scholarly journals Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yupeng Geng ◽  
Yabin Guan ◽  
La Qiong ◽  
Shugang Lu ◽  
Miao An ◽  
...  
Keyword(s):  
High Altitude ◽  
De Novo ◽  
High Elevation ◽  
Tibet Plateau ◽  
Middle Pleistocene ◽  
Oilseed Crop ◽  
Loss Of Function ◽  
Thlaspi Arvense ◽  
A Genome ◽  
Field Pennycress

Abstract Background Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.

scholarly journals Germination Patterns in Seeds Produced in Apical and Basal Fruits of Two Thlaspi arvense Populations

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 756
Author(s):  
Eva Edo-Tena ◽  
Russ W. Gesch ◽  
Aritz Royo-Esnal
Keyword(s):  
Germination Percentage ◽  
Temperate Climate ◽  
Oilseed Crop ◽  
Seed Selection ◽  
Thlaspi Arvense ◽  
Production Site ◽  
Field Pennycress ◽  
Selection For ◽  
The One ◽  
Two Populations

The aim of the present work is to study possible differences in the germination behavior of apical and basal seeds (produced in the upper and lower fruits of the infruitescence), of two populations of field pennycress (Thlaspi arvense), both produced in a Mediterranean and a continental temperate climate. The results showed that among the three studied factors (population, seed type, production site), only the production site was relevant for the total germination, germinating those produced in Morris in a greater amount than those produced in Lleida. Germination models could be applied only to seeds produced at Morris (>10% germination), and despite the lack of differences in the total germination percentage, germination rates (speed—b parameter—and time to 50% germination—G50) differed between population and seed types—apical seeds from the Spanish population germinated faster (lower b parameter) than the rest, while apical seeds of both populations germinated faster than the corresponding basal seeds (lower G50). The results show, on the one hand, the importance of the seed production site if this species was considered as a commercial oilseed crop and, on the other hand, differences that will help seed selection for seed germination and establishment improvement of pennycress.

scholarly journals CUX2 mutations in temporal lobe epilepsy; increased kainate susceptibility and excitatory input to hippocampus in deficient mice

2021 ◽  
Author(s):  
Toshimitsu Suzuki ◽  
Tetsuya Tatsukawa ◽  
Genki Sudo ◽  
Caroline Delandre ◽  
Yun Jin Pai ◽  
...  
Keyword(s):  
Synaptic Transmission ◽  
Temporal Lobe Epilepsy ◽  
Entorhinal Cortex ◽  
Temporal Lobe ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Cell Number ◽  
Loss Of Function ◽  
Genome Wide ◽  
A Genome

CUX2 gene encodes a transcription factor that controls neuronal proliferation, dendrite branching and synapse formation, locating at the epilepsy-associated chromosomal region 12q24 that we previously identified by a genome-wide association study (GWAS) in Japanese population. A CUX2 recurrent de novo variant p.E590K has been described in patients with rare epileptic encephalopathies and the gene is a candidate for the locus, however the mutation may not be enough to generate the genome-wide significance in the GWAS and whether CUX2 variants appear in other types of epilepsies and physiopathological mechanisms are remained to be investigated. Here in this study, we conducted targeted sequencings of CUX2, a paralog CUX1 and its short isoform CASP harboring a unique C-terminus on 271 Japanese patients with a variety of epilepsies, and found that multiple CUX2 missense variants, other than the p.E590K, and some CASP variants including a deletion, predominantly appeared in patients with temporal lobe epilepsy (TLE). Human cell culture and fly dendritic arborization analyses revealed loss-of- function properties for the CUX2 variants. Cux2- and Casp-specific knockout mice both showed high susceptibility to kainate, increased excitatory cell number in the entorhinal cortex, and significant enhancement in glutamatergic synaptic transmission to the hippocampus. CASP and CUX2 proteins physiologically bound to each other and co-expressed in excitatory neurons in brain regions including the entorhinal cortex. These results suggest that CUX2 and CASP variants contribute to the TLE pathology through a facilitation of excitatory synaptic transmission from entorhinal cortex to hippocampus.

scholarly journals Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Xu ◽  
Di Wu ◽  
Tianquan Yang ◽  
Chao Sun ◽  
Zaiqing Wang ◽  
...  
Keyword(s):  
Castor Bean ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Agronomic Traits ◽  
Ricinus Communis ◽  
Oilseed Crop ◽  
A Genome ◽  
Trait Locus ◽  
Wild Progenitors

Abstract Background Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. Results Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. Conclusions This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.

scholarly journals A genome-wide DNA methylation signature for SETD1B-related syndrome

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
I. M. Krzyzewska ◽  
S. M. Maas ◽  
P. Henneman ◽  
K. v. d. Lip ◽  
A. Venema ◽  
...  
Keyword(s):  
Clinical Utility ◽  
De Novo ◽  
Histone H3 ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Variant Of Uncertain Significance ◽  
Epigenetic Marker ◽  
Genome Wide ◽  
A Genome ◽  
Uncertain Significance

Abstract SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.

scholarly journals Spring flowering habit in field pennycress (Thlaspi arvense) has arisen multiple independent times

2017 ◽  
Author(s):  
Kevin M. Dorn ◽  
Evan B. Johnson ◽  
Erin Daniels ◽  
Donald L. Wyse ◽  
M. David Marks
Keyword(s):  
Cold Season ◽  
Oilseed Crop ◽  
Loss Of Function ◽  
Thlaspi Arvense ◽  
New Information ◽  
Annual Habit ◽  
History Of ◽  
Winter Annual ◽  
The Difference ◽  
New Alleles

Summary- Pennycress (Thlaspi arvense L.) is currently being developed as a new cold-season oilseed crop. Like many Brassicaceae, pennycress can exhibit either a winter or spring annual phenotype. In Arabidopsis, mutations in negative regulators of flowering, including FLOWERING LOCUS C (FLC) and FRIGIDA can cause the transition to a spring annual habit. The genetics underlying the difference between spring and winter annual pennycress are currently unknown.- Using whole genome sequencing across wild spring annual pennycress accessions, co-segregation analyses, and comparative genomics approaches, we identify new alleles of TaFLC and explore their geographic distribution.- We report that loss of function mutations in TaFLC confer the spring annual phenotype in pennycress. We have also identified four natural alleles of TaFLC that confer a spring annual growth habit. The two spring annual FLC alleles present in European accessions were only identified in accessions collected in Montana, USA.- In pennycress, the spring annual habit has arisen several independent times. Accessions harboring the two European alleles were introduced to North America, likely after the species became a widespread on the continent. These findings provide new information on the natural history of the introduction and spread of the spring annual phenotype in pennycress.

scholarly journals Genomic signature of shifts in selection in a sub-alpine ant and its physiological adaptations

2019 ◽  
Author(s):  
Francesco Cicconardi ◽  
Patrick Krapf ◽  
Ilda D’Annessa ◽  
Alexander Gamisch ◽  
Herbert C Wagner ◽  
...  
Keyword(s):  
High Altitude ◽  
Evolutionary Biology ◽  
Extreme Environments ◽  
Purifying Selection ◽  
High Elevation ◽  
Protein Coding ◽  
Strong Shift ◽  
Genomic Signatures ◽  
A Genome ◽  
Shock Proteins

AbstractUnderstanding how organisms adapt to extreme environments is fundamental and can provide insightful case studies for both evolutionary biology and climate-change biology. Here, we take advantage of the vast diversity of lifestyles in ants to identify genomic signatures of adaptation to extreme habitats such as high altitude. We hypothesised two parallel patterns would occur in a genome adapting to an extreme habitat: i) strong positive selection on genes related to adaptation and, ii) a relaxation of previous purifying selection. We tested this hypothesis by sequencing the high-elevation specialist Tetramorium alpestre and four other phylogenetic related species. In support of our hypothesis, we recorded a strong shift of selective forces in T. alpestre, in particular a stronger magnitude of diversifying and relaxed selection when compared to all other ants. We further disentangled candidate molecular adaptations in both gene expression and protein-coding sequence that were identified by our genome-wide analyses. In particular, we demonstrate that T. alpestre has i) a derived level of expression for stv and other heat-shock proteins in chill shock tests, and ii) enzymatic enhancement of Hex-T1, a rate-limiting regulatory enzyme that controls the entry of glucose into the glycolytic pathway. Together, our analyses highlight the adaptive molecular changes that support colonisation of high-altitude environments.

scholarly journals Rare loss-of-function variants in KMT2F are associated with schizophrenia and developmental disorders

2016 ◽  
Author(s):  
Tarjinder Singh ◽  
Mitja I. Kurki ◽  
David Curtis ◽  
Shaun M. Purcell ◽  
Lucy Crooks ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
De Novo ◽  
Learning Difficulties ◽  
Loss Of Function ◽  
H3k4 Methylation ◽  
Methylation Pathway ◽  
Genome Wide ◽  
Whole Exome ◽  
A Genome ◽  
Histone H3k4

Schizophrenia is a common, debilitating psychiatric disorder with a substantial genetic component. By analysing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls, and 1,077 parent-proband trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in KMT2F and risk for schizophrenia. In this dataset, we observed three de novo LoF mutations, seven LoF variants in cases, and none in controls (P=3.3x10^(-9)). To search for LoF variants in KMT2F in individuals without a known neuropsychiatric diagnosis, we examined the exomes of 45,376 individuals in the ExAC database and found only two heterozygous LoF variants, showing that KMT2F is significantly depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying KMT2F LoF variants also had varying degrees of learning difficulties. We further identified four KMT2F LoF carriers among 4,281 children with diverse, severe, undiagnosed developmental disorders, and two additional carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations show that LoF variants in KMT2F cause a range of neurodevelopmental disorders, including schizophrenia. Combined with previous common variant evidence, we more generally implicate epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, as an important mechanism in the pathogenesis of schizophrenia.

scholarly journals De Novo Transcriptomic and Metabolomic Analyses Reveal the Ecological Adaptation of High-Altitude Bombus pyrosoma

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 631
Author(s):  
Yanjie Liu ◽  
Huiyue Zhao ◽  
Qihua Luo ◽  
Yadong Yang ◽  
Guangshuo Zhang ◽  
...  
Keyword(s):  
High Altitude ◽  
Signaling Pathways ◽  
De Novo ◽  
Tibet Plateau ◽  
Joint Analysis ◽  
Cold Temperatures ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Low Altitude ◽  
Upregulated Genes

Bombus pyrosoma is one of the most abundant bumblebee species in China, with a distribution range of very varied geomorphology and vegetation, which makes it an ideal pollinator species for research into high-altitude adaptation. Here, we sequenced and assembled transcriptomes of B. pyrosoma from the low-altitude North China Plain and the high-altitude Tibet Plateau. Subsequent comparative analysis of de novo transcriptomes from the high- and low-altitude groups identified 675 common upregulated genes (DEGs) in the high-altitude B. pyrosoma. These genes were enriched in metabolic pathways and corresponded to enzyme activities involved in energy metabolism. Furthermore, according to joint analysis with comparative metabolomics, we suggest that the metabolism of coenzyme A (CoA) and the metabolism and transport of energy resources contribute to the adaptation of high-altitude B. pyrosoma. Meanwhile, we found many common upregulated genes enriched in the Toll and immune deficiency (Imd)signaling pathways that act as important immune defenses in insects, and hypoxia and cold temperatures could induce the upregulation of immune genes in insects. Therefore, we suppose that the Toll and Imd signaling pathways also participated in the high-altitude adaptation of B. pyrosoma. Like other organisms, we suggest that the high-altitude adaptation of B. pyrosoma is controlled by diverse mechanisms.

scholarly journals Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations

2020 ◽  
Vol 37 (8) ◽  
pp. 2211-2227
Author(s):  
Francesco Cicconardi ◽  
Patrick Krapf ◽  
Ilda D’Annessa ◽  
Alexander Gamisch ◽  
Herbert C Wagner ◽  
...  
Keyword(s):  
High Altitude ◽  
Evolutionary Biology ◽  
Extreme Environments ◽  
Purifying Selection ◽  
High Elevation ◽  
Protein Coding ◽  
Strong Shift ◽  
Genomic Signatures ◽  
A Genome ◽  
Shock Proteins

Abstract Understanding how organisms adapt to extreme environments is fundamental and can provide insightful case studies for both evolutionary biology and climate-change biology. Here, we take advantage of the vast diversity of lifestyles in ants to identify genomic signatures of adaptation to extreme habitats such as high altitude. We hypothesized two parallel patterns would occur in a genome adapting to an extreme habitat: 1) strong positive selection on genes related to adaptation and 2) a relaxation of previous purifying selection. We tested this hypothesis by sequencing the high-elevation specialist Tetramorium alpestre and four other phylogenetically related species. In support of our hypothesis, we recorded a strong shift of selective forces in T. alpestre, in particular a stronger magnitude of diversifying and relaxed selection when compared with all other ants. We further disentangled candidate molecular adaptations in both gene expression and protein-coding sequence that were identified by our genome-wide analyses. In particular, we demonstrate that T. alpestre has 1) a higher level of expression for stv and other heat-shock proteins in chill-shock tests and 2) enzymatic enhancement of Hex-T1, a rate-limiting regulatory enzyme that controls the entry of glucose into the glycolytic pathway. Together, our analyses highlight the adaptive molecular changes that support colonization of high-altitude environments.

scholarly journals Classification of Driving Fatigue in High-Altitude Areas

2019 ◽  
Vol 11 (3) ◽  
pp. 817 ◽  
Author(s):  
Zhihao Duan ◽  
Jinliang Xu ◽  
Han Ru ◽  
Menghui Li
Keyword(s):  
High Altitude ◽  
Traffic Safety ◽  
Traffic Accidents ◽  
High Elevation ◽  
Tibet Plateau ◽  
High Altitude Area ◽  
Driving Fatigue ◽  
Qinghai Tibet Plateau

Driving fatigue is one of the main causes of traffic accidents. Thus, to prevent traffic accidents and ensure traffic safety, the properties of driving fatigue at the wheel must be determined. The Qinghai–Tibet Plateau in China is known for its high elevation, causing hypoxia, and presence of severely cold areas; all these easily lead to fatigue during driving. This, in turn, seriously affects the traffic safety on the high-altitude highway. Therefore, the factors leading to driving fatigue and the influence of high-altitude on driving fatigue affecting the driver must be further studied. In this study, we classified and quantified driving fatigue according to the driving fatigue degree. We determined three levels of driving fatigues (i.e., mild, moderate, and severe fatigues) to present their influence on drivers. Our study shows that in this high-altitude area, drivers became fatigued within a significantly shorter time.

Sign in / Sign up

Export Citation Format

Share Document