scholarly journals The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 478 ◽  
Author(s):  
Yanli Xiong ◽  
Yi Xiong ◽  
Jun He ◽  
Qingqing Yu ◽  
Junming Zhao ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Genome Structure ◽  
Divergence Time ◽  
Global Alignment ◽  
Trifolium Alexandrinum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Annual Grasses ◽  
Cp Genome

Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species.

scholarly journals The chloroplast genome sequencing of two important annual Trifolium species T. alexandrinum and T. resupinatum and comparative analysis with other congeneric species

2020 ◽  
Author(s):  
yanli xiong ◽  
yi xiong ◽  
jun he ◽  
qingqing yu ◽  
junming zhao ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Evolutionary Process ◽  
Crustal Movement ◽  
Nucleotide Polymorphisms ◽  
Reading Frame ◽  
Cp Genome ◽  
Cretaceous Period ◽  
Land Changes

Abstract Background: Chloroplast (cp) genome of most plant species has two typical inverted-repeats (IRs) regions. However, in some species this IR structure is lost for unknown reasons and the consequence still needs to be revealed . Here, we present whole cp genome sequencing of Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover) from the IR lacking clade (IRLC) . Results: Global aligning of T. alexandrinum and T. resupinatum to other eight Trifolium species revealed a large amount of rearrangement and repetitive events in these ten species. We found that IR lacking species have lower GC content and higher percentage of repetition than IR containing species. Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits severally, two genes ycf1 and rpoC2 in the cp genomes, which both contain vast repetitive sequences and high Pi values (0.6656, 0.455) between T. alexandrinum and T. resupinatum , possessed highly variation among ten Trifolium species. Thus they could greatly influence evolutionary process of Trifolium species. In addition, IR containing and IR lacking Trifolium species were estimated to split during the upper Cretaceous period, which was potentially related to the violent crustal movement and sea-land changes. Conclusions: Cp genomes of T. alexandrinum and T. resupinatum, which belong to IRLC were sequenced and annotated in present study, and compared with cp genomes of other eight Trifolium species reported previously. This valuable information will provide insight into the evolution of IR lacking species. Nevertheless, further investigating of the detailed reason of IR lacking is still challenging, but it may be related to the violent crustal movement and sea-land changes of the Cretaceous period presented in this study.

scholarly journals Molecular Cloning, Expression Profiling, and Marker Validation of the Chicken Myoz3 Gene

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Maosen Ye ◽  
Fei Ye ◽  
Liutao He ◽  
Yiping Liu ◽  
Xiaoling Zhao ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Fiber Type ◽  
Breast Muscle ◽  
Nucleotide Polymorphisms ◽  
Amino Acid Sequence Analysis ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Marker Validation ◽  
Basic Characteristics ◽  
Fiber Type Differentiation

Myozenin3 (Myoz3) has been reported to bind multiple Z-disc proteins and hence play a key role in signal transduction and muscle fiber type differentiation. The purpose of current study is to better understand the basic characteristics of Myoz3. Firstly, we cloned the ORF (open reading frame) of the Myoz3 gene. AA (amino acid) sequence analysis revealed that the Myoz3 gene encodes a 26 kDa protein which have 97% identities with that of turkey. Expression profiling showed that Myoz3 mRNA is mainly expressed in leg muscle and breast muscle. Furthermore, we investigated Myoz3 gene polymorphisms in two broiler breeds, the Yellow Bantam (YB) and the Avian. Five SNPs (single nucleotide polymorphisms) were identified in the YB breed and 3 were identified in the Avian breed. Genotypes and haplotype were constructed and their associations with carcass traits were analyzed. In the YB breed, c.516 C>T had a strong effect on both shank bone length and the L⁎ value of breast muscle, and the H1H3 diplotype had the highest FC compared to other diplotypes. The markers identified in this study may serve as useful targets for the marker-assisted selection (MAS) of growth and meat quality traits in chickens.

scholarly journals Causal Role of Single Nucleotide Polymorphisms within themprFGene of Staphylococcus aureus in Daptomycin Resistance

2013 ◽  
Vol 57 (11) ◽  
pp. 5658-5664 ◽  
Author(s):  
Soo-Jin Yang ◽  
Nagendra N. Mishra ◽  
Aileen Rubio ◽  
Arnold S. Bayer
Keyword(s):  
Staphylococcus Aureus ◽  
Single Nucleotide Polymorphisms ◽  
Point Mutations ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Content Type ◽  
Reading Frame ◽  
A Charge

ABSTRACTSingle nucleotide polymorphisms (SNPs) within themprFopen reading frame (ORF) have been commonly observed in daptomycin-resistant (DAPr)Staphylococcus aureusstrains. Such SNPs are usually associated with a gain-in-function phenotype, in terms of either increased synthesis or enhanced translocation (flipping) of lysyl-phosphatidylglycerol (L-PG). However, it is unclear if suchmprFSNPs are causal in DAPrstrains or are merely a biomarker for this phenotype. In this study, we used an isogenic set ofS. aureusstrains: (i) Newman, (ii) its isogenic ΔmprFmutant, and (iii) several intransplasmid complementation constructs, expressing either a wild-type or point-mutated form of themprFORF cloned from two isogenic DAP-susceptible (DAPs)-DAPrstrain pairs (616-701 and MRSA11/11-REF2145). Complementation of the ΔmprFstrain with singly point-mutatedmprFgenes (mprFS295LormprFT345A) revealed that (i) individual and distinct point mutations within themprFORF can recapitulate phenotypes observed in donor strains (i.e., changes in DAP MICs, positive surface charge, and cell membrane phospholipid profiles) and (ii) these gain-in-function SNPs (i.e., enhanced L-PG synthesis) likely promote reduced DAP binding toS. aureusby a charge repulsion mechanism. Thus, for these two DAPrstrains, the definedmprFSNPs appear to be causally related to this phenotype.

scholarly journals Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiu-jie Li ◽  
Na Su ◽  
Ling Zhang ◽  
Ru-chang Tong ◽  
Xiao-hui Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Cp Genome

AbstractPulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.

scholarly journals The complete chloroplast genome of Limonium tetragonum (Plumbaginaceae) isolated in Korea

2021 ◽  
Vol 51 (3) ◽  
pp. 337-344
Author(s):  
Yongsung KIM ◽  
Hong XI ◽  
Jongsun PARK
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Trees ◽  
Sister Group ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Large Single Copy ◽  
Single Nucleotide ◽  
Complete Chloroplast Genome ◽  
Cp Genome

The chloroplast genome of Limonium tetragonum (Thunb.) Bullock, a halophytic species, was sequenced to understand genetic differences based on its geographical distribution. The cp genome of L. tetragonum was 154,689 bp long (GC ratio is 37.0%) and has four subregions: 84,572 bp of large single-copy (35.3%) and 12,813 bp of small singlecopy (31.5%) regions were separated by 28,562 bp of inverted repeat (40.9%) regions. It contained 128 genes (83 proteincoding genes, eight rRNAs, and 37 tRNAs). Thirty-five single-nucleotide polymorphisms and 33 INDEL regions (88 bp in length) were identified. Maximum-likelihood and Bayesian inference phylogenetic trees showed that L. tetragonum formed a sister group with L. aureum, which is incongruent with certain previous studies, including a phylogenetic analysis.

scholarly journals The First Report of Genetic Polymorphisms of the Equine SPRN Gene in Outbred Horses, Jeju and Halla Horses

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2574
Author(s):  
Sae-Young Won ◽  
Yong-Chan Kim ◽  
Kyoungtag Do ◽  
Byung-Hoon Jeong
Keyword(s):  
Prion Protein ◽  
Prion Disease ◽  
Protein Gene ◽  
Prion Diseases ◽  
Minimum Free Energy ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Direct Dna Sequencing ◽  
Thoroughbred Horses

Prion disease is a fatal infectious disease caused by the accumulation of pathogenic prion protein (PrPSc) in several mammals. However, to date, prion disease has not been reported in horses. The Sho protein encoded by the shadow of the prion protein gene (SPRN) plays an essential role in the pathomechanism of prion diseases. To date, the only genetic study of the equine SPRN gene has been reported in the inbred horse, Thoroughbred horse. We first discovered four SPRN single nucleotide polymorphisms (SNPs) in 141 Jeju and 88 Halla horses by direct DNA sequencing. In addition, we found that the genotype, allele and haplotype frequencies of these SNPs of Jeju horses were significantly different from those of Halla and Thoroughbred horses, this latter breed is also included in this study. Furthermore, we observed that the minimum free energy and mRNA secondary structure were significantly different according to haplotypes of equine SPRN polymorphisms by the RNAsnp program. Finally, we compared the SNPs in the coding sequence (CDS) of the SPRN gene between horses and prion disease-susceptible species. Notably, prion disease-susceptible animals had polymorphisms that cause amino acid changes in the open reading frame (ORF) of the SPRN gene, while these polymorphisms were not found in horses.

scholarly journals DNA analyses and their applications in plant breeding

2012 ◽  
Vol 38 (No. 1) ◽  
pp. 29-40 ◽  
Author(s):  
J. Ovesná ◽  
K. Poláková ◽  
L. Leišová
Keyword(s):  
Molecular Markers ◽  
Fragment Length ◽  
Genome Mapping ◽  
Genome Structure ◽  
Detailed Knowledge ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Expressed Sequence

In recent years, molecular markers have been developed based on the more detailed knowledge of genome structure. Considerable emphasis has been laid on the use of molecular markers in practical breeding and genotype identification. This review attempts to give an account of different molecular markers currently available for genome mapping and for tagging different traits – restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs) and microsatellites. Other markers, expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also mentioned. The importance of structural, functional genomic and comparative mapping is also discussed.

Single nucleotide polymorphisms in the open reading frame of the stearoyl-CoA desaturase gene and resulting genetic variants in Canadian Holstein and Jersey cows

DNA Sequence ◽  
2007 ◽  
Vol 18 (5) ◽  
pp. 357-362 ◽  
Author(s):  
Patrick M. Kgwatalala ◽  
Patrick M. Kgwatalala ◽  
Eveline M. Ibeagha-Awemu ◽  
Patrick M. Kgwatalala ◽  
Eveline M. Ibeagha-Awemu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variants ◽  
Open Reading Frame ◽  
Nucleotide Polymorphisms ◽  
Desaturase Gene ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Stearoyl Coa Desaturase ◽  
Jersey Cows

Molecular characterisation of the buffalo SCAP gene and its association with milk production traits in water buffaloes

2018 ◽  
Vol 85 (2) ◽  
pp. 133-137
Author(s):  
Tingxian Deng ◽  
Xiaoya Ma ◽  
Chunying Pang ◽  
Shasha Liang ◽  
Xingrong Lu ◽  
...  
Keyword(s):  
Milk Production ◽  
Gene Expression Analysis ◽  
Open Reading Frame ◽  
Molecular Characterisation ◽  
Early Lactation ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Single Nucleotide ◽  
Reading Frame

The study reported in this Research Communication was conducted to investigate the molecular characterisation of buffalo SCAP gene, expression analysis, and the association between single nucleotide polymorphisms and milk production traits in 384 buffaloes. Sequence analysis revealed the SCAP gene had an open reading frame of 3837 bp encoding 1279 amino acids. A ubiquitous expression profile of SCAP gene was detected in various tissues with extreme predominance in the mammary gland during early lactation. Moreover, eleven SNPs in buffalo SCAP gene were identified, six of them (g.1717600A>G, g.1757922C>T, g.1758953G>A, g.1759142C>T, g.1760740G>A, and g.1766036T>C) were found to be significantly associated with 305-day milk yield. Thus, buffalo SCAP could sever as a candidate gene affecting milk production traits in buffalo and the identified SNPs might potentially be genetic markers.

scholarly journals Coevolution of a Persistent Plant Virus and Its Pepper Hosts

2018 ◽  
Vol 31 (7) ◽  
pp. 766-776 ◽  
Author(s):  
Maliheh Safari ◽  
Marilyn J. Roossinck
Keyword(s):  
Hot Pepper ◽  
Capsicum Frutescens ◽  
Nucleotide Polymorphisms ◽  
Large Open Reading Frame ◽  
Rna Dependent Rna Polymerase ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Persistent Viruses ◽  
Capsicum Species ◽  
Viral Helicase

There are many nonpathogenic viruses that are maintained in a persistent lifestyle in plants. Plant persistent viruses are widespread, replicating in their hosts for many generations. So far, Endornaviridae is the only family of plant persistent viruses with a single-stranded RNA genome, containing one large open reading frame. Bell pepper endornavirus (BPEV), Hot pepper endornavirus, Capsicum frutescens endornavirus 1 (CFEV 1) have been identified from peppers. Peppers are native to Central and South America and, as domesticated plants, human selection accelerated their evolution. We investigated the evolution of these endornaviruses in different peppers including Capsicum annuum, C. chacoense, C. chinense, C. frutescens, C. baccutum, and C. pubescens using two fragments from the viral helicase (Hel) and RNA dependent RNA polymerase (RdRp) domains. In addition, using single nucleotide polymorphisms, we analyzed the pepper host populations and phylogenies. The endornaviruses phylogeny was correlated with its Capsicum species host. In this study, BPEV was limited to C. annuum species, and the RdRp and Hel phylogenies identified two clades that correlated with the host pungency. No C. annuum infected with CFEV 1 was found in this study, but the CFEV 1 RdRp fragment was recovered from C. chinense, C. frutescens, C. baccutum, and C. pubescens. Hence, during pepper speciation, the ancestor of CFEV 1 may have evolved as a new endornavirus, BPEV, in C. annuum peppers.

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