scholarly journals Populus trichocarpa (Black Cottonwood) As a Model for Plant Genomic Studies: A Review

2021 ◽  
pp. 270-275
Author(s):  
Navjit Kaur ◽  
Divya Dhawal Bhandari
Keyword(s):  
Populus Trichocarpa ◽  
Duplication Event ◽  
Plant Genomics ◽  
Black Cottonwood ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Model Plant ◽  
Genomics Research ◽  
Genomic Studies ◽  
Medicinal Properties

Numerous plants have been the subject of recent research in the pharmacological, cosmetic, and agro-alimentary domains due to their chemical composition and multiple therapeutic capabilities. Populus trichocarpa is one of the most common trees found in deciduous forests (Salicaceae family). The current study examines Populus trichocarpa as a model plant for plant genomics research, as well as the most recent findings on phytochemical composition and medicinal potential. More than 45,000 potential protein-coding genes were discovered. In the Populus genome, a whole-genome duplication event was discovered, with approximately 8,000 pairs of duplicated genes surviving. Furthermore, the reproductive biology of Populus provides new opportunities and challenges in the study and analysis of natural genetic and phenotypic variation. In the present review, we endeavour to describe and compile the available knowledge on Populus trichocarpa as a model plant for genomic investigations and to bring that material up to date of Populus trichocarpa's phytochemical and medicinal properties.

scholarly journals Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon (Acipenser baerii)

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1375
Author(s):  
Larisa S. Biltueva ◽  
Dmitry Yu. Prokopov ◽  
Svetlana A. Romanenko ◽  
Elena A. Interesova ◽  
Manfred Schartl ◽  
...  
Keyword(s):  
Duplication Event ◽  
Siberian Sturgeon ◽  
Genome Duplication Event ◽  
Acipenser Baerii ◽  
Whole Genome Duplications ◽  
Sturgeon Species ◽  
Genome Duplications ◽  
Size Groups ◽  
Genomic Studies ◽  
Syntenic Regions

Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.

scholarly journals A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Shubo Jin ◽  
Chao Bian ◽  
Sufei Jiang ◽  
Kai Han ◽  
Yiwei Xiong ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Evolutionary Biology ◽  
Sex Differentiation ◽  
Duplication Event ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Macrobrachium Nipponense ◽  
Oriental River Prawn ◽  
Chromosome Level

Abstract Background The oriental river prawn, Macrobrachium nipponense, is an economically important shrimp in China. Male prawns have higher commercial value than females because the former grow faster and reach larger sizes. It is therefore important to reveal sex-differentiation and development mechanisms of the oriental river prawn to enable genetic improvement. Results We sequenced 293.3 Gb of raw Illumina short reads and 405.7 Gb of Pacific Biosciences long reads. The final whole-genome assembly of the Oriental river prawn was ∼4.5 Gb in size, with predictions of 44,086 protein-coding genes. A total of 49 chromosomes were determined, with an anchor ratio of 94.7% and a scaffold N50 of 86.8 Mb. A whole-genome duplication event was deduced to have happened 109.8 million years ago. By integration of genome and transcriptome data, 21 genes were predicted as sex-related candidate genes. Conclusion The first high-quality chromosome-level genome assembly of the oriental river prawn was obtained. These genomic data, along with transcriptome sequences, are essential for understanding sex-differentiation and development mechanisms in the oriental river prawn, as well as providing genetic resources for in-depth studies on developmental and evolutionary biology in arthropods.

scholarly journals The ancient Salicoid genome duplication event: A platform for reconstruction of de Novo gene evolution in Populus trichocarpa

2021 ◽  
Author(s):  
Timothy B Yates ◽  
Kai Feng ◽  
Jin Zhang ◽  
Vasanth Singan ◽  
Sara S Jawdy ◽  
...  
Keyword(s):  
Genome Duplication ◽  
De Novo ◽  
Gene Evolution ◽  
Populus Trichocarpa ◽  
Duplication Event ◽  
Functional Enrichment ◽  
Orphan Genes ◽  
Genome Duplication Event ◽  
Orphan Gene ◽  
De Novo Gene

Abstract Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event (WGD) which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from inter-genera, inter-species, and intra-genomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel (GWAS), a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.

Poplar defense against insect herbivoresThis review is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

2007 ◽  
Vol 85 (12) ◽  
pp. 1111-1126 ◽  
Author(s):  
Ryan N. Philippe ◽  
Jörg Bohlmann
Keyword(s):  
Chemical Ecology ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Insect Pests ◽  
Populus Trichocarpa ◽  
Relevant Literature ◽  
Wood Formation ◽  
Genomic Research ◽  
Black Cottonwood ◽  
Genomics Research

The availability of a poplar ( Populus trichocarpa Torr & A. Gray, black cottonwood) genome sequence is enabling new research approaches in angiosperm tree biology. Much of the recent genomics research in poplars has been on wood formation, growth and development, resistance to abiotic stress and pathogens, motivated, at least in part, by the fact that poplars provide an important system for large-scale, short-rotation plantation forestry in the Northern Hemisphere. To sustain productivity and ecosystem health of natural and planted poplar forests it is of critical importance to also develop a better understanding of the molecular mechanisms of defense and resistance of poplars against insect pests. Previous research has established a solid foundation of the chemical ecology of poplar defense against insects. This review summarizes some of the relevant literature on defense against insect herbivores in poplars with an emphasis on molecular, biochemical, and emerging genomic research in this important field within forest biotechnology and chemical ecology. Following a general introduction, we provide a brief overview of some of the most relevant insect pests of poplars; we then describe some of the general defense strategies of poplars along with selected examples of their activities. We conclude with a summary of emerging results and perspectives from recent advances in genomics research on poplar defense against insects.

Populus trichocarpa MONOPTEROS/AUXIN RESPONSE FACTOR5 (ARF5) genes: comparative structure, sub-functionalization, and Populus–Arabidopsis microsyntenyThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

2007 ◽  
Vol 85 (11) ◽  
pp. 1058-1070 ◽  
Author(s):  
Lee A. Johnson ◽  
Carl J. Douglas
Keyword(s):  
Secondary Xylem ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Fold Increase ◽  
Duplication Event ◽  
Sequence Information ◽  
Auxin Response ◽  
Genome Duplication Event ◽  
Regulatory Module ◽  
Comparative Structure

The genome of Populus (poplar) has been shaped by a whole genome duplication event specific to the salicoid lineage. The MONOPTEROS (MP)/AUXIN RESPONSE FACTOR5 (ARF5) transcription factor plays a key role in auxin-mediated morphogenesis and vascular development in Arabidopsis , and may play a similar role in secondary xylem development in Populus. We used EST and genome sequence information to identify and characterize two duplicated Populus MP genes, PoptrMP1 and PoptrMP2. PoptrMP1 and PoptrMP2 DNA binding and other domains are highly conserved relative to Arabidopsis MP, while the glutamine-rich middle domains are divergent. The two PoptrMP genes are located on duplicated regions of linkage groups II and V. Comparative analysis of the surrounding genes in both the Populus and Arabidopsis genomes revealed a high degree of conservation of gene content and order extending over 11 genes in the immediate vicinity, but also specific changes to genomic regions surrounding each MP locus, providing insights into genome evolution. Expression studies showed that PoptrMP1 and PoptrMP2 have overlapping but distinct expression patterns, suggesting that subfunctionalization of the duplicated genes has occurred, with PoptrMP1 specialized for expression in developing secondary xylem. Transgenic Populus lines overexpressing PoptrMP1 exhibited a 2–4 fold increase in expression of a Populus AtHB8 homolog, a proposed MP target gene, confirming conservation of this regulatory module.

scholarly journals High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Yun Li ◽  
Hairong Wei ◽  
Jun Yang ◽  
Kang Du ◽  
Jiang Li ◽  
...  
Keyword(s):  
De Novo ◽  
Mevalonate Pathway ◽  
Genome Structure ◽  
Duplication Event ◽  
Eucommia Ulmoides ◽  
Long Terminal Repeats ◽  
High Quality ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Rubber Biosynthesis

Abstract We report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species, Eucommia ulmoides, which is known for its rubber biosynthesis and medicinal applications. The assembly was obtained by applying PacBio and Hi–C technologies to a haploid that we specifically generated. Compared to the initial genome release, this one has significantly improved assembly quality. The scaffold N50 (53.15 MB) increased 28-fold, and the repetitive sequence content (520 Mb) increased by 158.24 Mb, whereas the number of gaps decreased from 104,772 to 128. A total of 92.87% of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes. A new whole-genome duplication event was superimposed on the earlier γ paleohexaploidization event, and the expansion of long terminal repeats contributed greatly to the evolution of the genome. The more primitive rubber biosynthesis of this species, as opposed to that in Hevea brasiliensis, relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate, as the MEP pathway operates predominantly in trans-polyisoprene-containing leaves and central peels. Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark. This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution, gene mapping, epigenetic analysis and functional genomics but also efforts to improve E. ulmoides for industrial and medical uses through genetic engineering.

scholarly journals A high-quality chromosome-level genome of wild Rosa rugosa

DNA Research ◽  
2021 ◽  
Vol 28 (5) ◽  
Author(s):  
Fengqi Zang ◽  
Yan Ma ◽  
Xiaolong Tu ◽  
Ping Huang ◽  
Qichao Wu ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Duplication Event ◽  
Genome Sequences ◽  
Rosa Rugosa ◽  
High Quality ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Chromosome Level

Abstract Rosa rugosa is an important shrub with economic, ecological, and pharmaceutical value. A high-quality chromosome-scale genome for R. rugosa sequences was assembled using PacBio and Hi-C technologies. The final assembly genome sequences size was about 407.1 Mb, the contig N50 size was 2.85 Mb, and the scaffold N50 size was 56.6 Mb. More than 98% of the assembled genome sequences were anchored to seven pseudochromosomes (402.9 Mb). The genome contained 37,512 protein-coding genes, with 37,016 genes (98.68%) that were functionally annotated, and 206.67 Mb (50.76%) of the assembled sequences are repetitive sequences. Phylogenetic analyses indicated that R. rugosa diverged from Rosa chinensis ∼6.6 million years ago, and no lineage-specific whole-genome duplication event occurred after divergence from R. chinensis. Chromosome synteny analysis demonstrated highly conserved synteny between R. rugosa and R. chinensis, between R. rugosa and Prunus persica as well. Comparative genome and transcriptome analysis revealed genes related to colour, scent, and environment adaptation. The chromosome-level reference genome provides important genomic resources for molecular-assisted breeding and horticultural comparative genomics research.

PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions

2019 ◽  
Vol 14 (7) ◽  
pp. 621-627 ◽  
Author(s):  
Youhuang Bai ◽  
Xiaozhuan Dai ◽  
Tiantian Ye ◽  
Peijing Zhang ◽  
Xu Yan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Populus Trichocarpa ◽  
Noncoding Rnas ◽  
Reference Database ◽  
Protein Coding ◽  
Arabidopsis Lyrata ◽  
User Friendly

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface. Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.

scholarly journals A peroxisomal β-oxidative pathway contributes to the formation of C6–C1 aromatic volatiles in poplar

2021 ◽  
Author(s):  
Nathalie D Lackus ◽  
Axel Schmidt ◽  
Jonathan Gershenzon ◽  
Tobias G Köllner
Keyword(s):  
Cinnamic Acid ◽  
Aromatic Compounds ◽  
Populus Trichocarpa ◽  
Alternative Pathway ◽  
Gene Families ◽  
Defense Responses ◽  
In Planta ◽  
Black Cottonwood ◽  
Oxidative Pathway

AbstractBenzenoids (C6–C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6–C3). The biosynthesis of C6–C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6–C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

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