scholarly journals Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 63
Author(s):  
Xiu-Xiu Guo ◽  
Xiao-Jian Qu ◽  
Xue-Jie Zhang ◽  
Shou-Jin Fan
Keyword(s):  
Carbon Fixation ◽  
Repeat Sequence ◽  
Phylogenetic Position ◽  
Drought Event ◽  
Protein Coding ◽  
Variable Regions ◽  
Coding Sequences ◽  
The Difference ◽  
Usage Analysis ◽  
Phylogeny And Evolution

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.

Genetic variation in mRNA coding sequences of highly conserved genes

2001 ◽  
Vol 5 (3) ◽  
pp. 113-118 ◽  
Author(s):  
ANNELOOR L. M. A. TEN ASBROEK ◽  
JEFFREY OLSEN ◽  
DAVID HOUSMAN ◽  
FRANK BAAS ◽  
VINCE STANTON
Keyword(s):  
Disease Genes ◽  
Protein Coding ◽  
Coding Sequences ◽  
Human Genes ◽  
Evolutionarily Conserved ◽  
Conserved Genes ◽  
The Difference ◽  
Minimum Estimate ◽  
Human Disease Genes ◽  
Evolutionary Comparisons

The frequency and distribution of genetic polymorphism in the human genome is a question of major importance. We have studied this in highly conserved genes, which encode crucial functions such as DNA replication, mRNA transcription, and translation. Evolutionary comparisons suggest that these genes are under particularly strong selective pressure, and their frequency of nucleotide sequence polymorphism would be expected to represent a minimum estimate for sequence variation throughout the genome. We have analyzed the complete coding sequence and the 3′-untranslated region (3′-UTR) of 22 human genes, most of which have homologs in all cellular organisms and all of which are at least 25% amino acid identical to homologs in yeast. Comparisons with similar studies of less conserved human disease genes indicate that 1) evolutionarily conserved genes are, on average, less polymorphic than disease related genes; 2) the difference in polymorphism levels is attributable almost entirely to reduced levels of variation in protein coding sequences, whereas noncoding sequences have similar levels of polymorphism; and 3) the character of polymorphism, in terms of the spectrum and frequency of mutational changes, is similar.

scholarly journals Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1332
Author(s):  
Kai Jiang ◽  
Li-Yuan Miao ◽  
Zheng-Wei Wang ◽  
Zi-Yi Ni ◽  
Chao Hu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Protein Coding ◽  
Variable Regions ◽  
Sequencing Platform ◽  
Close Relationship

Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.

scholarly journals Characterization of the First Complete Mitochondrial Genome of Cyphonocerinae (Coleoptera: Lampyridae) with Implications for Phylogeny and Evolution of Fireflies

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 570
Author(s):  
Xueying Ge ◽  
Lilan Yuan ◽  
Ya Kang ◽  
Tong Liu ◽  
Haoyu Liu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Repeat Sequence ◽  
Protein Coding ◽  
Gc Skew ◽  
Complete Mitogenome ◽  
Phylogeny And Evolution ◽  
Complete Mitochondrial Genomes

Complete mitochondrial genomes are valuable resources for phylogenetics in insects. The Cyphonoceridae represents an important lineage of fireflies. However, no complete mitogenome is available until now. Here, the first complete mitochondrial genome from this subfamily was reported, with Cyphonocerus sanguineus klapperichi as a representative. The mitogenome of C. sanguineus klapperichi was conserved in the structure and comparable to that of others in size and A+T content. Nucleotide composition was A+T-biased, and all genes exhibited a positive AT-skew and negative GC-skew. Two types of tandem repeat sequence units were present in the control region (136 bp × 2; 171 bp × 2 + 9 bp). For reconstruction of Lampyridae’s phylogeny, three different datasets were analyzed by both maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, the same topology was produced by both ML analysis of 13 protein-coding genes and 2rRNA and BI analysis of 37 genes. The results indicated that Lampyridae, Lampyrinae, Luciolinae (excluding Emeia) were monophyletic, but Ototretinae was paraphyletic, of which Stenocladius was recovered as the sister taxon to all others, while Drilaster was more closely related to Cyphonocerinae; Phturinae + Emeia were included in a monophyletic clade, which comprised sister groups with Lampyridae. Vesta was deeply rooted in the Luciolinae.

scholarly journals Comparative analysis of whole chloroplast genomes of Ligusticum sinense and L. jeholense, Umbelliferae

2020 ◽  
Author(s):  
Shijie Wang ◽  
Tingting Zhang ◽  
Liang Xu ◽  
Zhilai Zhan ◽  
Guihua Bao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Higher Plants ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Atpase Subunit ◽  
Gene Group ◽  
Gene Variation ◽  
Chloroplast Genomes ◽  
The Difference ◽  
Cp Genome

Abstract Background Gaoben has a long history of application as medicine. There are few records of Liaogaoben in ancient books. The varieties of Ligusticum in practical application are confused. Therefore, it is very important to identify Ligusticum accurately. The phylogenetic position of Ligusticum in Umbelliferae needs to be determined. It is also of great significance to analyze the phylogeny of Ligusticum in Umbelliferae the difference of somatic genome. Methods Chloroplast (cp) genomic DNA was extracted from two species of Ligusticum and sequenced on Hiseq4000 light source. The sequence was assembled into contrags by soapenovo 2.04, aligned with reference genome by blast, and then corrected manually. Genereanation is performed by online dogma tools. The general characteristics of cp genomes of two species were analyzed, and compared with the relative species. The DNA of chloroplasts of higher plants is double stranded covalently closed loop molecule, and its length varies with species. According to the assembly genome sequence of the sequenced samples, combined with the prediction results of the coding genes, the genome of the samples was displayed in circles. After alignment, the evolutionary tree was constructed based on the single nucleotide polymorphism (SNP) of cp genome in 31 species by ML method. Results The whole chloroplast genome of Gaoben and Liaogaoben is 148,515 bp and 148,493 bp, both of which contain IR (IRa and IRb) LSC and SSC. 127 genes have been annotated, including 83 protein coding genes, 8 tRNA and 36 rRNA of all species, and 28 coding genes in IR region. There are six genes in the ATPase subunit of photosynthesis gene group, and there are obvious differences in the types of introns in NADH dehydrogenase subunit between them. In the comparative analysis of Pi value, two significant gene variation points are petG gene and psaL-ycf4 gene. The phylogenetic tree of the whole cp genome of SNP Umbelliferae was constructed, including 28 Umbelliferae and 3 Ligusticum. Conclusions In this study, the cp genomic characteristics of Ligusticum sinense and L. jeholense were identified, which provided a theoretical basis and documentation for the identification and phylogenetic analysis of Ligusticum.

Polymorphisms of the Plasminogen Activator Inhibitor- 1 Gene in Type 1 and Type 2 Diabetes, and in Patients with Diabetic Retinopathy

1994 ◽  
Vol 71 (06) ◽  
pp. 731-736 ◽  
Author(s):  
M W Mansfield ◽  
M H Stickland ◽  
A M Carter ◽  
P J Grant
Keyword(s):  
Diabetic Retinopathy ◽  
Plasminogen Activator Inhibitor ◽  
Allelic Frequency ◽  
Repeat Sequence ◽  
Dinucleotide Repeat ◽  
Plasminogen Activator Inhibitor 1 ◽  
The Difference ◽  
Pai 1

SummaryTo identify whether genotype contributes to the difference in PAI-1 levels in type 1 and type 2 diabetic subjects and whether genotype relates to the development of retinopathy, a Hind III restriction fragment length polymorphism and two dinucleotide repeat polymorphisms were studied. In 519 Caucasian diabetic subjects (192 type 1, 327 type 2) and 123 Caucasian control subjects there were no differences in the frequency of the Hind III restriction alleles (type 1 vs type 2 vs control: allele 1 0.397 vs 0.420 vs 0.448; allele 2 0.603 vs 0.580 vs 0.552) nor in the allelic frequency at either dinucleotide repeat sequence. In 86 subjects with no retinopathy at 15 years or more from diagnosis of diabetes and 190 subjects with diabetic retinopathy there was no difference in the frequency of Hind III restriction alleles (retinopathy present vs retinopathy absent: allele 1 0.400 vs 0.467; allele 2 0.600 vs 0.533) nor in the allelic frequencies at either dinucleotide repeat sequence. The results indicate that there is no or minimal influence of the PAI-1 gene on either PAI-1 levels or the development of diabetic retinopathy in patients with diabetes mellitus.

scholarly journals Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Si Chul Kim ◽  
Hyo Jung Lee
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gram Negative ◽  
Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

scholarly journals Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 326
Author(s):  
Yu-Jun Wang ◽  
Hua-Ling Wang ◽  
Xiao-Wei Wang ◽  
Shu-Sheng Liu
Keyword(s):  
Gene Expression ◽  
Slow Rate ◽  
Species Complex ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Coding Sequences ◽  
Species Comparisons ◽  
Differential Gene ◽  
Males And Females ◽  
And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

scholarly journals Land surface model photosynthesis and parameter calibration for boreal sites with adaptive population importance sampler

2019 ◽  
Author(s):  
Jarmo Mäkelä ◽  
Jürgen Knauer ◽  
Mika Aurela ◽  
Andrew Black ◽  
Martin Heimann ◽  
...  
Keyword(s):  
Stomatal Conductance ◽  
Land Surface ◽  
Carbon Fixation ◽  
Gross Primary Production ◽  
Effect Of Temperature ◽  
Coefficient Of Determination ◽  
Surface Model ◽  
Drought Event ◽  
Forest Site ◽  
Delayed Effect

Abstract. We calibrated the JSBACH model with six different stomatal conductance formulations using measurements from 10 FLUXNET coniferous evergreen sites in the Boreal zone. The parameter posterior distributions were generated by adaptive population importance sampler and the optimal values by a simple stochastic optimisation algorithm. The observations used to constrain the model are evapotranspiration (ET) and gross primary production (GPP). We identified the key parameters in the calibration process. These parameters control the soil moisture stress function and the overall rate of carbon fixation. We were able to improve the coefficient of determination and the model bias with all stomatal conductance formulations. There was no clear candidate for the best stomatal conductance model, although certain versions produced better estimates depending on the examined variable (ET, GPP) and the used metric. We were also able to significantly enhance the model behaviour during a drought event in a Finnish Scots pine forest site. The JSBACH model was also modified to use a delayed effect of temperature for photosynthetic activity. This modification enabled the model to correctly time and replicate the springtime increase in GPP (and ET) for conifers throughout the measurements sites used in this study.

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