Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata

Achlorophyllous plants are full mycoheterotrophic plants with no chlorophyll and they obtain their nutrients from soil fungi. Gastrodia elata is a perennial, achlorophyllous orchid that displays distinctive evolutionary strategy of adaptation to the non-photosynthetic lifestyle. Here in this study, the genome of G. elata was assembled to 1.12 Gb with a contig N50 size of 110 kb and a scaffold N50 size of 1.64 Mb so that it helped unveil the genetic basics of those adaptive changes. Based on the genomic data, key genes related to photosynthesis, leaf development, and plastid division pathways were found to be lost or under relaxed selection during the course of evolution. Thus, the genome sequence of G. elata provides a good resource for future investigations of the evolution of orchids and other achlorophyllous plants.

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A Study of the Coevolution of Digital Organisms with an Evolutionary Cellular Automaton

Biology ◽

10.3390/biology10111147 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1147

Author(s):

Javier Falgueras-Cano ◽

Juan-Antonio Falgueras-Cano ◽

Andrés Moya

Keyword(s):

Natural Selection ◽

Cellular Automaton ◽

Evolutionary Dynamics ◽

Evolutionary Strategy ◽

Phenotypic Flexibility ◽

Biological Interactions ◽

Fragmented Habitats ◽

Digital Organisms ◽

Effective Instrument ◽

Good Resource

This paper presents an Evolutionary Cellular Automaton (ECA) that simulates the evolutionary dynamics of biological interactions by manipulating strategies of dispersion and associations between digital organisms. The parameterization of the different types of interaction and distribution strategies using configuration files generates easily interpretable results. In that respect, ECA is an effective instrument for measuring the effects of relative adaptive advantages and a good resource for studying natural selection. Although ECA works effectively in obtaining the expected results from most well-known biological interactions, some unexpected effects were observed. For example, organisms uniformly distributed in fragmented habitats do not favor eusociality, and mutualism evolved from parasitism simply by varying phenotypic flexibility. Finally, we have verified that natural selection represents a cost for the emergence of sex by destabilizing the stable evolutionary strategy of the 1:1 sex ratio after generating randomly different distributions in each generation.

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Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role

BMC Genomics ◽

10.1186/s12864-020-06940-0 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Jose Alfredo Samaniego Castruita ◽

Michael V. Westbury ◽

Eline D. Lorenzen

Keyword(s):

De Novo ◽

Polar Bears ◽

De Novo Mutations ◽

Standing Variation ◽

Key Genes

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De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers

Biochemical Genetics ◽

10.1007/s10528-020-09983-w ◽

2020 ◽

Vol 58 (6) ◽

pp. 914-934

Author(s):

Yunsheng Wang ◽

Muhammad Qasim Shahid ◽

Fozia Ghouri ◽

Faheem Shehzad Baloch

Keyword(s):

Rna Sequencing ◽

Ssr Markers ◽

De Novo Assembly ◽

De Novo ◽

Gastrodia Elata

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De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids

Molecules ◽

10.3390/molecules22122155 ◽

2017 ◽

Vol 22 (12) ◽

pp. 2155 ◽

Cited By ~ 11

Author(s):

Megha Rai ◽

Amit Rai ◽

Noriaki Kawano ◽

Kayo Yoshimatsu ◽

Hiroki Takahashi ◽

...

Keyword(s):

Rna Sequencing ◽

Expression Analysis ◽

De Novo ◽

Diterpene Alkaloids ◽

Key Genes ◽

Sequencing And Expression ◽

Aconitum Carmichaelii

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Lack of mitochondria-generated acetyl-CoA by pyruvate dehydrogenase complex downregulates gene expression in the hepatic de novo lipogenic pathway

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00064.2016 ◽

2016 ◽

Vol 311 (1) ◽

pp. E117-E127 ◽

Cited By ~ 10

Author(s):

Saleh Mahmood ◽

Barbara Birkaya ◽

Todd C. Rideout ◽

Mulchand S. Patel

Keyword(s):

Gene Expression ◽

Fatty Acids ◽

Fatty Acid ◽

Pyruvate Dehydrogenase ◽

De Novo ◽

Pyruvate Dehydrogenase Complex ◽

Acid Oxidation ◽

Acetyl Coa ◽

Key Genes ◽

Dehydrogenase Complex

During the absorptive state, the liver stores excess glucose as glycogen and synthesizes fatty acids for triglyceride synthesis for export as very low density lipoproteins. For de novo synthesis of fatty acids from glucose, the mitochondrial pyruvate dehydrogenase complex (PDC) is the gatekeeper for the generation of acetyl-CoA from glucose-derived pyruvate. Here, we tested the hypothesis that limiting the supply of PDC-generated acetyl-CoA from glucose would have an impact on expression of key genes in the lipogenic pathway. In the present study, although the postnatal growth of liver-specific PDC-deficient (L-PDCKO) male mice was largely unaltered, the mice developed hyperinsulinemia with lower blood glucose levels in the fed state. Serum and liver lipid triglyceride and cholesterol levels remained unaltered in L-PDCKO mice. Expression of several key genes ( ACL, ACC1) in the lipogenic pathway and their upstream regulators ( LXR, SREBP1, ChREBP) as well as several genes in glucose metabolism ( Pklr, G6pd2, Pck1) and fatty acid oxidation ( FAT, Cpt1a) was downregulated in livers from L-PDCKO mice. Interestingly, there was concomitant upregulation of lipogenic genes in adipose tissue from L-PDCKO mice. Although, the total hepatic acetyl-CoA content remained unaltered in L-PDCKO mice, modified acetylation profiles of proteins in the nuclear compartment suggested an important role for PDC-generated acetyl-CoA in gene expression in de novo fatty acid synthesis in the liver. This finding has important implications for the regulation of hepatic lipid synthesis in pathological states.

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Identification of Genes Underlying the Resistance to Melampsora larici-populina in an R Gene Supercluster of the Populus deltoides Genome

Plant Disease ◽

10.1094/pdis-08-19-1699-re ◽

2020 ◽

Vol 104 (4) ◽

pp. 1133-1143

Author(s):

Suyun Wei ◽

Huaitong Wu ◽

Xiaoping Li ◽

Yingnan Chen ◽

Yonghua Yang ◽

...

Keyword(s):

Populus Deltoides ◽

De Novo ◽

Quantitative Resistance ◽

Rust Fungus ◽

Constitutive Expression ◽

Transcriptome Profiling ◽

R Gene ◽

R Genes ◽

Sequencing Data ◽

Key Genes

Identification of the particular genes in an R genes supercluster underlying resistance to the rust fungus Melampsora larici-populina in poplar genome remains challenging. Based on the de novo assembly of the Populus deltoides genome, all of the detected major genetic loci conferring resistance to M. larici-populina were confined to a 3.5-Mb region on chromosome 19. The transcriptomes of the resistant and susceptible genotypes were sequenced for a timespan from 0 to 168 hours postinoculation. By mapping the differentially expressed genes to the target genomic region, we identified two constitutive expression R genes and one inducible expression R gene that might confer resistance to M. larici-populina. Nucleotide variations were predicted based on the reconstructed haplotypes for each allele of the candidate genes. We also confirmed that salicylic acid was the phytohormone mediating signal transduction pathways, and PR-1 was identified as a key gene inhibiting rust reproduction. Finally, quantitative reverse transcription PCR assay revealed consistent expressions with the RNA-sequencing data for the detected key genes. This study presents an efficient approach for the identification of particular genes underlying phenotype of interest by the combination of genetic mapping, transcriptome profiling, and candidate gene sequences dissection. The identified key genes would be useful for host resistance diagnosis and for molecular breeding of elite poplar cultivars exhibiting resistance to M. larici-populina infection. The detected R genes are also valuable for testing whether the combination of individual R genes can induce durable quantitative resistance.

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De novo transcriptome sequencing of pakchoi (Brassica rapa L. chinensis) reveals the key genes related to the response of heat stress

Acta Physiologiae Plantarum ◽

10.1007/s11738-016-2269-5 ◽

2016 ◽

Vol 38 (10) ◽

Cited By ~ 3

Author(s):

Hai Xu ◽

Longzheng Chen ◽

Bo Song ◽

Xiaoxue Fan ◽

Xihan Yuan ◽

...

Keyword(s):

Heat Stress ◽

Brassica Rapa ◽

Transcriptome Sequencing ◽

De Novo ◽

De Novo Transcriptome ◽

De Novo Transcriptome Sequencing ◽

Key Genes

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The Anti-RA Activities of a Couplet Medicinals, Gastrodia Elata and Radix Aconitic Lateralis preparata, Explored by Untargeted Metabolomics and Network Pharmacology.

10.21203/rs.3.rs-29055/v1 ◽

2020 ◽

Author(s):

Jie Yang ◽

Xiang-Chun SHEN ◽

Wei-Hong LI ◽

Guang-Zhong FAN ◽

Bu-Fa GUO ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Endothelial Function ◽

Unsaturated Fatty Acids ◽

Untargeted Metabolomics ◽

Network Pharmacology ◽

Gastrodia Elata ◽

Fundamental Process ◽

Key Genes ◽

Combined Strategy ◽

Anti Inflammation

Abstract Background The couplet Medicinals, Gastrodia Elata and Radix Aconitic Lateralis preparata (GERA), is an established formula extensively used in Chinese medicine for treating rheumatoid arthritis (RA). However, the anti-RA mechanisms of GERA are still unclear. This paper aims to explore the anti-RA mechanisms of GERA by a combined strategy of untargeted metabolomics and network pharmacology. Methods Three water extracts were prepared as propotions: Gastrodia Elata compared with Radix Aconitic Lateralis (w/w): 1:1, 3:2, or 2:3. The untargeted metabolomics were executed with UPLC-MS. The metabolites were annotated and identified by Human metabolome database (HMDB) and Lipid maps database. Finally, key genes and pathways related to anti-RA activities of GERA were mined by network pharmacology. Results The untargeted metabolomics profile displayed that four differentially expressed metabolites were involved in isoflavonoid biosynthesis and biosynthesis of unsaturated fatty acids (p < 0.05). Among these differential metabolites, the essential ingredients of GERA were linoleic acid, daidzein, and daidzin. The principal targets of anti-RA activities of GERA were IL-6, TNF, VEGFA, TP53, CASP3 and PTGS2. Thirty anti-RA targets of GERA were majorly belonged to pathways response for anti-inflammation, endothelial function and apoptosis, suggesting the fundamental process of RA treatment. Conclusion The anti-RA activities of GERA were based on the inhibition of inflammation and regulation of endothelial function and apoptosis.

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Transcriptome analysis and identification of key genes involved in 1-deoxynojirimycin biosynthesis of mulberry (Morus alba L.)

PeerJ ◽

10.7717/peerj.5443 ◽

2018 ◽

Vol 6 ◽

pp. e5443 ◽

Cited By ~ 7

Author(s):

Dujun Wang ◽

Li Zhao ◽

Dan Wang ◽

Jia Liu ◽

Xiaofeng Yu ◽

...

Keyword(s):

Biosynthetic Pathway ◽

De Novo ◽

Amine Oxidase ◽

Average Length ◽

Morus Alba ◽

Cdna Libraries ◽

Alkaloid Biosynthesis ◽

Mulberry Leaf ◽

Primary Amine Oxidase ◽

Key Genes

Mulberry (Morus alba L.) represents one of the most commonly utilized plants in traditional medicine and as a nutritional plant used worldwide. The polyhydroxylated alkaloid 1-deoxynojirimycin (DNJ) is the major bioactive compounds of mulberry in treating diabetes. However, the DNJ content in mulberry is very low. Therefore, identification of key genes involved in DNJ alkaloid biosynthesis will provide a basis for the further analysis of its biosynthetic pathway and ultimately for the realization of synthetic biological production. Here, two cDNA libraries of mulberry leaf samples with different DNJ contents were constructed. Approximately 16 Gb raw RNA-Seq data was generated and de novo assembled into 112,481 transcripts, with an average length of 766 bp and an N50 value of 1,392. Subsequently, all unigenes were annotated based on nine public databases; 11,318 transcripts were found to be significantly differentially regulated. A total of 38 unique candidate genes were identified as being involved in DNJ alkaloid biosynthesis in mulberry, and nine unique genes had significantly different expression. Three key transcripts of DNJ biosynthesis were identified and further characterized using RT-PCR; they were assigned to lysine decarboxylase and primary-amine oxidase genes. Five CYP450 transcripts and two methyltransferase transcripts were significantly associated with DNJ content. Overall, the biosynthetic pathway of DNJ alkaloid was preliminarily speculated.

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