Comparison of peach and Arabidopsis genomic sequences: fragmentary conservation of gene neighborhoods

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 268-276 ◽  
Author(s):  
Laura L Georgi ◽  
Ying Wang ◽  
Gregory L Reighard ◽  
Long Mao ◽  
Rod A Wing ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Evolution ◽  
Gene Order ◽  
Prunus Persica ◽  
Sequence Data ◽  
Coding Regions ◽  
Thale Cress ◽  
Gene Level ◽  
Genomic Regions ◽  
Exon Structure

We examined the degree of conservation of gene order in two plant species, Prunus persica (peach) and Arabidopsis thaliana (thale cress), whose lineages diverged more than 90 million years ago. In the three peach genomic regions studied, segments with a gene order congruent with A. thaliana were short (two to three genes in length); and for any peach region, corresponding segments were found in diverse locations in the A. thaliana genome. At the gene level and lower, the A. thaliana sequence was enormously useful for identifying likely coding regions in peach sequences and in determining their intron–exon structure. The peach BAC sequence data reported here contained a BLAST-detectable putative coding sequence an average of every 7 kb, and the peach introns identified in this study were, on average, almost twice the length of the corresponding introns in A. thaliana.Key words: conserved microsynteny, genome evolution.

scholarly journals Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

2019 ◽  
Vol 8 (1) ◽  
pp. 36 ◽  
Author(s):  
Giovanni Lorenzin ◽  
Franco Gargiulo ◽  
Arnaldo Caruso ◽  
Francesca Caccuri ◽  
Emanuele Focà ◽  
...  
Keyword(s):  
Public Health ◽  
Sequence Data ◽  
Human Mobility ◽  
Heterosexual Couples ◽  
Molecular Surveillance ◽  
Coalescence Model ◽  
Coding Regions ◽  
Hiv Epidemic ◽  
Viral Subtypes ◽  
Hiv 1

HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools; the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was used on the datasets, to determine clusters and evolution. We detected 304 (43%) patients infected with HIV-1 non-B variants, of which only 293 sequences were available, with four pure subtypes and five recombinant forms; subtype F1 (17%) and CRF02_AG (51.1%) were most common. Twenty-five transmission clusters were identified, three of which included >10 patients, belonging to subtype CRF02_AG and subtype F. Most cases of alleged transmission were between heterosexual couples. Probably due to strong migratory flows, we have identified different subtypes with particular patterns of recombination or, as in the case of the subtype G (18/293, 6.1%), to a complete lack of relationship between the sequenced strains, revealing that they are all singletons. Continued HIV molecular surveillance is most important to analyze the dynamics of the boost of transmission clusters in order to implement public health interventions aimed at controlling the HIV epidemic.

46 Footprints of Selection in Angus and Hanwoo Beef Cattle Using Imputed Whole Genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 25-25
Author(s):  
Muhammad Yasir Nawaz ◽  
Rodrigo Pelicioni Savegnago ◽  
Cedric Gondro
Keyword(s):  
Beef Cattle ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Whole Genome ◽  
Extended Haplotype Homozygosity ◽  
Extended Haplotype ◽  
Genome Sequence Data ◽  
Genomic Regions

Abstract In this study, we detected genome wide footprints of selection in Hanwoo and Angus beef cattle using different allele frequency and haplotype-based methods based on imputed whole genome sequence data. Our dataset included 13,202 Angus and 10,437 Hanwoo animals with 10,057,633 and 13,241,550 imputed SNPs, respectively. A subset of data with 6,873,624 common SNPs between the two populations was used to estimate signatures of selection parameters, both within (runs of homozygosity and extended haplotype homozygosity) and between (allele fixation index, extended haplotype homozygosity) the breeds in order to infer evidence of selection. We observed that correlations between various measures of selection ranged between 0.01 to 0.42. Assuming these parameters were complementary to each other, we combined them into a composite selection signal to identify regions under selection in both beef breeds. The composite signal was based on the average of fractional ranks of individual selection measures for every SNP. We identified some selection signatures that were common between the breeds while others were independent. We also observed that more genomic regions were selected in Angus as compared to Hanwoo. Candidate genes within significant genomic regions may help explain mechanisms of adaptation, domestication history and loci for important traits in Angus and Hanwoo cattle. In the future, we will use the top SNPs under selection for genomic prediction of carcass traits in both breeds.

scholarly journals Mapping and Characterization QTLs for Phenological Traits in Seven Pedigree-connected Peach Families

2020 ◽  
Author(s):  
Zena Rawandoozi ◽  
Timothy Hartmann ◽  
Silvia Carpenedo ◽  
Ksenija Gasic ◽  
Cassia da Silva Linge ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Large Tree ◽  
Early Seedling ◽  
Sib Families ◽  
Functional Alleles ◽  
Genomic Regions ◽  
Marker Identification

Abstract BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F1 low to medium chill full-sib families were collected over two years at two locations and genotyped using the 9K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172 – 182 cM), LG4 (48 – 54 cM), and LG7 (62 – 70 cM), explaining 17-54%, 11-55%, and 11-18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40 - 46 cM) and explained between 40-75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL for the creation of predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

scholarly journals Genome evolution of SARS-CoV-2 and its virological characteristics

2020 ◽  
Vol 40 (1) ◽  
Author(s):  
So Nakagawa ◽  
Takayuki Miyazawa
Keyword(s):  
Genome Evolution ◽  
Genome Sequence ◽  
Causative Agent ◽  
Sequence Data ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
Global Prevalence ◽  
Horseshoe Bats

AbstractCoronavirus disease of 2019 (COVID-19), which originated in China in 2019, shows mild cold and pneumonia symptoms that can occasionally worsen and result in deaths. SARS-CoV-2 was reported to be the causative agent of the disease and was identified as being similar to SARS-CoV, a causative agent of SARS in 2003. In this review, we described the phylogeny of SARS-CoV-2, covering various related studies, in particular, focusing on viruses obtained from horseshoe bats and pangolins that belong to Sarbecovirus, a subgenus of Betacoronavirus. We also describe the virological characteristics of SARS-CoV-2 and compare them with other coronaviruses. More than 30,000 genome sequences of SARS-CoV-2 are available in the GISAID database as of May 28, 2020. Using the genome sequence data of closely related viruses, the genomic characteristics and evolution of SARS-CoV-2 were extensively studied. However, given the global prevalence of COVID-19 and the large number of associated deaths, further computational and experimental virological analyses are required to fully characterize SARS-CoV-2.

scholarly journals SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

2020 ◽  
Vol 21 (24) ◽  
pp. 9421
Author(s):  
Lidia Skuza ◽  
Ewa Filip ◽  
Izabela Szućko ◽  
Jan Bocianowski
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Markers ◽  
Related Species ◽  
Economic Importance ◽  
Closely Related Species ◽  
Coding Sequences ◽  
Coding Regions ◽  
Genomic Regions ◽  
Tribe Triticeae

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

scholarly journals Identification and Characterization of Botryosphaeria spp. Causing Gummosis of Peach Trees in Hubei Province, Central China

Plant Disease ◽  
2011 ◽  
Vol 95 (11) ◽  
pp. 1378-1384 ◽  
Author(s):  
Fan Wang ◽  
Lina Zhao ◽  
Guohuai Li ◽  
Junbin Huang ◽  
Tom Hsiang
Keyword(s):  
Prunus Persica ◽  
Elongation Factor ◽  
Fruit Trees ◽  
Hubei Province ◽  
Central China ◽  
Internal Transcribed Spacer Region ◽  
Fusicoccum Aesculi ◽  
Peach Trees ◽  
Production Areas ◽  
Genomic Regions

Peach (Prunus persica) is one of the most important and widely grown fruit trees in China; however, perennial gummosis on trunks and branches is a major problem in peach orchards of Hubei Province, one of the most important peach production areas of China. In order to identify the gummosis-causing agents, diseased trunks and branches were collected from 11 peach orchards in Hubei Province. Fungal isolates were obtained from these samples, yielding three species: Botryosphaeria dothidea (anamorph Fusicoccum aesculi), B. rhodina (anamorph Lasiodiplodia theobromae), and B. obtusa (anamorph Diplodia seriata). They were identified based on conidial morphology and cultural characteristics, as well as analyses of nucleotide sequences of three genomic regions: the internal transcribed spacer region, a partial sequence of the β-tubulin gene, and the translation elongation factor 1-α gene. Fusicoccum aesculi was found in all 11 orchards but L. theobromae was found only in Shayang County in the Jingmen region and D. seriata only in Gong'an County in the Jingzhou region. Via artificial inoculation using mycelia on wounded twigs or branches, these three species were all found to be pathogenic, causing dark lesions on the twigs and branches and, sometimes, gum exudation from diseased parts. Isolates of L. theobromae were the most virulent and caused the largest lesions and most copious gummosis, and D. seriata had less gum than the other two species. This report represents the first description of L. theobromae and D. seriata as causal agents of gummosis on peach in China.

scholarly journals A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽  
2020 ◽  
Vol 4748 (1) ◽  
pp. 182-194 ◽  
Author(s):  
JING ZHANG ◽  
ERNST BROCKMANN ◽  
QIAN CONG ◽  
JINHUI SHEN ◽  
NICK V. GRISHIN
Keyword(s):  
Dna Sequences ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Type Specimens ◽  
African Species ◽  
Protein Coding ◽  
Coding Regions ◽  
As Species ◽  
Close Relatives ◽  
Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]). 

scholarly journals Applying comparative genomics to plant disease epidemiology

2004 ◽  
Vol 85 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Linda M. Kohn
Keyword(s):  
Magnaporthe Grisea ◽  
Sequence Data ◽  
Population Level ◽  
Avirulence Genes ◽  
Genome Database ◽  
Disease Epidemiology ◽  
Dna Sequence Data ◽  
Specific Pathogen ◽  
Pathogen Populations ◽  
Genomic Regions

Astract Phylogenetic or genealogical interpretation of DNA sequence data from multiple genomic regions has become the gold standard for species delimitation and population genetics. Precise species concepts can inform quarantine decisions but are likely to reflect evolutionary events too far in the past to impact disease management. On the other hand, multilocus approaches at the population level can identify patterns of endemism or migration directly associated with episodes of disease, including host shifts and associated changes in determinants of pathogenicity and avirulence. We used the genome database of Magnaporthe grisea to frame a comparative, multilocus genomics approach from which we demonstrate a single origin for rice infecting genotypes with concomitant loss of sex in pandemic clonal lineages, and patterns of gain and loss of avirulence genes. In the Sclerotinia sclerotiorum pathosystem, we identified significant associations of multilocus haplotypes with specific pathogen populations in North America. Following the introduction of a new crop, endemic pathogen genotypes and newly evolved migrant genotypes caused novel, early-season symptoms.

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