our bioinformatic studies. Second, GATA-1 induces epigenetic changes in chromatin structure that are associated with gene activation, including formation of a DNase I hypersensitive site, hyperacetylation of histones H3 and H4, and methylation of histone H3 lysine-4. Together, these findings begin to establish the DNA region and mechanisms that control Ahsp transcription, allowing for further studies to map the cis elements responsible for population variations in gene expression.

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