Comparative analyses of chloroplast genomes of Theobroma cacao and Theobroma grandiflorum

Biologia ◽  
2019 ◽  
Vol 75 (5) ◽  
pp. 761-771 ◽  
Author(s):  
Abdullah ◽  
Shahid Waseem ◽  
Bushra Mirza ◽  
Ibrar Ahmed ◽  
Mohammad Tahir Waheed
Keyword(s):  
Theobroma Cacao ◽  
Comparative Analyses ◽  
Theobroma Grandiflorum ◽  
Chloroplast Genomes

Comparative analyses of the complete chloroplast genomes of nymphoides and menyanthes species (menyanthaceae)

2019 ◽  
Vol 156 ◽  
pp. 73-81 ◽  
Author(s):  
Ann W. Njuguna ◽  
Zhi-Zhong Li ◽  
Josphat K. Saina ◽  
Justus M. Munywoki ◽  
Andrew W. Gichira ◽  
...  
Keyword(s):  
Comparative Analyses ◽  
Chloroplast Genomes

scholarly journals ESTIMACIÓN DE LA BIOMASA CON RELACIONES ALOMÉTRICAS EN DOS ESPECIES DE FRUTALES: THEOBROMA CACAO L. (CACAO) Y THEOBROMA GRANDIFLORUM (WILLD. EX SPRENG.) K.SCHUM. (COPOAZÚ)

2013 ◽  
Vol 22 (1-2) ◽  
pp. 67
Author(s):  
Percy MARTÍNEZ-DÁVILA ◽  
Jorge SOLIGNAC-RUIZ ◽  
Ricardo ZÁRATE ◽  
Lizardo FACHÍN ◽  
José T. MACO-GARCÍA ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Theobroma Grandiflorum ◽  
Theobroma Cacao L

Se elaboró un modelo alométrico para estimar la biomasa aérea total a partir de la variable altura en dos especies de frutales de dos años de edad: Theobroma cacao L. (cacao) y Theobroma grandiflorum (Willd. ex Spreng.) K.Schum. (copoazú). Estas especies se cultivan, asociadas con otras especies, en sistemas frutales de algunas áreas cercanas a la carretera Iquitos – Nauta. El estudio utilizó un método destructivo con 18 individuos por especie. Se extrajeron submuestras del  fuste, hojas, ramas y ramillas que fueron sometidas a un proceso de secado en hornos para obtener su peso seco y finalmente ordenar, tabular y analizar los datos para generar los modelos por especie. A partir de los resultados obtenidos de la biomasa total y por cada componente, se formaron modelos alométricos para cada una de las especies en función de la variable altura total. Las ecuaciones alométricas con el coeficiente de determinación (R2) mayor a 0,80 fueron las cúbicas: Y = 0,16 +  (-2,74X2) + 1,52X3, y Y = 0,62 + 4,04X - 0,49X2 + 2,062X3 para Theobroma cacao y Theobroma grandiflorum donde Y es la biomasa aérea (t) y X es la altura total (m). En las dos ecuaciones el coeficiente de determinación (R2) fue mayor a 0,80.

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants

2019 ◽  
Author(s):  
Ting Yang ◽  
Xuezhu Liao ◽  
Lingxiao Yang ◽  
Yang Liu ◽  
Weixue Mu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Structure ◽  
Strong Support ◽  
Gc Content ◽  
Taxon Sampling ◽  
Data Sets ◽  
Green Plants ◽  
Comparative Analyses ◽  
Chloroplast Genomes ◽  
The Matrix

AbstractBackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.ResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.ConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.

scholarly journals Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus Dalbergia (Fabacaeae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood

2021 ◽  
Author(s):  
Zhou Hong ◽  
Dan Peng ◽  
Wenchuang He ◽  
Ningnan Zhang ◽  
Zengjiang Yang ◽  
...  
Keyword(s):  
Nucleotide Polymorphisms ◽  
Dna Barcodes ◽  
Variable Regions ◽  
Comparative Analyses ◽  
Illicit Trade ◽  
Traditional Medicines ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Plastid Markers ◽  
Simple Sequence

Abstract The genus Dalbergia contains more than 120 species several of which are trees that produce traditional medicines and extremely high value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade CITES has listed the entire genus in appendix II and the species D. nigra in appendix I because it is considered threatened with extinction. Given this and the fact that species or even genus level determination is nearly impossible from cut timber alternative molecular methods are needed to identify and track intercepted rosewood. In order to improve molecular identification of rosewood, we sequenced and assembled eight chloroplast genomes including D. nigra as well as conducted comparative analyses with all other available chloroplast genomes in Dalbergia and closely related lineages. From these analyses numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis using the CDS of 77 coding genes the groups Siam rosewood and scented rosewood based mainly on wood characteristics were supported as monophyletic. In addition, several instances of paraphyly and polyphyly resulting from mismatch between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of Dalbergia species including those frequently intercepted in illegal trade.

scholarly journals COMPARAÇÃO ENTRE AS CARACTERÍSTICAS BROMATOLÓGICAS DAS AMÊNDOAS DE CACAU (Theobroma cacao), CUPUAÇU (Theobroma grandiflorum) E CUPUÍ (Theobroma subincanum)

2018 ◽  
Vol 15 (28) ◽  
pp. 312-317
Author(s):  
Jessé Silva ◽  
Maria Santos ◽  
Fabrício Mesquita ◽  
William Alves ◽  
Adauto Pena Junior
Keyword(s):  
Theobroma Cacao ◽  
Theobroma Grandiflorum
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