Origins and chromosome differentiation of Thinopyrum elongatum revealed by PepC, Pgk1 genes and ND-FISH

Thinopyrum elongatum is an important gene pool for wheat genetic improvement. However, the origins of the Thinopyrum genomes and the nature of the genus’ intraspecific relationships are still controversial. In this study, we used single-copy nuclear genes and non-denaturing fluorescence in situ hybridization (ND-FISH) to characterize genome constitution and chromosome differentiation in Th. elongatum. According to phylogenetic analyses based on PepC and Pgk1 genes, there was an E genome with three versions (Ee, Eb, Ex) and St genomes in the polyploid Th. elongatum. The ND-FISH results of pSc119.2 and pAs1 revealed that the karyotypes of diploid Th. elongatum and Th. bessarabicum were different and the chromosome differentiation occurred among accessions of the diploid Th. elongatum. In addition, the tetraploid Th. elongatum has two groups of ND-FISH karyotype, indicating that the tetraploid Th. elongatum might be a segmental allotetraploid. In summary, our results suggested that the diploid Th. elongatum, Th. bessarabicum and Pseudoroegneria were the donors of the Ee, Eb and St genome to polyploid Th. elongatum species, respectively.

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Genomic constitution and phylogenetic position of several New Zealand Triticeae species revealed by two single copy nuclear genes

Australian Journal of Botany ◽

10.1071/bt10195 ◽

2011 ◽

Vol 59 (1) ◽

pp. 1 ◽

Cited By ~ 3

Author(s):

Aimee G. Oliver ◽

Kara Harnish ◽

Genlou Sun

Keyword(s):

New Zealand ◽

North American ◽

Diploid Species ◽

Single Copy ◽

Nuclear Genes ◽

Phylogenetic Position ◽

Genome Constitution ◽

Elymus Species ◽

New Zealand Flora ◽

Hordeum Species

Three genera of Triticeae, Elymus, Stenostachys and Australopyrum, are described in the New Zealand flora. Cytological analyses suggested that five basic genomes (St, H, Y, P and W) donated by different diploid species in different combinations exist in the genera Elymus and Stenostachys, whereas Australopyrum species contain the W genome only. Morphological and cytogenetic data suggested that the genome constitution for both E. apricus and E. multiflorus is StYW. Chloroplast DNA and ITS data supported the genome constitution of these Elymus species, but the HW genome constitution was assigned to the Stenostachys species. In this study, sequences of two single copy nuclear genes, RPB2 and DMC1, were used to confirm or refute the genome constitutions of the two Stenostachys species and the two Elymus species from New Zealand, and to analyse their phylogenetic relationships with other Elymus species. Our RPB2 and DMC1 data confirmed that the genome constitution of hexaploid E. apricus is StWY, and tetraploid S. gracilis is HW. The presence of the StW genome in hexaploid E. multiflorus, and the W genome in tetraploid S. laevis is also confirmed. No obvious St genome differentiation between New Zealand and non-New Zealand species is observed. The H genomes in the S. gracilis and S. laevis are closely related to the H genome from North American species, indicating that the H genomes in these two New Zealand species might originate from North American Hordeum species.

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Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

10.1101/2021.02.25.432805 ◽

2021 ◽

Author(s):

Bin-Bin Liu ◽

Zhi-Yao Ma ◽

Chen Ren ◽

Richard G.J. Hodel ◽

Miao Sun ◽

...

Keyword(s):

Ribosomal Dna ◽

Phylogenetic Analyses ◽

Single Copy ◽

Sequencing Depth ◽

Nuclear Genes ◽

Nuclear Ribosomal Dna ◽

Plant Systematics ◽

Genome Skimming ◽

Enrichment Experiments ◽

And Performance

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage in silico. We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10x coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.

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Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Journal of Systematics and Evolution ◽

10.1111/jse.12806 ◽

2021 ◽

Author(s):

Bin‐Bin Liu ◽

Zhi‐Yao Ma ◽

Chen Ren ◽

Richard G.J. Hodel ◽

Miao Sun ◽

...

Keyword(s):

Ribosomal Dna ◽

Single Copy ◽

Nuclear Genes ◽

Nuclear Ribosomal Dna ◽

Organellar Genomes ◽

Genome Skimming ◽

Plant Phylogenetics

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Fluorescence in situ hybridization on plant extended chromatin DNA fibers for single-copy and repetitive DNA sequences

Plant Cell Reports ◽

10.1007/s00299-011-1086-y ◽

2011 ◽

Vol 30 (9) ◽

pp. 1779-1786 ◽

Cited By ~ 5

Author(s):

Kun Yang ◽

Hecui Zhang ◽

Richard Converse ◽

Yong Wang ◽

Xiaoying Rong ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Repetitive Dna ◽

Dna Sequences ◽

Single Copy ◽

Repetitive Dna Sequences

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A Full-Ocean-Depth Sampler for Hadal Microbes Based on Multistage Membrane Filters With In-Situ Preservation

Marine Technology Society Journal ◽

10.4031/mtsj.55.2.10 ◽

2021 ◽

Vol 55 (2) ◽

pp. 25-34

Author(s):

Jiawang Chen ◽

Weitao He ◽

Peng Zhou ◽

Jiasong Fang ◽

Dahai Zhang ◽

...

Keyword(s):

Ribonucleic Acid ◽

Gene Pool ◽

Special Structure ◽

High Quality ◽

Mariana Trench ◽

Membrane Filters ◽

In Situ Preservation ◽

Microbial Samples ◽

Flow Pump

Abstract In order to obtain high-quality microbial samples from the hadal zone, which has a depth of over 6,000 m, a full-ocean-depth sampler with the function of in-situ filtration and preservation was developed. A flow pump and several membrane filters were used for in-situ filtration under the sea. With a multistage filtering structure, the microbes can be initially screened according to their sizes. To avoid the degradation of microbial ribonucleic acid (RNA), a special structure was designed to inject the RNAlater solution into the samples immediately after the filtration. The sampler was tested in our laboratory and deployed during Mariana TS-15 in 2019. It was installed on a hadal lander of Shanghai Ocean University and deployed at MBR02 (11.371°N, 142.587°E, 10,931 m) in the Mariana Trench. A total of 20 L of in-situ seawater was filtered, and membranes with pore sizes of 3 and 0.2 μm were preserved. The study is expected to provide important support for the establishment of a hadal microbial gene pool.

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Primed in situ labeling for detecting single-copy genes

Genetics and Molecular Research ◽

10.4238/vol10-3gmr1391 ◽

2011 ◽

Vol 10 (3) ◽

pp. 1884-1890 ◽

Cited By ~ 5

Author(s):

J.-L. Gao ◽

Y. Nie ◽

X.-P. Ding

Keyword(s):

Single Copy

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Enhancement of antimicrobial diversity in situ through relaxed symbiont specificity in an insect/actinomycete partnership

10.1101/2020.12.02.394189 ◽

2020 ◽

Author(s):

Rita de Cassia Pessotti ◽

Bridget L. Hansen ◽

Jewel N. Reaso ◽

Javier A. Ceja-Navarro ◽

Laila El-Hifnawi ◽

...

Keyword(s):

Social Behavior ◽

Metarhizium Anisopliae ◽

Phylogenetic Analyses ◽

Pathogen Resistance ◽

Transmission Mechanism ◽

Fecal Material ◽

Fungal Entomopathogen ◽

Symbiont Transmission ◽

Chemical Strategies

ABSTRACTSome insects form symbioses in which actinomycetes provide defense against pathogens by making antimicrobials. The range of chemical strategies employed across these symbioses, and how these strategies relate to insect social behavior and mechanisms of symbiont transmission, remains underexplored. Here, we assess subsocial passalid beetles Odontotaenius disjunctus (known as bessbugs), and their frass (fecal material), as a model insect/actinomycete system. Through chemical and phylogenetic analyses, we found that O. disjunctus associates with an exceptionally wide variety of actinomycetes and antimicrobials. Metabolites detected directly in frass displayed both synergistic and antagonistic inhibition of a fungal entomopathogen, Metarhizium anisopliae, and multiple streptomycete isolates inhibited this pathogen when co-cultivated directly in frass. Together, these findings support a model in which coprophagy as a vertical transmission mechanism leads to relaxed symbiote specificity, resulting in a rich and dynamic repertoire of antimicrobials that insulates O. disjunctus against the evolution of pathogen resistance.

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