scholarly journals Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 27 ◽  
Author(s):  
Sunil Sahu ◽  
Min Liu ◽  
Anna Yssel ◽  
Robert Kariba ◽  
Samuel Muthemba ◽  
...  
Keyword(s):  
Starch Synthesis ◽  
Gene Families ◽  
Genomic Information ◽  
High Quality ◽  
Specific Expression ◽  
Closely Related Species ◽  
Important Species ◽  
Specific Composition ◽  
Western Ghats Of India ◽  
The Western Ghats

Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

scholarly journals Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

2019 ◽  
Author(s):  
Sunil Kumar Sahu ◽  
Min Liu ◽  
Anna Yssel ◽  
Robert Kariba ◽  
Sanjie Jiang ◽  
...  
Keyword(s):  
Starch Synthesis ◽  
Gene Families ◽  
Genomic Information ◽  
High Quality ◽  
Specific Expression ◽  
Closely Related Species ◽  
Important Species ◽  
Specific Composition ◽  
Western Ghats Of India ◽  
The Western Ghats

AbstractTwo of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 100 pounds). To date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2,822 and 2,034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch- and sucrose metabolism, photosynthesis and others. The copy number of several starch synthesis related genes were found increased in jackfruit and breadfruit compared to closely related species, and the tissue specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.

scholarly journals Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1465
Author(s):  
Ramon de Koning ◽  
Raphaël Kiekens ◽  
Mary Esther Muyoka Toili ◽  
Geert Angenon
Keyword(s):  
Common Bean ◽  
Seed Development ◽  
Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Raffinose Family Oligosaccharides ◽  
Specific Expression ◽  
Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

scholarly journals A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

2021 ◽  
Author(s):  
Tomas N Generalovic ◽  
Shane A McCarthy ◽  
Ian A Warren ◽  
Jonathan M D Wood ◽  
James Torrance ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Animal Feed ◽  
Repetitive Sequences ◽  
Genomic Variation ◽  
Runs Of Homozygosity ◽  
High Quality ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Chromosome Conformation ◽  
Important Species

Abstract Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome five. Release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterisation of genes of interest and genetic modification of this economically important species.

scholarly journals Use of wastes from the tea and coffee industries for the production of cellulases using fungi isolated from the Western Ghats of India

2020 ◽  
Vol 1 (1) ◽  
pp. 33-41
Author(s):  
S. A. Saldaña-Mendoza ◽  
J. A. Ascacio-Valdés ◽  
A. S. Palacios-Ponce ◽  
J. C. Contreras-Esquivel ◽  
R. Rodríguez-Herrera ◽  
...  
Keyword(s):  
Western Ghats ◽  
Western Ghats Of India ◽  
The Western Ghats

scholarly journals Rapid mapping of landslides in the Western Ghats (India) triggered by 2018 extreme monsoon rainfall using a deep learning approach

Landslides ◽  
2021 ◽  
Author(s):  
Sansar Raj Meena ◽  
Omid Ghorbanzadeh ◽  
Cees J. van Westen ◽  
Thimmaiah Gudiyangada Nachappa ◽  
Thomas Blaschke ◽  
...  
Keyword(s):  
Deep Learning ◽  
Western Ghats ◽  
Auxiliary Information ◽  
Optical Data ◽  
Spectral Information ◽  
Topographic Slope ◽  
Western Ghats Of India ◽  
Landslide Inventory Map ◽  
Inventory Map ◽  
The Western Ghats

AbstractRainfall-induced landslide inventories can be compiled using remote sensing and topographical data, gathered using either traditional or semi-automatic supervised methods. In this study, we used the PlanetScope imagery and deep learning convolution neural networks (CNNs) to map the 2018 rainfall-induced landslides in the Kodagu district of Karnataka state in the Western Ghats of India. We used a fourfold cross-validation (CV) to select the training and testing data to remove any random results of the model. Topographic slope data was used as auxiliary information to increase the performance of the model. The resulting landslide inventory map, created using the slope data with the spectral information, reduces the false positives, which helps to distinguish the landslide areas from other similar features such as barren lands and riverbeds. However, while including the slope data did not increase the true positives, the overall accuracy was higher compared to using only spectral information to train the model. The mean accuracies of correctly classified landslide values were 65.5% when using only optical data, which increased to 78% with the use of slope data. The methodology presented in this research can be applied in other landslide-prone regions, and the results can be used to support hazard mitigation in landslide-prone regions.

Native coffee agroforestry in the Western Ghats of India maintains higher carbon storage and tree diversity compared to exotic agroforestry

2018 ◽  
Vol 265 ◽  
pp. 461-469 ◽  
Author(s):  
Joannès Guillemot ◽  
Guerric le Maire ◽  
Manjunatha Munishamappa ◽  
Fabien Charbonnier ◽  
Philippe Vaast
Keyword(s):  
Carbon Storage ◽  
Western Ghats ◽  
Tree Diversity ◽  
Coffee Agroforestry ◽  
Western Ghats Of India ◽  
The Western Ghats
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