Phylogenetic relationships of sorghum taxa inferred from mitochondrial DNA restriction fragment analysis

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 1027-1034 ◽  
Author(s):  
J. H. Guo ◽  
D. Z. Skinner ◽  
G. H. Liang
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Dna Analysis ◽  
Multiple Correspondence Analysis ◽  
Restriction Enzymes ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Group Iii ◽  
Group I ◽  
Taxonomic Research

To elucidate the evolutionary history and affinity of sorghum species, 41 sorghum taxa were analyzed using variability in mitochondrial DNA. Analysis of species relationships at the molecular level can provide additional data to supplement the existing classification based on morphological characters and may also furnish unexpected but useful information. Total DNA extracted from each of the sorghum accessions was digested with each of five restriction enzymes, BamHI, HindIII, EcoRI, EcoRV, and XbaI, and probed with five mitochondrial DNAs cloned from Sorghumbicolor. A total of 180 restriction fragments was detected by the 25 probe–enzyme combinations. Forty-three fragment bands were phylogenetically informative. Multiple correspondence analysis was performed to visualize associations among the accessions and suggested that section Eusorghum species may be divided into four groups, with Sorghumlaxiflorum (section Heterosorghum) and Sorghumnitidum (section Parasorghum) appearing as outliers. A phylogenetic tree was assembled from mitochondrial restriction fragment data. The taxa analyzed formed three major groups comprising section Heterosorghum (group I), section Parasorghum (group II), and all accessions in section Eusorghum (group III). Group III is further divided into four groups: (i) two sweet sorghums and shattercane; (ii) Sorghumhalepense, Sorghummiliaceum, Sorghumhewisonii, Sorghumaethiopicum, Sorghumverticilliflorum, and S. bicolor, including Sorghumsudanense (sudangrass), the Chinese Kaoliangs, and a number of commercial sorghum inbreds from the U.S.A.; (iii) Sorghumpropinquum; and (iv) Sorghumarundinaceum, Sorghumniloticum, Sorghumalmum, Sorghumcontroversum, and the Chinese material C-401 and 5-27. Results indicate that the analysis of fragmented mitochondrial DNA was diagnostic and useful in sorghum phylogenetic and taxonomic research at the species, subspecies, and race levels, and can complement results from those analyses using nuclear ribosomal DNA and chloroplast DNA that effectively distinguish taxa at species and genus levels. Key words : Sorghum, mitochondrial DNA, phylogeny, restriction fragment.

scholarly journals DNA Analysis of Ralstonia solanacearum and Related Bacteria Based on 282-bp PCR-Amplified Fragment

Plant Disease ◽  
2003 ◽  
Vol 87 (11) ◽  
pp. 1337-1343 ◽  
Author(s):  
Joselito Villa ◽  
Kenichi Tsuchiya ◽  
Mitsuo Horita ◽  
Marina Natural ◽  
Nenita Opina ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Dna Analysis ◽  
Restriction Analysis ◽  
Polymerase Chain Reaction Amplification ◽  
Restriction Enzymes ◽  
The Philippines ◽  
Restriction Fragments ◽  
Group Iii ◽  
Group I ◽  
Group 2

Strains of Ralstonia solanacearum, Pseudomonas syzygii, and the blood disease bacterium (BDB) from different countries were tested for polymerase chain reaction amplification of the 282-bp fragment using the primer pair 759 and 760. These 282-bp fragments from 49 strains of R. solanacearum, six strains of P. syzygii, and two strains of BDB were sequenced. A phylogenetic tree was generated based on the sequence alignment. The R. solanacearum strains were divided into three groups. Group I was composed of strains belonging to biovars 3, 4, 5, and biovar N2 from Japan. Most of the strains from this group were of Asian origin except for two strains from Australia and Guyana (GMI 1000), the type strain. Group II was composed of strains belonging to biovars 1 and 2 and biovar N2 from Brazil. Group III was composed of strains belonging to biovar N2 from Japan and the Philippines. All strains of P. syzygii and BDB clustered in group III. Based on nucleotide differences of the 282-bp fragments, restriction enzyme NlaIII was capable of differentiating R. solanacearum strains into the three groups. Restriction analysis of 165 R. solanacearum isolates from the Philippines using NlaIII showed that all biovar 3 and 4 (group 1) strains had restriction fragments of 116 and 166 bp, strains belonging to biovars 1 and 2 (group 2) showed no restriction, and one strain belonging to biovar 2 (group 3) showed restriction fragments of 54 and 228 bp in size. Thus, NlaIII could be used for rapid differentiation of R. solanacearum strains. Additionally, other restriction enzymes, such as McrI, BsiEI, and MnlI could be used to differentiate R. solanacearum strains from P. syzygii strains.

Mitochondrial and nuclear DNA variation, genotype fingerprinting and genetic relationships in lentil (Lens culinaris Medik.)

1997 ◽  
Vol 77 (4) ◽  
pp. 515-521 ◽  
Author(s):  
Om P. Rajora ◽  
John D. Mahon
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Lens Culinaris ◽  
Nuclear Dna ◽  
Genetic Relationships ◽  
Restriction Enzymes ◽  
Dna Variation ◽  
Apocytochrome B ◽  
Nuclear Dna Variation ◽  
Mean Similarity

Mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) variations were examined in six cultivars of Lens culinaris ssp. culinaris and two (mtDNA) or one (nuDNA) accession(s) of L. culinaris ssp. orientalis. Total leaf DNA was digested with up to 15 restriction endonucleases, separated by agarose gel electrophoresis and trasferred to nylon membranes. To examine mtDNA variation, blots were probed with mtDNA coding for cytochrome c oxidase I (coxI) and ATPase 6 (atp6) of both wheat and maize as well as apocytochrome b (cob) and Orf25 (orf25) of wheat. Sixteen combinations of mtDNA probes and restriction enzymes revealed 34 fragments that discriminated between at least two lentil accessions. For nuDNA analysis, probes from cDNA and genomic DNA clones of lentil were used to probe the same blots, and identified 46 diagnostic fragments from 19 probe/enzyme combinations. Each lentil accession could be unequivocably distinguished from all others on the basis of both mitochondrial and nuclear DNA fragment patterns. The mitochondrial restriction fragment similarities ranged from 0.944 to 0.989, with a mean of 0.970 but nuclear restriction fragment similarities varied from 0.582 to 0.987, with a mean of 0.743. The apparent genetic relationships among accessions differed according to the source of DNA examined, although the commercial varieties Laird, Brewer and Redchief showed similarly high levels of mean similarity with both nuclear (0.982) and mitochondrial DNA (0.983). Key words: Lens culinaris Medik., genetic variation, mitochondrial, nuclear, DNA, lentil

Six new species of the genus Chevalia Walker, 1904 (Amphipoda, Corophiidea, Chevaliidae) from Brazilian waters, with a key to world species of the genus

Zootaxa ◽  
2019 ◽  
Vol 2713 (1) ◽  
pp. 25
Author(s):  
JESSER F. SOUZA-FILHO ◽  
ANA MARIA T. SOUZA ◽  
MARIA TERESA VALÉRIO-BERARDO
Keyword(s):  
New Species ◽  
Morphological Characters ◽  
Species Group ◽  
Brazilian Coast ◽  
Proximal Margin ◽  
World Species ◽  
Group Iii ◽  
Cephalic Lobe ◽  
Group I ◽  
The World

Six new species of the genus Chevalia are described from the Brazilian coast using all morphological characters proposed by Barnard & Thomas (1987) and Lazo-Wazen (1999) with two more: the shape of head proximal margin of lateral cephalic lobe and length ratio of uropod 2 rami: C. anomala sp. nov.; C. caetes sp. nov.; C. convexa sp. nov.; C. marajoara sp. nov.; C. thomasi sp. nov.; and C. setosa sp. nov. This paper raises the total number of recognized world species in this genus to 13. The genus is herein subdivided into three groups, based only on the shape of the basis of pereopod 7: group I – rectangular basis of pereopod 7 with a protuberant posteroventral corner, comprises four species; group II – rectangular basis of pereopod 7 lacking a protuberant posteroventral corner, comprises three species; and group III – ovate basis of pereopod 7, comprises seven species. A key of the world Chevalia species is also provided.

scholarly journals Geographic Discrimination of Paracoccidioides brasiliensis Strains by Randomly Amplified Polymorphic DNA Analysis

1998 ◽  
Vol 36 (6) ◽  
pp. 1733-1736 ◽  
Author(s):  
Ana María Calcagno ◽  
Gustavo Niño-Vega ◽  
Felipe San-Blas ◽  
Gioconda San-Blas
Keyword(s):  
Dna Analysis ◽  
Paracoccidioides Brasiliensis ◽  
Epidemiological Studies ◽  
Randomly Amplified Polymorphic Dna ◽  
Group V ◽  
Group Iii ◽  
Group I ◽  
Geographical Regions ◽  
High Degree ◽  
Discriminatory Index

Randomly amplified polymorphic DNA (RAPD) analysis of 33Paracoccidioides brasiliensis strains from Argentina, Brazil, Colombia, Peru, and Venezuela produced reproducible amplification products which were sufficiently polymorphic to allow differentiation of the strains. Types generated with five primers (OPG 03, OPG 05, OPG 14, OPG 16, and OPG 18) resulted in a high discriminatory index (0.956). The discriminatory index was slightly reduced (0.940) when only two primers (OPG 3 and OPG 14) were used. A dendrogram based on these results showed a high degree of similarity among the strains, and genetic differences were expressed in clusters related to geographical regions but not to pathological features of the disease. With a few exceptions, strains were sorted into five groups by geographical origin as follows: group I, Venezuelan strains; group II, Brazilian strains; group III, Peruvian strains; group IV, Colombian strains; and group V, Argentinian strains. The group containing the most disparate strains was group V (discriminatory index, 0.633); the discriminatory index for the other four groups was 0.824. The use of primer OPG 18 by itself was sufficient to discriminate species specificity, and the use of primer OPG 14 by itself was sufficient to discriminate among the geographical locations of the strains in the sample. This method may be helpful for epidemiological studies ofP. brasiliensis.

scholarly journals Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)

ZooKeys ◽  
2018 ◽  
Vol 763 ◽  
pp. 1-111 ◽  
Author(s):  
Tricia C. Goulding ◽  
Munawar Khalil ◽  
Shau Hwai Tan ◽  
Benoît Dayrat
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Comparative Anatomy ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
The Philippines ◽  
Coral Triangle ◽  
Yellow Orange

A new genus of onchidiid slugs,WallaconchisGoulding & Dayrat,gen. n., is described, including ten species. Five species were previously described but known only from the type material:Wallaconchisater(Lesson, 1830),W.graniferum(Semper, 1880),W.nangkauriense(Plate, 1893),W.buetschlii(Stantschinsky, 1907), andW.gracile(Stantschinsky, 1907), all of which were originally classified inOnchidiumBuchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new:WallaconchisachleitneriGoulding,sp. n.,W.comendadoriGoulding & Dayrat,sp. n.,W.melanesiensisGoulding & Dayrat,sp. n.,W.sinanuiGoulding & Dayrat,sp. n., andW.uncinusGoulding & Dayrat,sp. n.Nine of the tenWallaconchisspecies are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia).Wallaconchisis distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify allWallaconchisspecies. The copulatory organs ofWallaconchisspecies are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed,nomina dubiaare discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.

Allozyme and mitochondrial DNA separation of Pacific northern bluefin tuna, Thunnus thynnus orientalis (Temminck and Schlegel), from southern bluefin tuna, Thunnus maccoyii (Castelnau)

1995 ◽  
Vol 46 (6) ◽  
pp. 921 ◽  
Author(s):  
RD Ward ◽  
NG Elliott ◽  
PM Grewe
Keyword(s):  
Mitochondrial Dna ◽  
Fishery Management ◽  
Dna Analysis ◽  
Haplotype Frequency ◽  
Restriction Enzymes ◽  
Bluefin Tuna ◽  
Allozyme Variation ◽  
Site Variation ◽  
Southern Bluefin Tuna ◽  
Allozyme Loci

Northern and southern bluefin tunas are morphologically similar and can be misidentified, posing problems for fishery management and marketing. Allozyme variation and restriction-site variation in mitochondrial DNA (mtDNA) were used to distinguish between the two species. A survey of 36 allozyme loci active in white muscle and liver tissue showed that the genetic identity between the species was high (Nei's I = 0.907). One diagnostic locus (sAH*) and two nearly diagnostic loci (ADA* and GDA*) were found, and four loci showed highly significant allele frequency differences (FH*, GPI-A*, PGDH* and sSOD*). A survey of the mtDNA genome, using 15 restriction enzymes and southern blotting, revealed five restriction enzymes that gave species-diagnostic restriction digest profiles (Ban I, Bcl I, Dra I, Pvu II, Xba I) and a further three enzymes (Pst I, Barn HI and Nco I) with large haplotype frequency differences. Mitochondrial DNA analysis provided more reliable discrimination of specimens than did allozyme analysis, although the more rapid allozyme identification will be accurate for most specimens. The two biochemical genetic methods were then used to identify Australian-caught fish of uncertain identity. Six of 12 tuna originally considered to be northern bluefin tuna were confirmed as northern bluefin and six were identified as southern bluefin. The presence of northern bluefin tuna as far south as south-western Tasmania was confirmed.

Eulepida mbala, a new species from Zambia (Coleoptera: Scarabaeidae: Melolonthinae)

Zootaxa ◽  
2018 ◽  
Vol 4399 (4) ◽  
pp. 591
Author(s):  
RICHARD SEHNAL
Keyword(s):  
New Species ◽  
Type Species ◽  
Morphological Characters ◽  
Species Group ◽  
Undescribed Species ◽  
Group Iii ◽  
Group I ◽  
Group Ii ◽  
One New Species ◽  
A New Species

The genus Eulepida Kolbe, 1894 (Coleoptera: Scarabaeidae: Melolonthinae: Leucopholini) was established to accommodate 10 Afrotropical species, seven new and three previously placed in Lepidiota Kirby, 1828, Proagosternus Blanchard, 1851, and Tricholepis Hampson, 1891. Lacroix (2010) designated Leucopholis lepidota Klug, 1855 as the type species of the genus Eulepida. Currently the genus contains 20 species divided into three groups based on morphological characters (Lacroix 2010, 2013): species group I includes Eulepida lepidota (Klug, 1855), E. minor Moser, 1913, E. nitidicollis Kolbe, 1894, E. nyassica Kolbe, 1894, E. sinuatifrons (Fairmaire, 1887), and E. zambiensis Lacroix, 2010; species group II includes E. anatina Brenske, 1896, E. tschindeana Péringuey, 1904, and E. werneri Lacroix, 2010; and species group III includes E. baumanni Kolbe, 1894, E. flavovestita Moser, 1913, E. gracilipes Kolbe, 1894, E. kameruna (Frey, 1972), E. kenyensis Lacroix, 2010, E. mamboiae Brenske, 1896, E. manowensis Moser, 1913, E. mashona Arrow, 1902, E. montana Kolbe, 1894, E. reichei (Thomson, 1858), and E. savagei (Hope, 1842). Examination of material recently collected in Zambia revealed an undescribed species belonging to species group II (sensu Lacroix 2010). This group is defined by the combination of the following characters: protibia bidentate; antennal club distinctly longer than antennal shaft; pygidium narrow, longer than wide, with a pronounced elongate terminal invagination; and parameres symmetrical, long, evenly curved in ventral aspect (Lacroix 2010). The purpose of this paper is to describe one new species, to add new geographic records for some Eulepida species of group II, and to update the key for this group. New faunistic records are reported for Eulepida tschindeana and Eulepida werneri from Zimbabwe. 

scholarly journals Rapid Identification and Differentiation of the Soft Rot Erwinias by 16S-23S Intergenic Transcribed Spacer-PCR and Restriction Fragment Length Polymorphism Analyses

2001 ◽  
Vol 67 (9) ◽  
pp. 4070-4076 ◽  
Author(s):  
I. K. Toth ◽  
A. O. Avrova ◽  
L. J. Hyman
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Soft Rot ◽  
Group Iii ◽  
Group I ◽  
Its Pcr ◽  
Restriction Fragment Length

ABSTRACT Current identification methods for the soft rot erwinias are both imprecise and time-consuming. We have used the 16S-23S rRNA intergenic transcribed spacer (ITS) to aid in their identification. Analysis by ITS-PCR and ITS-restriction fragment length polymorphism was found to be a simple, precise, and rapid method compared to current molecular and phenotypic techniques. The ITS was amplified fromErwinia and other genera using universal PCR primers. After PCR, the banding patterns generated allowed the soft rot erwinias to be differentiated from all other Erwinia and non-Erwinia species and placed into one of three groups (I to III). Group I comprised all Erwinia carotovorasubsp. atroseptica and subsp.betavasculorum isolates. Group II comprised allE. carotovora subsp. carotovora,subsp. odorifera, and subsp. wasabiae andE. cacticida isolates, and group III comprised allE. chrysanthemi isolates. To increase the level of discrimination further, the ITS-PCR products were digested with one of two restriction enzymes. Digestion with CfoI identified E. carotovora subsp.atroseptica and subsp. betavasculorum(group I) and E. chrysanthemi (group III) isolates, while digestion with RsaI identified E. carotovora subsp. wasabiae, subsp. carotovora, and subsp.odorifera/carotovora and E. cacticida isolates (group II). In the latter case, it was necessary to distinguishE. carotovora subsp. odorifera and subsp. carotovora using the α-methyl glucoside test. Sixty suspected soft rot erwinia isolates from Australia were identified as E. carotovora subsp.atroseptica, E. chrysanthemi,E. carotovora subsp. carotovora, and non-soft rot species. Ten “atypical” E. carotovora subsp. atroseptica isolates were identified as E. carotovora subsp.atroseptica, subsp. carotovora, and subsp. betavasculorum and non-soft rot species, and two “atypical” E. carotovora subsp.carotovora isolates were identified as E. carotovora subsp. carotovora and subsp.atroseptica.

Allozyme and mitochondrial DNA analysis of carp, Cyprinus carpio L., from south-eastern Australia

1999 ◽  
Vol 50 (3) ◽  
pp. 253 ◽  
Author(s):  
Karyn M. Davis ◽  
Patricia I. Dixon ◽  
John H. Harris
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Cyprinus Carpio ◽  
Dna Analysis ◽  
Restriction Enzymes ◽  
South Eastern ◽  
Eastern Australia ◽  
Carp Cyprinus Carpio ◽  
Allozyme Loci ◽  
South Eastern Australia

Carp (Cyprinus carpio L.) were introduced to Australia on at least three occasions over the past 100 years. These introductions were to the Prospect Reservoir, Sydney (1907), the Murrumbidgee Irrigation Area, New South Wales (NSW) (1940s), and to Boolarra, Victoria (1960). Koi, a colourful variety of carp, have been introduced to several areas as well. Carp are now widely spread throughout south-eastern Australia. This study aimed to investigate genetic variation of carp in south-eastern Australia. Carp from several localities were examined at seven polymorphic allozyme loci and with three restriction enzymes detecting polymorphic sites in mitochondrial DNA. Three composite mtDNA haplotypes were found. Haplotype 1 was spread throughout the study area, occurring in 72% of all individuals examined. Haplotype 2 was localized to south-western NSW and occurred in 4% of individuals. Haplotype 3 was found in the Australian Capital Territory and Tasmania and accounted for 24% of individuals. Little genetic variation within and among carp populations was observed in the mitochondrial DNA data. The allozyme data showed greater variation within populations than did the mitochondrial DNA data.

scholarly journals Characterization of Botryosphaeria dothidea Isolates Collected from Pistachio and Other Plant Hosts in California

2002 ◽  
Vol 92 (5) ◽  
pp. 519-526 ◽  
Author(s):  
Zhonghua Ma ◽  
Themis J. Michailides
Keyword(s):  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Botryosphaeria Dothidea ◽  
Internal Transcribed Spacer Region ◽  
Group Iii ◽  
Group I ◽  
Plant Group ◽  
Plant Hosts ◽  
Shoot Blight ◽  
Group Ii

Eighty-six isolates of Botryosphaeria dothidea, the causal agent of Botryosphaeria panicle and shoot blight of pistachio, were collected from pistachio and other plant hosts in California. The isolates were characterized by microsatellite-primed polymerase chain reaction (MP-PCR), sequences of the nuclear ribosomal DNA internal transcribed spacer region (ITS1, 5.8S gene, and ITS2), morphological and cultural characters, osmotic and fungicide sensitivity, and pathogenicity on pistachio. Three groups of these isolates were identified based upon analysis of MP-PCR data and ITS sequences. Group I contained 43 pycnidiospore-derived isolates collected from pistachio and other hosts. Group II consisted of 20 ascosporic isolates obtained from a single sequoia plant. Group III consisted of 20 ascosporic isolates from three shoots on a single blackberry plant, two pycnidiospore-derived isolates from incense cedar, and one from pistachio. Group I predominated over the other two groups in California pistachio orchards. B. dothidea isolates of group III grew faster on acidified potato dextrose agar (APDA) than the isolates of groups I and II. Isolates of group III produced pycnidia on both APDA and autoclaved pistachio shoots, but the isolates of the other two groups produced pycnidia on only autoclaved pistachio shoots. Additionally, significant differences in osmotic and fungicide sensitivities were observed among these three groups. Results from lathhouse inoculations demonstrated that the representative isolates for each of the three groups were all capable of infecting pistachio and producing characteristic disease symptoms of Botryosphaeria blight. The virulence of group II isolates on pistachio was, however, significantly lower than that of group I isolates.

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