Diversity of microcystin-producing genotypes in Brazilian strains of Microcystis (Cyanobacteria)

Microcystis Kützing ex Lemmermann is among the genera of cyanobacteria often associated to toxic blooms with the release of microcystins. A gene cluster codes for microcystin synthetases, which are involved in the biosynthesis of this toxin. The aim of the present study was to investigate the genetic diversity of the mcyB gene, specifically the B1 module, in Brazilian strains of Microcystis spp. and its microcystin variants. Broad genetic diversity was revealed in this region. From the phylogenetic analysis, three clusters were obtained that were not related to the geographic origin or morphospecies of the strains, nor with the variant of the microcystin produced. A group of strains that did not produce microcystins was found, despite the presence of the mcyB1 fragment. Eight microcystin isoforms were detected: MC-LR, [D-Asp³]-MC-LR, [Asp³]-MC-LR, MC-RR, [Dha7]-MC-LR, MC-LF, MC-LW and [D-Asp³, EtAdda5]-MC-LH, the latter of which is described for the first time in Brazil. Moreover, five other variants were not identified and indicate being new.

Download Full-text

Genetic diversity of green algal and cyanobacterial photobionts in Nephroma (Peltigerales)

The Lichenologist ◽

10.1016/s0024-2829(03)00051-3 ◽

2003 ◽

Vol 35 (4) ◽

pp. 325-339 ◽

Cited By ~ 41

Author(s):

Katileena Lohtander ◽

Ilona Oksanen ◽

Jouko Rikkinen

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Gene Cluster ◽

Ginkgo Biloba ◽

Ribosomal Gene ◽

Ssu Rdna ◽

Evolutionary Change ◽

Phylogenetic Groups ◽

Evolutionary Transitions ◽

Green Algal

AbstractGenetic diversity of green algal and cyanobacterial photobionts in Nephroma was examined by using nucleotide sequences of the ribosomal gene cluster. The lichens studied included both bipartite and tripartite species. There was very little variation in green algal-ITS sequences of N. arcticum and N. expallidum. Almost identical sequences were obtained from all thalli analysed and also from two tripartite Peltigera species. On the basis of SSU rDNA data the green algal photobionts of N. arcticum are closely related to the primary photobiont of P. britannica, and also to an endophytic alga of Ginkgo biloba. The SSU rDNA region of lichen-forming cyanobacteria was rather variable. A phylogenetic analysis indicated that the Nostoc specimens formed a monophyletic group and the strains were divided into two main groups. One clade included only cyanobionts of lichens, including those of all bipartite Nephroma species. The second group was genetically more heterogeneous and included mainly cyanobionts of terricolous cyanolichens, including those of both tripartite Nephroma species studied. The distinction between bi- and tripartite Nephroma species is significant as the mycobionts of tripartite species are not monophyletic. It implies that within Nephroma, evolutionary transitions between symbiosis types cannot have been achieved simply via an acquisition or loss of the green algal photobiont. As the Nostoc symbionts of bi- and tripartite species belong to different phylogenetic groups, an evolutionary change in green algal association has required a concurrent change in cyanobiont composition.

Download Full-text

Genetic Diversity of Grapevine virus A in Washington and California Vineyards

Phytopathology ◽

10.1094/phyto-06-13-0179-r ◽

2014 ◽

Vol 104 (5) ◽

pp. 548-560 ◽

Cited By ~ 17

Author(s):

Olufemi J. Alabi ◽

Maher Al Rwahnih ◽

Tefera A. Mekuria ◽

Rayapati A. Naidu

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Sequence Data ◽

Management Strategies ◽

Geographic Origin ◽

Phylogenetic Network ◽

Grapevine Virus ◽

Grapevine Virus A ◽

Strong Negative Selection ◽

Epidemiological Characteristics

Grapevine virus A (GVA; genus Vitivirus, family Betaflexiviridae) has been implicated with the Kober stem grooving disorder of the rugose wood disease complex. In this study, 26 isolates of GVA recovered from wine grape (Vitis vinifera) cultivars from California and Washington were analyzed for their genetic diversity. An analysis of a portion of the RNA-dependent RNA polymerase (RdRp) and complete coat protein (CP) sequences revealed intra- and inter-isolate sequence diversity. Our results indicated that both RdRp and CP are under strong negative selection based on the normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. A global phylogenetic analysis of CP sequences revealed segregation of virus isolates into four major clades with no geographic clustering. In contrast, the RdRp-based phylogenetic tree indicated segregation of GVA isolates from California and Washington into six clades, independent of geographic origin or cultivar. Phylogenetic network coupled with recombination analyses showed putative recombination events in both RdRp and CP sequence data sets, with more of these events located in the CP sequence. The preponderance of divergent variants of GVA co-replicating within individual grapevines could increase viral genotypic complexity with implications for phylogenetic analysis and evolutionary history of the virus. The knowledge of genetic diversity of GVA generated in this study will provide a foundation for elucidating the epidemiological characteristics of virus populations at different scales and implementing appropriate management strategies for minimizing the spread of genetic variants of the virus by vectors and via planting materials supplied to nurseries and grape growers.

Download Full-text

Genetic diversity in a Brazilian bovine herd based on four microsatellite loci

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000200018 ◽

2000 ◽

Vol 23 (2) ◽

pp. 345-350 ◽

Cited By ~ 2

Author(s):

Sabrina E. Matos Almeida ◽

Márcia S.N. Machado ◽

Clara Sabina Steigleder ◽

Cleonice L. Gama ◽

Mara Helena Hutz ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Tandem Repeats ◽

Geographic Origin ◽

Low Diversity ◽

Taurine Cattle ◽

Red Angus ◽

High Degree ◽

First Time ◽

Short Tandem

Microsatellites or short tandem repeats (STRs), DNA markers relatively abundant in the genome, have a high degree of polymorphism and therefore great potential for characterizing populations. The present study estimates genetic variability in a set of four microsatellites (BMS3013, BMS3004, HEL10 and TGLA122) in a Brazilian hybrid bovine breed (5/8 Aberdeen Angus x 3/8 Nelore). The objectives were to determine the effect of crossbreeding and selection in these animals' genetic diversity as well as to discover the herd's genetic relationship with that of other breeds. Low diversity was verified in BMS3013 and high diversity was detected in BMS3004, HEL10 and TGLA122. Two alleles in TGLA122 are described here for the first time (TGLA122*155 and TGLA122*163). These genes are possibly characteristics of Zebu animals since they have not been found in other taurine samples so far investigated. Low interpopulational diversity was observed among taurine cattle populations, and clusters obtained on TGLA122 phylogenetic trees agreed with the bovine herd's geographic origin. Therefore, despite TGLA122's high polymorphism and high levels of intrapopulational diversity, the system engenders consistent bovine phylogenies. We detected an intriguingly high similarity between Brangus Ibagé and Red Angus since the former is a hybrid having 3/8 of Nelore genes. Either these animals' environment or genetic selective practices applied to the breed probably favor the Angus genotype.

Download Full-text

Phylogenetic Analysis and Molecular Typing of Trichothecene-Producing Fusarium Fungi from Russian Collections

Acta Naturae ◽

10.32607/20758251-2018-10-2-79-92 ◽

2018 ◽

Vol 10 (2) ◽

pp. 79-92

Author(s):

A. A. Stakheev ◽

L. V. Samokhvalova ◽

O. D. Mikityuk ◽

S. K. Zavriev

Keyword(s):

Phylogenetic Analysis ◽

Fusarium Species ◽

Geographic Origin ◽

Elongation Factor ◽

Intraspecific Variability ◽

North Caucasus ◽

The North ◽

Group I ◽

High Level ◽

First Time

We performed a three-locus phylogenetic analysis of Fusarium strains presumably capable of trichothecene production, which were deposited in the Russian national collections. The intra- and interspecific polymorphism of partial sequences of the translation elongation factor 1 alpha (TEF1) gene and two genes from the trichothecene cluster TRI5 and TRI14 was studied. A study of 60 strains of different origins using DNA markers confirmed, and in the case for several strains, clarified their taxonomic characteristics. As a result, a strain of F. commune (F-900) was identified in Russia for the first time. Furthermore, the strain F-846 proved to be phylogenetically distinct from any of the known Fusarium species. F. equiseti strains from Northwest Russia were found to belong to the North European group (I), whereas a strain from the North Caucasus - to the South European one (II). Partial TRI14 sequences from 9 out of 12 species were determined for the first time. Their comparative analysis demonstrated a relatively high level of intraspecific variability in F. graminearum and F. sporotrichioides, but no correlation between the sequence polymorphism and the geographic origin of the strains or their chemotype was found. Specific chemotypes of trichothecene B producers were characterized using two primer sets. The chemotyping results were verified by HPLC.

Download Full-text

Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N

BMC Research Notes ◽

10.1186/s13104-021-05874-4 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Amer Al-Jawabreh ◽

Suheir Ereqat ◽

Kamal Dumaidi ◽

Hanan Al-Jawabreh ◽

Abedelmajeed Nasereddin

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genome Sequencing ◽

Rna Virus ◽

Haplotype Network ◽

Health Concern ◽

Diversity Analysis ◽

High Genetic Diversity ◽

Genetic Diversity Analysis ◽

First Time

Abstract Objectives SARS-CoV-2, severe respiratory syndrome coronavirus-2, is an RNA virus that emerged from China sweeping the globe in the form of a pandemic that became an international public health concern. This pilot study aimed to describe the genetic variation and molecular epidemiology of SARS-CoV-2 in Palestine in fall 2020. Results To achieve these aims, whole genome sequencing of SARS-CoV-2, phylogenetic analysis, haplotype networking and genetic diversity analysis were performed. These analyses revealed a unique spike mutation H245N that has never been reported before. The phylogenetic analysis depicted that three clusters existed in Palestinian SARS-CoV-2 genome sequences, in which cluster-I comprised the majority of clusters by 90%. Congruently, the haplotype network analysis depicted the same three clusters with a total of 39 haplotypes. The genetic diversity analysis showed that Cluster-I is highly diverse as confirmed by statistically significant mutation rate indices, Tajima’s D and Fu-Li’s-F tests (− 2.11 and 2.74, respectively), highest number of mutations (Eta = 120), highest number of haplotypes (h = 17), and highest average number of nucleotide differences between any two sequences (S = 118). The study confirmed the high genetic diversity among the Palestinian of SARS-CoV-2 which possessed high number of mutations including one which was reported for the first time.

Download Full-text

New record of Tulostoma squamosum (Agaricales: Basidiomycota) from India based on morphological features and phylogenetic analysis

Journal of Threatened Taxa ◽

10.11609/jott.5663.12.3.15375-15381 ◽

2020 ◽

Vol 12 (3) ◽

pp. 15375-15381

Author(s):

Arun Kumar Dutta ◽

Soumitra Paloi ◽

Krishnendu Acharya

Keyword(s):

Phylogenetic Analysis ◽

Nucleotide Sequence ◽

Sequence Comparison ◽

New Record ◽

Geographic Origin ◽

Morphological Description ◽

Evolutionary Divergence ◽

Nucleotide Sequence Comparison ◽

First Time ◽

Description Field

Tulostoma squamosum is reported for the first time from India. A comprehensive macro-morphological description, field photographs along with microscopic observations, and comparisons with morphologically similar and phylogenetically related taxa are provided. Nucleotide sequence comparison and an estimation of evolutionary divergence between Tulostoma squamosum sequences across different geographic origin are also provided.

Download Full-text

New and noteworthy lichen-forming and lichenicolous fungi 10

Acta Botanica Hungarica ◽

10.1556/034.62.2020.1-2.6 ◽

2020 ◽

Vol 62 (1-2) ◽

pp. 69-108

Author(s):

S. Y. Kondratyuk ◽

D. K. Upreti ◽

G. K. Mishra ◽

S. Nayaka ◽

K. K. Ingle ◽

...

Keyword(s):

Phylogenetic Analysis ◽

South Korea ◽

Eastern Europe ◽

South Asia ◽

New Combinations ◽

Eastern Asia ◽

Forest Zone ◽

Mediterranean Europe ◽

First Time ◽

India And China

Eight species, new for science, i.e.: Lobothallia gangwondoana S. Y. Kondr., J.-J. Woo et J.-S. Hur and Phyllopsora dodongensis S. Y. Kondr. et J.-S. Hur from South Korea, Eastern Asia, Ioplaca rinodinoides S. Y. Kondr., K. K. Ingle, D. K. Upreti et S. Nayaka, Letrouitia assamana S. Y. Kondr., G. K. Mishra et D. K. Upreti, and Rusavskia indochinensis S. Y. Kondr., D. K. Upreti et S. Nayaka from India and China, South Asia, Caloplaca orloviana S. Y. Kondr. and Rusavskia drevlyanica S. Y. Kondr. et O. O. Orlov from Ukraine, Eastern Europe, as well as Xanthoria ibizaensis S. Y. Kondr. et A. S. Kondr. from Ibiza Island, Spain, Mediterranean Europe, are described, illustrated and compared with closely related taxa. Fominiella tenerifensis S. Y. Kondr., Kärnefelt, A. Thell et Feuerer is for the first time recorded from Mediterranean Europe, Huriella loekoesiana S. Y. Kondr. et Upreti is provided from Russia for the first time, and H. pohangensis S. Y. Kondr., L. Lőkös et J.-S. Hur for the first time from China, Phoma candelariellae Z. Kocakaya et Halıcı is new to Ukraine, and Staurothele frustulenta Vain. is recorded from the Forest Zone of Ukraine for the first time. Twelve new combinations, i.e.: Bryostigma apotheciorum (for Sphaeria apotheciorum A. Massal.), Bryostigma biatoricola (for Arthonia biatoricola Ihlen et Owe-Larss.), Bryostigma dokdoense (for Arthonia dokdoensis S. Y. Kondr., L. Lőkös, B. G. Lee, J.-J. Woo et J.-S. Hur), Bryostigma epiphyscium (for Arthonia epiphyscia Nyl.), Bryostigma lobariellae (for Arthonia lobariellae Etayo), Bryostigma lapidicola (for Lecidea lapidicola Taylor), Bryostigma molendoi (for Tichothecium molendoi Heufl. ex Arnold), Bryostigma neglectulum (for Arthonia neglectula Nyl.), Bryostigma parietinarium (for Arthonia parietinaria Hafellner et Fleischhacker), Bryostigma peltigerinum (for Arthonia vagans var. peltigerina Almq.), Bryostigma phaeophysciae (for Arthonia phaeophysciae Grube et Matzer), Bryostigma stereocaulinum (for Arthonia nephromiaria var. stereocaulina Ohlert), are proposed based on results of combined phylogenetic analysis based on mtSSU and RPB2 gene sequences. Thirty-one new combinations for members of the genus Polyozosia (i.e.: Polyozosia actophila (for Lecanora actophila Wedd.), Polyozosia agardhiana (for Lecanora agardhiana Ach.), Polyozosia altunica (for Myriolecis altunica R. Mamut et A. Abbas), Polyozosia antiqua (for Lecanora antiqua J. R. Laundon), Polyozosia bandolensis (for Lecanora bandolensis B. de Lesd.), Polyozosia behringii (for Lecanora behringii Nyl.), Polyozosia caesioalutacea (for Lecanora caesioalutacea H. Magn.), Polyozosia carlottiana (for Lecanora carlottiana C. J. Lewis et Śliwa), Polyozosia congesta (for Lecanora congesta Clauzade et Vězda), Polyozosia eurycarpa (for Lecanora eurycarpa Poelt, Leuckert et Cl. Roux), Polyozosia expectans (Lecanora expectans Darb.), Polyozosia flowersiana (Lecanora flowersiana H. Magn.), Polyozosia fugiens (for Lecanora fugiens Nyl.), Polyozosia invadens (for Lecanora invadens H. Magn.), Polyozosia juniperina (for Lecanora juniperina Śliwa), Polyozosia latzelii (for Lecanora latzelii Zahlbr.), Polyozosia liguriensis (for Lecanora liguriensis B. de Lesd.), Polyozosia massei (for Myriolecis massei M. Bertrand et J.-Y. Monnat), Polyozosia mons-nivis (for Lecanora mons-nivis Darb.), Polyozosia oyensis (for Lecanora oyensis M.-P. Bertrand et Cl. Roux), Polyozosia percrenata (for Lecanora percrenata H. Magn.), Polyozosia persimilis (for Lecanora hagenii subsp. persimilis Th. Fr.), Polyozosia poeltiana (for Lecanora poeltiana Clauzade et Cl. Roux), Polyozosia prominens (for Lecanora prominens Clauzade et Vězda), Polyozosia prophetae-eliae (for Lecanora prophetae-eliae Sipman), Polyozosia salina (for Lecanora salina H. Magn.), Polyozosia schofieldii (for Lecanora schofieldii Brodo), Polyozosia sverdrupiana (for Lecanora sverdrupiana Øvstedal), Polyozosia torrida (for Lecanora torrida Vain.), Polyozosia wetmorei (for Lecanora wetmorei Śliwa), Polyozosia zosterae (for Lecanora subfusca? zosterae Ach.)) are proposed.

Download Full-text

Genetic Diversity of Basil (Ocimum spp. - Lamiaceae) Based on RAPD Markers and Volatile Oil Constituents

HortScience ◽

10.21273/hortsci.33.3.492f ◽

1998 ◽

Vol 33 (3) ◽

pp. 492f-493

Author(s):

Roberto F. Vieira ◽

James E. Simon ◽

Peter Goldsbrough ◽

Antonio Figueira

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Rapd Markers ◽

Volatile Oil ◽

Essential Oil Composition ◽

Oil Composition ◽

Traditional Medicines ◽

The Tropics ◽

High Degree ◽

First Time

Essential oils extracted from basil (Ocimum spp.) by steam distillation are used to flavor foods, oral products, in fragrances, and in traditional medicines. The genus Ocimum contains around 30 species native to the tropics and subtropics, with some species naturalized and/or cultivated in temperate areas. Interand intraspecific hybridization have created significant confusion in the botanical systematics of this genus. Taxonomy of basil (O. basilicum) is also complicated by the existence of numerous varieties, cultivars, and chemotypes within the species that do not differ significantly in morphology. In this study we are using RAPD markers and volatile oil composition to characterize the genetic diversity among the most economically important Ocimum species. We hypothesize that the genetic similarity revealed by molecular markers will more accurately reflect the morphological and chemical differences in Ocimum than essential oil composition per se. Preliminary research using five Ocimum species, four undetermined species, and eight varieties of O. basilicum (a total of 19 accessions) generated 107 polymorphic fragments amplified with 19 primers. RAPDs are able to discriminate between Ocimum species, but show a high degree of similarity between O. basilicum varieties. The genetic distance between nine species and among 55 accessions within the species O. americanum, O. basilicum, O. campechianum, O. × citriodorum, O. gratissimum, O. kilimandscharium, O. minimum, O. selloi, and O. tenuiflorum will be analyzed by matrix of similarity and compared to the volatile oil profile. This research will for the first time apply molecular markers to characterize the genetic diversity of Ocimum associate with volatile oil constituent.

Download Full-text

Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil (Lens culinaris Medik.)

Plants ◽

10.3390/plants10010015 ◽

2020 ◽

Vol 10 (1) ◽

pp. 15

Author(s):

Badreddine Sijilmassi ◽

Abdelkarim Filali-Maltouf ◽

Hassan Boulahyaoui ◽

Aymane Kricha ◽

Kenza Boubekri ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

16S Rrna ◽

Rhizobium Leguminosarum ◽

Sequence Similarity ◽

P Value ◽

Rrna Gene ◽

Research Station ◽

Symbiotic Efficiency ◽

Rhizobium Strains

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.

Download Full-text

Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽

10.3390/pathogens10020089 ◽

2021 ◽

Vol 10 (2) ◽

pp. 89

Author(s):

Jiayu Li ◽

Fuxian Yang ◽

Ruobing Liang ◽

Sheng Guo ◽

Yaqiong Guo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Characterization ◽

Zoonotic Potential ◽

Common Occurrence ◽

High Genetic Diversity ◽

Gp60 Gene ◽

The Common ◽

Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

Download Full-text