scholarly journals Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Chenxin Li ◽  
Chaonan Cai ◽  
Yutian Tao ◽  
Zhongshuai Sun ◽  
Ming Jiang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Western China ◽  
Germplasm Resources ◽  
High Similarity ◽  
Illumina Platform ◽  
High Quality ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Group A ◽  
Group B

Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.

scholarly journals Emergence of Prochloraz-Resistant Populations of Calonectria pauciramosa and Calonectria polizzii in Ornamental Nurseries of Southern Italy

Plant Disease ◽  
2014 ◽  
Vol 98 (3) ◽  
pp. 344-350 ◽  
Author(s):  
Vladimiro Guarnaccia ◽  
Dalia Aiello ◽  
Giancarlo Polizzi ◽  
Giancarlo Perrone ◽  
Gaetano Stea ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Red Clover ◽  
Translation Elongation ◽  
Group A ◽  
Sterol Demethylation Inhibitors ◽  
Benzimidazole Carbamates ◽  
Group B ◽  
Translation Elongation Factor 1Α

Management of Calonectria spp. infections in nurseries requires scheduled fungicide applications, particularly with methyl benzimidazole carbamates (MBCs) and sterol demethylation inhibitors (DMIs). Due to rising concerns about the occurrence of MBC resistance in different Calonectria populations and variability in prochloraz efficacy in controlling these pathogens, a detailed study on prochloraz sensitivity distributions of Calonectria isolates belonging to the Calonectria scoparia complex was carried out. In total, 105 isolates collected in two distinct periods (1993 to 1996 and 2005 to 2009) were analyzed for prochloraz sensitivity. Based on DNA sequencing and phylogenetic analyses of β-tubulin, histone H3, and translation elongation factor-1α gene sequences, 69 and 36 isolates were identified as C. pauciramosa and C. polizzii, respectively. The isolates collected more recently (group B) had a reduced prochloraz sensitivity, as indicated by greater values for the effective dose to reduce growth by 50% than those collected earlier (group A). The reduced sensitivity detected in vitro corresponded to partial loss of fungicide efficacy in controlling infections in red clover and feijoa under controlled and semi-field conditions, respectively. Frequent prochloraz application in nurseries for controlling Calonectria spp. infections is discouraged.

scholarly journals Whole Genome Classification and Phylogenetic Analyses of Rotavirus B strains from the United States

Pathogens ◽  
2018 ◽  
Vol 7 (2) ◽  
pp. 44 ◽  
Author(s):  
Frances Shepherd ◽  
Diana Herrera-Ibata ◽  
Elizabeth Porter ◽  
Nitipong Homwong ◽  
Richard Hesse ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Middle Layer ◽  
The United States ◽  
Viral Gastroenteritis ◽  
Pairwise Identity ◽  
Cutoff Values ◽  
Group A ◽  
Group B

Rotaviruses (RVs) are a major etiological agent of acute viral gastroenteritis in humans and young animals, with rotavirus B (RVB) often detected in suckling and weaned pigs. Group A rotavirus classification is currently based on the two outer capsid proteins, VP7 and VP4, and the middle layer protein, VP6. Using RVB strains generated in this study and reference sequences from GenBank, pairwise identity frequency graphs and phylogenetic trees were constructed for the eleven gene segments of RVB to estimate the nucleotide identity cutoff values for different genotypes and determine the genotype diversity per gene segment. Phylogenetic analysis of VP7, VP4, VP6, VP1–VP3, and NSP1–NSP5 identified 26G, 5P, 13I, 5R, 5C, 5M, 8A, 10N, 6T, 4E, and 7H genotypes, respectively. The analysis supports the previously proposed cutoff values for the VP7, VP6, NSP1, and NSP3 gene segments (80%, 81%, 76% and 78%, respectively) and suggests new cutoff values for the VP4, VP1, VP2, VP3, NSP2, NSP4, and NSP5 (80%, 78%, 79%, 77% 83%, 76%, and 79%, respectively). Reassortment events were detected between the porcine RVB strains from our study. This research describes the genome constellations for the complete genome of Group B rotaviruses in different host species.

scholarly journals The influence of balanced complex chromosomal rearrangements on preimplantation embryonic development potential and molecular karyotype

2019 ◽  
Author(s):  
Gang Li ◽  
Weiyi Shi ◽  
Wenbin Niu ◽  
Jiawei Xu ◽  
Yihong Guo ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Formation Rate ◽  
Early Embryonic Development ◽  
High Quality ◽  
Abnormal Embryo ◽  
Molecular Karyotype ◽  
Group A ◽  
The Difference ◽  
Group B ◽  
Euploid Embryo

Abstract Background: Balanced complex chromosome rearrangements (BCCR) are balanced chromosomal structural aberrations that involve two or more chromosomes and at least three breakpoints. It is very rare in the population. The objective is to explore the difference of influence of three types of BCCR on early embryonic development and molecular karyotype. Results: Twelve couples were recruited including four couples of three-way rearrangements carriers (group A), three couples of double two-way translocations carriers (group B) and five couples of exceptional CCR carriers (group C). A total of 243 oocytes were retrieved in the seventeen preimplantation genetic testing (PGT) cycles, and 207 of these were available for fertilization. After intracytoplasmic sperm injection, 181 oocytes normally fertilized.The rates of embryos forming on day3 in three groups were 87.88%, 97.78% and 77.14%, which was significantly different (P=0.01). Compared with group B, the rate of embryo formation was statistically significantly lower in group C (P=0.01). Furthermore, the rates of high-quality blastocysts in three group were 14.71%, 48.15% and 62.96%, respectively, which was significantly different (P=0.00). Compared with group B and C, the rate of high-quality blastocysts in group A was statistically significantly lower (P=0.00; P=0.00). Comprehensive chromosome analysis was performed on 83 embryos, including 75 trophectoderm cells and 8 blastomeres. Except 7 embryos failed to amplify, 9.01% embryos were diagnosed as euploidy, and 90.91% were diagnosed as abnormal. As for group A, the euploid embryo rate was 10.71% and the abnormal embryo rate was 89.29%. In group B, the euploid embryo rate was 3.85%, the abnormal embryo rate was 96.15%. The euploid embryo rate was 13.04%, the abnormal embryo rate was 86.96% in group C. There were no significant differences among the three groups (P = 0.55). Conclusions: The double two-way translocations couples have more chance to get balanced or normal embryos probably, and there may be more high-quality blastocysts in exceptional CCRs, but the blastocyst formation rate was similar among the three type of BCCR. Different types of BCCR maybe have little effect on the embryonic molecular karyotype. The difference of influence of BCCR on early embryonic development and molecular karyotype should be further studied.

scholarly journals The influence of balanced complex chromosomal rearrangements on preimplantation embryonic development potential and molecular karyotype

2020 ◽  
Author(s):  
Gang Li ◽  
Weiyi Shi ◽  
Wenbin Niu ◽  
Jiawei Xu ◽  
Yihong Guo ◽  
...  
Keyword(s):  
Embryonic Development ◽  
High Quality ◽  
Preimplantation Genetic Testing ◽  
Abnormal Embryo ◽  
Significant Difference ◽  
Molecular Karyotype ◽  
Group A ◽  
The Difference ◽  
Group B ◽  
Euploid Embryo

Abstract Background: Balanced complex chromosome rearrangements (BCCR) are balanced chromosomal structural aberrations that involve two or more chromosomes and at least three breakpoints. It is very rare in the population.The objective is to explore the difference of influence of three types of BCCR on early embryonic development and molecular karyotype.Results:Twelve couples were recruited including four couples of three-way rearrangements carriers (group A), three couples of double two-way translocations carriers (group B) and five couples of exceptional CCR carriers (group C). A total of 243 oocytes were retrievedin the seventeen preimplantation genetic testing (PGT) cycles, and 207 of these were available for fertilization.After intracytoplasmic sperm injection, 181oocytes normally fertilized. The rates of embryos forming on day3 in three groups were 87.88%, 97.78% and77.14%, which was significantly different (P=0.01). Compared with group B, the rate of embryo formation was statistically significantly lower in group C(P=0.01).Furthermore, the rates of high-quality blastocysts in three group were 14.71%, 48.15% and 62.96%, respectively, which was significantly different (P=0.00). Compared with group B andC, the rate of high-quality blastocysts in group A was statistically significantly lower (P=0.00;P=0.00). Comprehensive chromosome analysis was performed on 83 embryos, including 75 trophectodermcellsand 8 blastomeres. Except 7 embryos failed to amplify, 9.01%embryos were diagnosed as euploidy, and 90.91% were diagnosed as abnormal. As for group A, the euploid embryo rate was 10.71%and the abnormal embryo rate was 89.29%. In group B,the euploid embryo rate was 3.85%, the abnormal embryo rate was 96.15%. The euploid embryo rate was 13.04%, the abnormal embryo rate was 86.96% in group C.There were no significant differences among the three groups (P = 0.55).Conclusions:The lowest rate of high quality blastocysts has been for three-way rearrangements and the lowest rate of euploidy has been for double two-way translocations, although no significant difference. Different types of BCCR maybe have little effect on the embryonic molecular karyotype. The difference of influence of BCCR on early embryonic developmentandmolecular karyotypeshould be further studied.

scholarly journals Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection

2016 ◽  
Author(s):  
My VT Phan ◽  
Pham Hong Anh ◽  
Nguyen Van Cuong ◽  
Bas B. Oude Munnink ◽  
Lia van der Hoek ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Phylogenetic Analyses ◽  
Mekong Delta ◽  
Viral Gastroenteritis ◽  
Human Patient ◽  
Virus Diversity ◽  
Genotype Constellation ◽  
Group A ◽  
Stool Samples ◽  
Group B

AbstractCoordinated and synchronous virological surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus is an important cause of viral gastroenteritis in humans and animals. We have documented the rotavirus diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of 60 human rotaviruses (all group A) and 31 porcine rotaviruses (13 group A, 7 group B, 6 group C and 5 group H). Phylogenetic analyses showed the co-circulation of multiple distinct rotavirus group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C and H, none of which have been previously reported in Vietnam. Furthermore the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event

scholarly journals Functional Characterization of a L-2-Haloacid Dehalogenase From Zobellia galactanivorans DsijT Suggests a Role in Haloacetic Acid Catabolism and a Wide Distribution in Marine Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Eugénie Grigorian ◽  
Agnès Groisillier ◽  
François Thomas ◽  
Catherine Leblanc ◽  
Ludovic Delage
Keyword(s):  
Marine Bacteria ◽  
Gene Knockout ◽  
Phylogenetic Analyses ◽  
Functional Characterization ◽  
Marine Environments ◽  
Direct Role ◽  
Marine Habitats ◽  
Group A ◽  
Group B

L-2-halocid dehalogenases (L-2-HADs) have been mainly characterized from terrestrial polluted environments. By contrast, knowledge is still scarce about their role in detoxification of predominant halocarbons in marine environments. Here, phylogenetic analyses showed a wide diversity of homologous L-2-HADs, especially among those belonging to marine bacteria. Previously characterized terrestrial L-2-HADs were part of a monophyletic group (named group A) including proteins of terrestrial and marine origin. Another branch (named group B) contained mostly marine L-2-HADs, with two distinct clades of Bacteroidetes homologs, closely linked to Proteobacteria ones. This study further focused on the characterization of the only L-2-HAD from the flavobacterium Zobellia galactanivorans DsijT (ZgHAD), belonging to one of these Group B clades. The recombinant ZgHAD was shown to dehalogenate bromo- and iodoacetic acids, and gene knockout in Z. galactanivorans revealed a direct role of ZgHAD in tolerance against both haloacetic acids. Analyses of metagenomic and metatranscriptomic datasets confirmed that L-2-HADs from group A were well-represented in terrestrial and marine bacteria, whereas ZgHAD homologs (group B L-2-HADs) were mainly present in marine bacteria, and particularly in host-associated species. Our results suggest that ZgHAD homologs could be key enzymes for marine Bacteroidetes, by conferring selective advantage for the recycling of toxic halogen compounds produced in particular marine habitats, and especially during interactions with macroalgae.

scholarly journals Similarity level of Nepenthes spp. based on the qualitative characters

2020 ◽  
Vol 5 (3) ◽  
pp. 140
Author(s):  
Putri Lukmanasari ◽  
Aziz Purwantoro ◽  
Rudi Hari Murti ◽  
Zulkifli Zulkifli
Keyword(s):  
Genetic Relationship ◽  
Ornamental Plants ◽  
Morphological Characterization ◽  
Similarity Coefficient ◽  
High Similarity ◽  
Pitcher Plant ◽  
Group A ◽  
Qualitative Characters ◽  
Group B ◽  
The Relationship

Nepenthes, also known as pitcher plant, are unique and interesting flora developed as ornamental plants. This species has an attraction not only on the flowers but also on the diverse shapes and colors of the pitchers. Each Nepenthes species and hybrid has a variety of characters. The genetic relationship and diversity in Nepenthes species and hybrids can be determined based on the morphological characterization. The purpose of this study was to determine the similarity level among the Nepenthes accessions based on 31 qualitative characters. In this study, 30 Nepenthes species and 11 hybrids were used. The range of the similarity coefficient of Nepenthes species was 0.28-0.65, and divided into two major groups namely group A and B. Group A was the Nepenthes population which had petioles consisted of 17 accessions, while group B had folius consisting of 24 accessions. It indicated that when the similarity value is higher, the similarity level between each plant becomes higher. Principle Coordinates Analysis (PCoA) provided an overview of the relationship among the genotypes in coordinates. Species with a high similarity coefficient were in a close position, whereas species with a low similarity coefficient were in a remote position. Based on the PCoA, the species were grouped based on the similar characters, which was supported by the dendrograms.

scholarly journals The influence of balanced complex chromosomal rearrangements on preimplantation embryonic development potential and molecular karyotype

2020 ◽  
Author(s):  
Gang Li ◽  
Weiyi Shi ◽  
Wenbin Niu ◽  
Jiawei Xu ◽  
Yihong Guo ◽  
...  
Keyword(s):  
Embryonic Development ◽  
High Quality ◽  
Preimplantation Genetic Testing ◽  
Abnormal Embryo ◽  
Significant Difference ◽  
Molecular Karyotype ◽  
Group A ◽  
The Difference ◽  
Group B ◽  
Euploid Embryo

Abstract Background: Balanced complex chromosome rearrangements (BCCR) are balanced chromosomal structural aberrations that involve two or more chromosomes and at least three breakpoints. It is very rare in the population.The objective is to explore the difference of influence of three types of BCCR on early embryonic development and molecular karyotype.Results:Twelve couples were recruited including four couples of three-way rearrangements carriers (group A), three couples of double two-way translocations carriers (group B) and five couples of exceptional CCR carriers (group C). A total of 243 oocytes were retrievedin the seventeen preimplantation genetic testing (PGT) cycles, and 207 of these were available for fertilization.After intracytoplasmic sperm injection, 181oocytes normally fertilized. The rates of embryos forming on day3 in three groups were 87.88%, 97.78% and77.14%, which was significantly different (P=0.01). Compared with group B, the rate of embryo formation was statistically significantly lower in group C(P=0.01).Furthermore, the rates of high-quality blastocysts in three group were 14.71%, 48.15% and 62.96%, respectively, which was significantly different (P=0.00). Compared with group B andC, the rate of high-quality blastocysts in group A was statistically significantly lower (P=0.00;P=0.00). Comprehensive chromosome analysis was performed on 83 embryos, including 75 trophectodermcellsand 8 blastomeres. Except 7 embryos failed to amplify, 9.01%embryos were diagnosed as euploidy, and 90.91% were diagnosed as abnormal. As for group A, the euploid embryo rate was 10.71%and the abnormal embryo rate was 89.29%. In group B,the euploid embryo rate was 3.85%, the abnormal embryo rate was 96.15%. The euploid embryo rate was 13.04%, the abnormal embryo rate was 86.96% in group C.There were no significant differences among the three groups (P = 0.55).Conclusions:The lowest rate of high quality blastocysts has been for three-way rearrangements and the lowest rate of euploidy has been for double two-way translocations, although no significant difference. Different types of BCCR maybe have little effect on the embryonic molecular karyotype. The difference of influence of BCCR on early embryonic developmentandmolecular karyotypeshould be further studied.

scholarly journals The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3919 ◽  
Author(s):  
Hui Cheng ◽  
Jinfeng Li ◽  
Hong Zhang ◽  
Binhua Cai ◽  
Zhihong Gao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
Chloroplast Genomes

Compared with other members of the family Rosaceae, the chloroplast genomes ofFragariaspecies exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing ofFragariaspecies is needed. In this study, we sequenced the complete chloroplast genome ofF. × ananassa‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination ofde novoassembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of theF. × ananassa‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallestFragariachloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content inFragaria, particularly among three octoploid strawberries which wereF. × ananassa‘Benihoppe’,F.chiloensis(GP33) andF.virginiana(O477). However, when the sequences of the coding and non-coding regions ofF. × ananassa‘Benihoppe’ were compared in detail with those ofF.chiloensis(GP33) andF.virginiana(O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK,trnS-trnG,atpF-atpH,trnC-petN,trnT-psbDandtrnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genusFragaria.

scholarly journals Comparative Chloroplast Genome Analysis of Rhubarb Botanical Origins and the Development of Specific Identification Markers

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2811 ◽  
Author(s):  
Yuxin Zhou ◽  
Jing Nie ◽  
Ling Xiao ◽  
Zhigang Hu ◽  
Bo Wang
Keyword(s):  
Chinese Medicine ◽  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Genetic Identification ◽  
Protein Coding ◽  
Variable Regions ◽  
Specific Identification ◽  
Coding Regions ◽  
Botanical Species ◽  
Chloroplast Genomes

Rhubarb is an important ingredient in traditional Chinese medicine known as Rhei radix et rhizome. However, this common name refers to three different botanical species with different pharmacological effects. To facilitate the genetic identification of these three species for their more precise application in Chinese medicine we here want to provide chloroplast sequences with specific identification sites that are easy to amplify. We therefore sequenced the complete chloroplast genomes of all three species and then screened those for suitable sequences describing the three species. The length of the three chloroplast genomes ranged from 161,053 bp to 161,541 bp, with a total of 131 encoded genes including 31 tRNA, eight rRNA and 92 protein-coding sequences. The simple repeat sequence analysis indicated the differences existed in these species, phylogenetic analyses showed the chloroplast genome can be used as an ultra-barcode to distinguish the three botanical species of rhubarb, the variation of the non-coding regions is higher than that of the protein coding regions, and the variations in single-copy region are higher than that in inverted repeat. Twenty-one specific primer pairs were designed and eight specific identification sites were experimentally confirmed that can be used as special DNA barcodes for the identification of the three species based on the highly variable regions. This study provides a molecular basis for precise medicinal plant selection, and supplies the groundwork for the next investigation of the closely related Rheum species comparing and correctly identification on these important medicinal species.

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