Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus

Deb, Saptarathi; Jayaprasad, Suvratha; Ravi, Samathmika; Rao, Kanchan; Whadgar, Saurabh; Hariharan, Nivedita; Dixit, Swati; Sunil, Meeta; Choudhary, Bibha; Stevanato, Piergiorgio; Ramireddy, Eswarayya; Srinivasan, Subhashini

doi:10.3389/fpls.2020.579529

Cited by 7 publications

(6 citation statements)

References 38 publications

(74 reference statements)

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“…For example, A. cruentus is thought to have a basic chromosome set of n = 17 versus n = 16 for A. hypochondriacus. Based on whole-genome sequencing (WGS), there are other differences (Deb et al, 2020); however, the same SNP markers function across both clades as we saw in this research. A better definition of the primary and secondary gene pools for each Amaranthus species is needed through crossing studies with a wide range of germplasm.…”

Section: Discussionmentioning

confidence: 70%

“…In contrast, these studies used selected sets of markers to evaluate diversity, two genotyping by sequencing (GBS) studies ( Stetter and Schmid, 2017 ; Wu and Blair, 2017 ) found similar results when evaluating random SNP. Later, Deb et al. (2020) used WGS to place six re-sequenced Indian cultivars in the dendrogram of genotypes studied by Wu and Blair (2017) and to compare their A. cruentus and A. hypochondriacus representatives to the reference genome from Lightfoot et al.…”

Section: Discussionmentioning

confidence: 99%

“…As our number of SNP marker number was limited (but highly polymorphic), we recommend re-sequencing with PacBio or Illumina skimSeq but using multiple reference genomes for more SNP discovery. Previous studies for SNPs (Maughan et al, 2011, Stetter and Schmid, 2017, Wu and Blair, 2017Thapa et al, 2021) referenced the Plainsman variety, which is possibly of mixed Mesoamerican ancestry (Lightfoot et al, 2017;Deb et al, 2020). Maughan et al (2009), in contrast, emphasized A. caudatus for genomics.…”

Section: Discussionmentioning

confidence: 99%

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Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

et al. 2023

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Grain amaranths are made up of three New World species of pseudo-cereals with C4 photosynthesis from the dicotyledonous family Amaranthaceae and the genus Amaranthus. They originate in two ecoregions of the Americas, namely, the inter-Andean valleys of South America and the volcanic axis and lowlands of Mexico and Central America. These correspond to two centers of domestications for Andean and Mesoamerican crops, with one cultivated species found in the first region and two found in the latter region. To date, no core collection has been made for the grain amaranths in the United States Department of Agriculture (USDA) germplasm system. In this study, our objective was to create a core for the 2,899 gene bank accessions with collection site data by town or farm site of which 1,090 have current geo-referencing of latitude and longitude coordinates. We constituted the core with 260 genotypes of Amaranthus, which we evaluated with 90 single-nucleotide polymorphism markers. Our goal was to distinguish between Andean and Mesoamerican gene pools of amaranths, including the cultivated species and three possible progenitor or wild relative ancestors along with two more species in an outgroup. Population structure, clustering, and discriminant analysis for principal components showed that Andean species Amaranthus caudatus and Amaranthus quitensis shared fewer alleles with Mesoamerican species Amaranthus cruentus and Amaranthus hypochondriacus, compared to each group individually. Amaranthus hybridus was a bridge species that shared alleles with both regions. Molecular markers have the advantage over morphological traits at quickly distinguishing the Andean and Mesoamerican cultivars and have the added benefit of being useful for following inter-species crosses and introgression.

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Section: Discussionmentioning

confidence: 70%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

et al. 2023

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“…Synteny has been used to filter, organize and process local similarities between genome sequences of related organisms to build a coherent global chromosomal context ( Deb et al, 2020 ). Each genus of prokaryotes possesses characteristic genomic gene synteny information, and its patterns are broadly associated with many bacterial functional traits ( Brbić et al, 2016 ).…”

Section: Resultsmentioning

confidence: 99%

PPA-GCN: A Efficient GCN Framework for Prokaryotic Pathways Assignment

2022

Front. Genet.

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With the rapid development of sequencing technology, completed genomes of microbes have explosively emerged. For a newly sequenced prokaryotic genome, gene functional annotation and metabolism pathway assignment are important foundations for all subsequent research work. However, the assignment rate for gene metabolism pathways is lower than 48% on the whole. It is even lower for newly sequenced prokaryotic genomes, which has become a bottleneck for subsequent research. Thus, the development of a high-precision metabolic pathway assignment framework is urgently needed. Here, we developed PPA-GCN, a prokaryotic pathways assignment framework based on graph convolutional network, to assist functional pathway assignments using KEGG information and genomic characteristics. In the framework, genomic gene synteny information was used to construct a network, and ideas of self-supervised learning were inspired to enhance the framework’s learning ability. Our framework is applicable to the genera of microbe with sufficient whole genome sequences. To evaluate the assignment rate, genomes from three different genera (Flavobacterium (65 genomes) and Pseudomonas (100 genomes), Staphylococcus (500 genomes)) were used. The initial functional pathway assignment rate of the three test genera were 27.7% (Flavobacterium), 49.5% (Pseudomonas) and 30.1% (Staphylococcus). PPA-GCN achieved excellence performance of 84.8% (Flavobacterium), 77.0% (Pseudomonas) and 71.0% (Staphylococcus) for assignment rate. At the same time, PPA-GCN was proved to have strong fault tolerance. The framework provides novel insights into assignment for metabolism pathways and is likely to inform future deep learning applications for interpreting functional annotations and extends to all prokaryotic genera with sufficient genomes.

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“…More recently, this plainsman reference genome together with low-coverage PacBio reads and the contigs of amaranth draft genome [ 20 ] were used to assemble A . hypochondriacus (A.hyp_K_white), a landrace cultivated in India [ 21 ]. This assembly offers a better reference genome for the improvement of grain and vegetable amaranth crops in South Asia as it is genetically closer to most landraces and accessions originated from India and South Asia.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis and marker-trait associations in Amaranthus species

et al. 2022

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Amaranth (Amaranthus spp.) is a highly nutritious, underutilized vegetable and pseudo-cereal crop. It possesses diverse abiotic stress tolerance traits, is genetically diverse and highly phenotypically plastic, making it an ideal crop to thrive in a rapidly changing climate. Despite considerable genetic diversity there is a lack of detailed characterization of germplasm or population structures. The present study utilized the DArTSeq platform to determine the genetic relationships and population structure between 188 amaranth accessions from 18 agronomically important vegetable, grain, and weedy species. A total of 74, 303 SNP alleles were generated of which 63, 821 were physically mapped to the genome of the grain species A. hypochondriacus. Population structure was inferred in two steps. First, all 188 amaranth accessions comprised of 18 species and second, only 120 A. tricolor accessions. After SNP filtering, a total of 8,688 SNPs were generated on 181 amaranth accessions of 16 species and 9,789 SNPs generated on 118 A. tricolor accessions. Both SNP datasets produced three major sub-populations (K = 3) and generate consistent taxonomic classification of the amaranth sub-genera (Amaranthus Amaranthus, Amaranthus Acnida and Amaranthus albersia), although the accessions were poorly demarcated by geographical origin and morphological traits. A. tricolor accessions were well discriminated from other amaranth species. A genome-wide association study (GWAS) of 10 qualitative traits revealed an association between specific phenotypes and genetic variants within the genome and identified 22 marker trait associations (MTAs) and 100 MTAs (P≤0.01, P≤0.001) on 16 amaranth species and 118 A.tricolor datasets, respectively. The release of SNP markers from this panel has produced invaluable preliminary genetic information for phenotyping and cultivar improvement in amaranth species.

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Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus

Cited by 7 publications

References 38 publications

Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

PPA-GCN: A Efficient GCN Framework for Prokaryotic Pathways Assignment

Genetic diversity analysis and marker-trait associations in Amaranthus species

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