scholarly journals Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study

2019 ◽  
Vol 97 (4) ◽  
pp. 754-760
Author(s):  
Eduardo Ruiz-Sanchez ◽  
Carlos Alonso Maya-Lastra ◽  
Victor W. Steinmann ◽  
Sergio Zamudio ◽  
Eleazar Carranza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Information ◽  
Public Repository ◽  
Phylogenetic Studies ◽  
Meta Information ◽  
Study Case ◽  
Scripting Language ◽  
Diversity Studies ◽  
Extract Information

Background: GenBank is a public repository that houses millions of nucleotide sequences. Several software have been developed to extract information stored in GenBank. However, none of them are useful to extract and organize GenBank accession based on metadata. We developed a new script called Datataxa, which works to mine GenBank information. The checklist of the Flora del Bajío y de Regiones Adyacentes (FBRA) was used as a case study to apply our script.Questions: How many species occurring in the FBRA have records in GenBank? What percentage of those records have been used for phylogenetic, phylogeographic, phylogenomic, barcoding, genetic diversity, and biogeographic studies?Methods: Datataxa was written in AutoIt Scripting Language in order to facilitate the extraction of information from GenBank. This information was classified in six study categories. A checklist of species published fascicles of FBRA was used as study case to apply our new script, and the previous categories were applied to the FBRA species list.Results: The script allowed us to search for meta information, like publication titles, for 2,558 species that were included in the FBRA. Of these, 1,575 had a least one record in GenBank. A total of 1,322 species were used in phylogenetic studies, followed by barcoding studies (326) and biogeographic studies (298). Phylogenomic (41), phylogeographic (34), and diversity studies (34) were the least represented.Conclusions: Datataxa was useful for mining metadata sequence information from GenBank and can be used with any list of species to get the GenBank accessions’ metadata.

scholarly journals Genetic diversity of high and low molecular weight glutenin subunits in Saharan bread and durum wheats from Algerian oases

2012 ◽  
Vol 48 (No. 1) ◽  
pp. 23-32 ◽  
Author(s):  
I. Bellil ◽  
M. Chekara Bouziani ◽  
D. Khelifi
Keyword(s):  
Genetic Diversity ◽  
Molecular Weight ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Allelic Variation ◽  
Low Molecular Weight ◽  
Glutenin Subunits ◽  
Lmw Glutenin Subunits ◽  
Genotypic Identification ◽  
Diversity Studies

Saharan wheats have been studied particularly from a botanical viewpoint. Genotypic identification, classification and genetic diversity studies to date were essentially based on the morphology of the spike and grain. For this, the allelic variation at the glutenin loci was studied in a set of Saharan bread and durum wheats from Algerian oases where this crop has been traditionally cultivated. The high molecular weight and low molecular weight glutenin subunit composition of 40 Saharan bread and 30 durum wheats was determined by SDS-PAGE. In Saharan bread wheats 32 alleles at the six glutenin loci were detected, which in combination resulted in 36 different patterns including 17 for HMW and 23 for LMW glutenin subunits. For the Saharan durum wheats, 29 different alleles were identified for the five glutenin loci studied. Altogether, 29 glutenin patterns were detected, including 13 for HMW-GS and 20 for LMW-GS. Three new alleles were found in Saharan wheats, two in durum wheat at the Glu-B1 and Glu-B3 loci, and one in bread wheat at the Glu-B1 locus. The mean indices of genetic variation at the six loci in bread wheat and at the five loci in durum wheat were 0.59 and 0.63, respectively, showing that Saharan wheats were more diverse. This information could be useful to select Saharan varieties with improved quality and also as a source of genes to develop new lines when breeding for quality.

Thinning in mature eastern white pine: 43-year case study

2002 ◽  
Vol 78 (4) ◽  
pp. 539-549 ◽  
Author(s):  
Paul D Anderson ◽  
John C Zasada ◽  
Glen W Erickson ◽  
Zigmond A Zasada
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Large Diameter ◽  
White Pine ◽  
Thinning Intensity ◽  
Pine Regeneration ◽  
Volume Production ◽  
Pine Stands ◽  
Over Time

A white pine (Pinus strobus L.) stand at the western margin of the species range, approximately 125 years of age at present, was thinned in 1953 from 33.5 m2 ha-1 to target residual basal areas of 18.4, 23.0, 27.5, and 32.1 m2 ha-1 . Repeated measurement over the following 43-years indicated that the greatest total volume production and the greatest number of large diameter trees occurred in the unit of highest residual density. Over time, the distribution of stems was predominantly random although mortality between 1979 and 1996 resulted in a tendency for clumping in the 23.0 and 27.5 m2 ha-1 treatments. DNA analysis indicated that thinning intensity had little effect on the genetic diversity of residual white pine. This study suggests that mature white pine stands in northern Minnesota may be managed at relatively high densities without loss of productivity. However, regardless of overstory density, there was little or no white pine regeneration occurring in this stand. Key words: thinning, growth, genetic diversity, molecular markers, spatial pattern, regeneration

Do the importations of crop products affect the genetic diversity from landraces? A study case in garlic (Allium sativum L.)

2020 ◽  
Author(s):  
João Paulo Gomes Viana ◽  
Carolline de Jesús Pires ◽  
Miklos Maximiliano Bajay ◽  
Sérgio Emílio dos Santos Valente ◽  
José Baldin Pinheiro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Allium Sativum ◽  
Study Case

scholarly journals The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species

2005 ◽  
Vol 3 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Sally L. Dillon ◽  
Peter K. Lawrence ◽  
Robert J. Henry
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Ssr Markers ◽  
Diversity Indices ◽  
Basic Knowledge ◽  
Apparent Lack ◽  
Breeding Programmes ◽  
Diversity Studies ◽  
Potential Use ◽  
Simple Sequence

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

Impact of the choices of calibration points for molecular dating: a case study of Ensifera

2021 ◽  
Vol 4 (3) ◽  
Author(s):  
ANDRÉ NEL
Keyword(s):  
Molecular Dating ◽  
Rigorous Approach ◽  
Phylogenetic Studies

Fossils are crucial for molecular clade dating (Warnock et al., 2012, 2015). But it is necessary to have a rigorous approach, without rejecting taxa on poor arguments or ignoring some of them without any reasons. Here we show through two very recent examples of phylogenetic studies on the Orthoptera, that such behaviours can have dramatic consequences on the value of the results of the studies.

Coppice forests and genetic diversity: A case study in Quercus pyrenaica Willd. from Central Spain

2008 ◽  
Vol 254 (2) ◽  
pp. 225-232 ◽  
Author(s):  
M. Valbuena-Carabaña ◽  
S.C. González-Martínez ◽  
L. Gil
Keyword(s):  
Genetic Diversity ◽  
Quercus Pyrenaica ◽  
Central Spain

scholarly journals Study Case: Productivity of Catched Fish in Locations around the Construction of Coal Power Plant, Jepara Indonesia

2021 ◽  
pp. 52-63
Author(s):  
Slamet Isworo ◽  
Slamet Febrianto ◽  
Tosan Aji ◽  
Poerna Sri Oetari ◽  
Ekannisa Jasmiene
Keyword(s):  
Power Plant ◽  
Fish Production ◽  
Catch Per Unit Effort ◽  
Potential Conflict ◽  
Marine Fishery ◽  
Simple Regression Analysis ◽  
Study Case ◽  
The Government ◽  
Descriptive Method

Background and objective: The productivity of fishing in marine waters provides an overview of the level of ability of the fishing gear used by fishermen to obtain optimal fish catches. This study aims to determine the productivity of fishing in locations around the construction of the coal-fired power plant, Jepara Indonesia. Methods: The method used is a descriptive method which is a case study. This research case is about annual marine fishery productivity by calculating Catch Per Unit Effort (CPUE), then predictions are made using simple regression analysis. Results: Based on the results of the study, a positive modeling trend (increase) was obtained for total fishery production, total demersal fishery production, and total pelagic fish production. Conclusion: capture fisheries productivity in Jepara waters is generally quite good and is not affected due to the development of Tanjung Jati coal-fired power plant B-Unit 5 -6. This is because it is not a fishing operation area for fishermen so there is no potential conflict with fishermen. Suggestion: The results of this study can be used by the Government of Jepara Regency in determining sustainable fishing policies and not overfishing

scholarly journals Promoting sustainable development of poverty-alleviation policies based on high-quality cultural tourism by digital economy — A case study of Chishui City in Guizhou Province

2021 ◽  
Vol 251 ◽  
pp. 02015
Author(s):  
Fawen Yang ◽  
Cheng Yang ◽  
Qian Xie
Keyword(s):  
Poverty Alleviation ◽  
Development Trend ◽  
Cultural Tourism ◽  
Digital Economy ◽  
Guizhou Province ◽  
Moore’S Law ◽  
Moore's Law ◽  
Study Case ◽  
The Development Trend

Digital economy follows three laws — the Metcalfe’s law. the Moore’s law. and the Davidow effect, which are practically in line with China’s poverty-alleviation initiative by developing cultural tourism. The Moore’s law, however, is paradoxical in given contexts, and thus, we proposed the “reverse-Moore’s law” to analyze the current cultural tourism-based poverty-alleviation policies. The features of digital economy can be employed to support the cultural tourism-based poverty-alleviation work: the development trend of digital economy also coincides with China’s cultural tourism-based poverty alleviation initiatives. With the poverty-alleviation work at Chishui City in Guizhou Province as the study case, this paper made an analysis from the perspective of digital economy to confirm the practical and surreal significance of applying digital economy to China’s poverty alleviation endeavors.

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