Diverse Forms of Guanylyl Cyclases in Medaka Fish – Their Genomic Structure and Phylogenetic Relationships to those in Vertebrates and Invertebrates

Abstract BackgroundThe perennial shrub of Calligonum mongolicum is a dominant native plant in all Calligonum species, which has the largest and most widespread geographic distribution in arid deserts of northern China. Understanding the phylogenetic relationship between C. mongolicum and closely related plant species will offer guidance on the classification and identification of inter-species and their varieties. The chloroplast (cp) genome is an optimal model to decipher phylogenetic relationships and genome evolution in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced, and the characteristics were described, then the genomic structure was compared to other three Polygonaceae species.ResultsThe cp genome of C. mongolicum was 162,124 bp in length with a quadripartite structure. A total of 131 functional genes were annotated, 14 different genes of which harbored introns and exons, 50 long repeat sequences and 244 simple sequences repeats were identiﬁed. Synonymous codon usage (SCU) analysis exhibited A/T preference, and 7 codons were identified as the optimal codons. Multivariate statistical analysis of parity rule 2, ENC-plot, and neutrality plot were combined conducted to imply natural selection as the crucial constraint in SCU bias in C. mongolicum cp genome.The phylogenetic tree showed that Rumex acetosa was the most related plant to C. mongolicum. From the comparative analysis of genomic structures, the inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions was relatively conserved than non-coding regions. Compared to other species in the Polygonaceae, the borders of IRb/SSC and SSC/IRa in C. mongolicum changed greatly. Furthermore, adaptive evolution analysis of 75 orthologous protein-coding genes indicated that only the psbK gene was under positive selection, which might be crucial in the adaptive evolution of C. mongolicum.ConclusionsOur results comprehensively depicts the architecture of C. mongolicum cp genome, and will lay a vigorous foundation for further study on molecular marker selection, phylogenetic analysis, and population researches in Calligonum species.

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Genomic Structure and Expression of the Soluble Guanylyl Cyclase α2Subunit Gene in the Medaka Fish Oryzias latipes

ZOOLOGICAL SCIENCE ◽

10.2108/zsj.20.1293 ◽

2003 ◽

Vol 20 (10) ◽

pp. 1293-1304 ◽

Cited By ~ 4

Author(s):

Yuko Yao ◽

Takehiro Yamamoto ◽

Makiko Tsutsumi ◽

Masaru Matsuda ◽

Hiroshi Hori ◽

...

Keyword(s):

Guanylyl Cyclase ◽

Genomic Structure ◽

Soluble Guanylyl Cyclase ◽

Oryzias Latipes ◽

Medaka Fish

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Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

10.21203/rs.3.rs-49271/v1 ◽

2020 ◽

Author(s):

Huirong Duan ◽

Qian Zhang ◽

Hongshan Yang ◽

Fuping Tian ◽

Yu Hu ◽

...

Keyword(s):

Codon Usage ◽

Adaptive Evolution ◽

Phylogenetic Relationships ◽

Genomic Structure ◽

Native Plant ◽

Coding Regions ◽

Evolution Analysis ◽

Optimal Codons ◽

Related Plant ◽

Cp Genome

Abstract Background The perennial shrub of Calligonum mongolicum is a dominant native plant in all Calligonum species, which has the largest and most widespread geographic distribution in arid deserts of northern China. Understanding the phylogenetic relationship between C. mongolicum and closely related plant species will offer guidance on the classification and identification of inter-species and their varieties. The chloroplast (cp) genome is an optimal model to decipher phylogenetic relationships and genome evolution in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced, and the characteristics were described, then the genomic structure was compared to other three Polygonaceae species.Results The cp genome of C. mongolicum was 162,124 bp in length with a quadripartite structure. A total of 131 functional genes were annotated, 14 different genes of which harbored introns and exons, 50 long repeat sequences and 244 simple sequences repeats were identified. Synonymous codon usage (SCU) analysis exhibited A/T preference, and 7 codons were identified as the optimal codons. Multivariate statistical analysis of parity rule 2, ENC-plot, and neutrality plot were combined conducted to imply natural selection as the crucial constraint in SCU bias in C. mongolicum cp genome.The phylogenetic tree showed that Rumex acetosa was the most related plant to C. mongolicum. From the comparative analysis of genomic structures, the inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions was relatively conserved than non-coding regions. Compared to other species in the Polygonaceae, the borders of IRb/SSC and SSC/IRa in C. mongolicum changed greatly. Furthermore, adaptive evolution analysis of 75 orthologous protein-coding genes indicated that only the psbK gene was under positive selection, which might be crucial in the adaptive evolution of C. mongolicum.Conclusions Our results comprehensively depicts the architecture of C. mongolicum cp genome, and will lay a vigorous foundation for further study on molecular marker selection, phylogenetic analysis, and population researches in Calligonum species.

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The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

BMC Genomics ◽

10.1186/s12864-021-07968-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhongyu Du ◽

Ke Lu ◽

Kai Zhang ◽

Yiming He ◽

Haitao Wang ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Higher Plants ◽

Genomic Structure ◽

Divergence Time ◽

Gc Content ◽

Single Copy ◽

Genome Sequences ◽

Cp Genome ◽

Small Single Copy ◽

Large Single Copy Region

Abstract Background Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus. Results The results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya. Conclusion Our results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time.

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Architecture of Radiolitid Rudist (Mollusca) Shell-Wall Structures and its Phylogenetic Implications

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100117054 ◽

1975 ◽

Vol 33 ◽

pp. 686-687

Author(s):

David H. Sturm ◽

Bob F. Perkins

Keyword(s):

Phylogenetic Relationships ◽

Outer Wall ◽

Shell Microstructure ◽

Shell Wall ◽

Wall Structures ◽

Phylogenetic Implications ◽

Cellular Wall ◽

Superfamily Analysis ◽

Central Texas

Each of the seven families of rudists (Mollusca, Bivalvia, Hippuritacea) is characterized by distinctive shell-wall architectures which reflect phylogenetic relationships within the superfamily. Analysis of the complex, calcareous, cellular wall of the attached valve of the radiolite rudist Eoradiolites davidsoni (Hill) from the Comanche Cretaceous of Central Texas indicates that its wall architecture is an elaboration of the simpler monopleurid rudist wall and supports possible radiolite-monopleurid relationships.Several well-preserved specimens of E. davidsoni were sectioned, polished, etched, and carbon and gold coated for SEM examination. Maximum shell microstructure detail was displayed by etching with a 0.7% HC1 solution from 80 to 100 seconds.The shell of E. davidsoni comprises a large, thick-walled, conical, attached valve (AV) and a small, very thin, operculate, free valve (FV) (Fig. 1a). The AV shell is two-layered with a thin inner wall, in which original structures are usually obliterated by recrystallization, and a thick, cellular, outer wall.

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