Here, we present the most contiguous draft assemblies of these three species to date. Amaranthus hybridus subsp. (2017) from 16 developmental stages including leave, stem and root from 15,20,25 and 30 day plant, bud, flower, young seed and mature seed were mapped to AhKP reference using bowtie2 (Langmead and Salzberg, 2012). Amaranthaceae – Plant Classification Group – Famine Foods - Plants that are not normally considered as crops are consumed in times of famine - Purdue University, West Lafayette, Indiana doi: 10.1101/gr.094607.109, Smit, A.F. The sequence alignment/map format and SAMtools. Genome Biol. Post demultiplexing, the reads were mapped to AhKP using bowtie2 (Langmead and Salzberg, 2012) and SNP calling was done using the method described in the above section. boiRxiv [Preprint]. A., Van Heusden, P., et al. At K = 4 and 5 there is no resolution between species except A. hypochondriacus. Nucleic Acids Res. A, and Hubley, R (2008–2015). Genome Res. Briefly, for PE libraries, the fragmented DNA was end-repaired, 3′-adenylated, ligated with Illumina adapters, and PCR enriched with Illumina sequencing indexes. Avaliable at: https://hort.purdue.edu/newcrop/proceedings1999/v4-184.html (accessed October 4, 2020). For example, there is a component (Figure 4B, pink) only present in all A. hypochondriacus from India, which is missing in Plainsman. 12:e1006500. Fingerprints for two grain amaranthus varieties KBGA1 and Suvarna using RAPD and legume based SSR markers. In traditional medicinal system different parts of the plant Amaranthus hybridus (A. hybridus) The bam files of each sample can be visualized in the respective genome browser (link to the same is available in the data availability section) Also, the expression profiles of all the 12 predicted genes from the lysine pathway across developmental stages is provided in Figure 5A along with the corresponding exon number and sizes compared to Arabidopsis Figure 5B. J. Hum. Cladus: Amaranthaceae s.str. (2009). DNA was sheared using Adaptive Focused Acoustic technology (Covaris, Inc.) to generate fragments of desired insert size. Amaranthus chlorostachys var. The scaffolds from this step are further improved with simulated mate pairs using wgsim (Li, 2020) from Plainsman with SSPACE. Although easily controlled and not particularly competitive, it is recognized as a harmful weed of North American crops. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman (A.hyp.V.2.1). This section is divided into three parts. Classification schemes have varied between a single species approach, Amaranthus hybridus s.l., and a five At a time when gluten-free, protein-rich, high-fiber, and high nutritional values are becoming attractive labels in supermarkets around the globe, grain amaranths deserving all these labels cannot be ignored as a future crop. Phytochemical Studies of Rajigara Amaranthus Species for its Potential use in Medicine. However, at K = 5 and 6 components of A. quitensis is profound only in A. caudatus. doi: 10.1073/pnas.1107739108, Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J., and Holmes, I. H. (2009). For example, mate-pair libraries from one Arabidopsis thaliana strain were shared across many strains to build super-scaffolds for all individuals (Schneeberger et al., 2011). Polysaccharides extracted from traditional Chinese medicines may be effective substances with antioxidant activity. As a second approach, the phylogenetic tree shown in Figure 4A and generated using AhKP as reference (Figure 4A) combines variants called for the 94 accessions using both raw genotyping-by-sequencing (GBS) data from public sources (Wu and Blair, 2017) and whole-genome sequencing (WGS) data for listed accessions in Supplementary Table S2. The draft genomes of four species including bushbaby, African elephant, rabbit and guinea pig from the “Mammal 24 - 2X” project were built using both human and canine references (Gnerre et al., 2009). Plainsman reference: Phytozome1 A. hypochondriacus genome V.2.1(A.hyp.V.2.1) (Lightfoot et al., 2017) GBS: Blair et al. JBrowse: a next-generation genome browser. State of knowledge on amaranth grain: a comprehensive review. Amaranthus hybridus subsp. Suvarna, an accession/landrace from India, often classified as A. hypochondriacus in the literature, clearly clusters with A. cruentus and shows high similarity to the accession A.cru_Mexico_PI477913, also classified as A. cruentus. In the first approach we have attempted to create a classification tree with WGS data for landraces sequenced here and only those accessions for which WGS data was available (NCBI Project accession SRP061623). (A) Synteny of assemblies with respect to the Plainsman reference A.hyp.V.2.1 against AhK20. Nat. 15:e1007273. Amaranthus aureus Moq. (B) Genetic admixture analysis of A. hypochondriacus, A. caudatus, A. cruentus, and A. quitensis. From the mapped reads, variants were called using samtools (v1.9) mpileup (Li et al., 2009) and bcftools (v1.9) (Li et al., 2009). Here, a chromosome level assembly (AhKP) of a landrace, A.hyp_K_white, under contiguous cultivation in India for over several centuries is reported. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. The reads were demultiplexed using GBSX (Herten et al., 2015) using the provided barcode sequences. Gigascience 1:18. doi: 10.1186/2047-217X-1-18. (accessed 23 Septemper 2015).∗, Soderlund, C., Bomhoff, M., and Nelson, W. M. (2011). Since this landrace is more closely similar to all other landraces and accessions for A. hypochondriacus from India and South Asia (Supplementary Table S1), AhKP offers a better reference for the improvement of grain amaranth crops in South Asia. Effect of plant density and planting geometry on growth and yield of grain amaranths. In Argentina this weed first evolved multiple resistance (to 2 herbicide sites of action) in 2014 and infests Corn (maize), and Soybean. Also, the two landraces under A. hypochondriacus, A.hyp_K_white and A.hyp_K_red, cluster apart within the same clade validating our observation that the seeds of these two varieties faithfully produce plants with inflorescence unique to the respective phenotype. Only 97 out of 107 samples from both GBS and WGS data were filtered based on their good clustering and bigger sample size. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Food Sci. (2009). The assembly statistics of the initial assembly was sufficient for reference-based scaffolding using both the simulated mate-pairs from the reference genome and raw HiC data for Plainsman from public resources (Lightfoot et al., 2017). Schneeberger, K., Ossowski, S., and Ott, F. (2011). The Amaranth database is running on EC2 instances of Amazon cloud service (AWS). This was supported by the solid stem characteristics of A. cruentus for A.cru_Suvarna as reported by Malligawad and Patil (2010). For MP libraries, the fragmented DNA was end-repaired, followed by end labeling using the biotin-dNTP mix, size selected and later, circularized using circularization ligase. Interestingly, similar to Figure 2, A.hyp_K_white and A.hyp_K_red, both landraces from India cluster closely together along with accessions A.hyp_Nepal_PI619259 and A.hyp_India_PI481125. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few. PacBio reads using RSII technologies sequenced in 2013 with an average length of 7.5 kb with a coverage of 25X for A.hyp_K_white were assembled using state-of-the-art tools CANU (Koren et al., 2017)and FLYE (Kolmogorov et al., 2019) to obtain an assembly with L50 values of 1395 and 944, respectively, as shown in the flowchart in section “Materials and Methods” (Figure 6). The accession PI490752 originally classified as A. hypochondriacus now classifies under A. quitensis. It is believed that these landraces, which are in contiguous cultivation in distal geographical locations in India, have already adapted to diverse environmental conditions prevalent in Nepal, as well as in East and South India. ADMIXTURE analysis shown in Figure 4B, also suggests that there is significant gene flow between A. caudatus and A. quitensis. U.S.A. 108, 10249–10254. (2017). A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few. Bos taurus. Interestingly, the only A. hybridus accession from Greece (A.hyb_Greece_PI605351) included in the classification is not in the same clade as Plainsman but, instead, clusters along with all accessions from A. cruentus (near blue arrow in Figure 4A). The files were then merged, and the genotype matrix was created using a custom script. doi: 10.1093/nar/gkr123, Sunil, M., Hariharan, A. K., and Nayak, S. (2014). We used multiple assembly tools adapted/developed recently to handle error-prone long reads and merged these assemblies with the contigs from our previously reported draft assembly. This plant originated in America, but it has spread all over the world. Amaranthus hecticus Willd. The database is also integrated with graphical visualization for gene expression data of 16 developmental stages with query search options. RepeatModeler Open-1.0. Biol. doi: 10.1186/gb-2009-10-8-r88. Annotation of AhKP was done using multiple approaches (i) Augustus (Hoff and Stanke, 2019) (v3.2.3) prediction using Arabidopsis as model and (ii) MAKER (Campbell et al., 2014) genome annotation pipeline with (with and without Augustus) default parameters, was used for AhKP annotation. Interestingly, grain amaranths, domesticated around 8000 years ago, enjoyed equal status as corn during the Aztec and Inca civilizations (Caselato-Sousa and Amaya-Farfán, 2012). On the other hand, the phylogenetic trees shown in Figures 3B,C, generated using ∼6 million SNP variants, which shows some bias from the references used to generate variants, also clusters A.hyp_K_white in a distal clade from A.hyp_Plainsman_PI558499. Recently, a chromosome level genome of Lates calcarifer was assembled from a draft genome using long-read sequencing, transcriptome data, optical/genetic mapping and synteny to two closely related seabasses (Vij et al., 2016). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. Amaranthus batalleri Sennen Amaranthus bellardii Moq. The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. Genome annotation and curation using MAKER and MAKER-P. Curr. A draft genome for the same landrace was reported by our group in 2014 (Sunil et al., 2014). batalleri (Sennen) J.L.Carretero (synonym) Amaranthus hybridus subvar multispiculatus (Sennen) J.L.Carretero (synonym) Amaranthus incurvatus Tim. Sci. The red arrow indicates the position of A.hyp_Plainsman_PI558499 WGS sample next to its corresponding GBS, green arrow indicates position of A.hyp_K_white and blue arrow indicates the position of A.cru_Suvarna in the phylogenetic tree. Amaranthus hybridus grows from a short taproot and can be up to 2.5 m in height. (2015). JBrowse (Skinner et al., 2009) is JavaScript and html based genome browser provides the solution for visualization of various kinds of genomic data such as FASTA, BAM, GFF, VCF, and bigwig etc., Data for downloading and JBrowse is stored on the cloud and made available for research purposes. Curr. (2019). Amaranthus hybridus var. It has been reported to have been found in every state except Wyoming, Utah, and Alaska. doi: 10.1101/856591, Ghurye, J., Rhie, A., and Walenz, B. P. (2019). A. hybridus with accession of PI605351 clusters in the same clade as Suvarna with another accessions (PI477913) from A. cruentus. The size selection for all the libraries were done using solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP Beads) from Beckman Coulter. Methods: In this study, we isolated crude polysaccharides from A. hybridus … 1a, g), origin of flower bud from doi: 10.1038/s41587-019-0072-8, Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., and Phillippy, A. M. (2017). NH: transcriptome analysis. The first section describes the results from our efforts to assemble a near-chromosome level assembly for a landrace A.hyp_K_white using contigs from previously reported draft genome of A.hyp_K_white (Sunil et al., 2014), low-coverage PacBio reads and a high-quality reference genome of Plainsman (Lightfoot et al., 2017). Toward this end, our lab had initiated sequencing the genome of Amaranthus (A.) In the third and last section, results from classification of the landraces/varieties sequenced here with sequencing data for many accessions from public resources including GBS and WGS technologies are discussed. Sci. In Figure 4A, an attempt was made to decorate the classification of 94 accessions generated both using GBS data with WGS data for landraces generated here. Protoc. Possible aliases, alternative names and misspellings for Amaranthus hybridus. Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus. In a previous report, our lab had sequenced and reported developmental transcriptome of A.hyp_K_white from several tissues (Sunil et al., 2014, 2017). ER: forinitiating translational work and validating transcripts. A. ... Amaranthus caudatus, Amaranthus cruentus, and Amaranthus hybridus (Lightfoot et al., 2017). A whole-genome assembly of the domestic cow. The assembly reported here is obtained using relatively low coverage of long reads from PacBio RSII technologies in conjunction with a high-quality reference for another distal accession of the same species A.hyp_Plainsman_PI558499. Further, the regions covered in sequencing were identified using bedtools genomecov (Quinlan and Hall, 2010) from bam files, and the regions, which were not covered in sequencing in any of the samples, were removed from the genotype matrix. Smooth Pigweed (Amaranthus hybridus (syn: quitensis)) is a dicot weed in the Amaranthaceae family. In this article, we report a de novo assembly of a landrace (A.hyp_K_white) and demonstrate that, in the presence of a reference genome for a distal variety, a chromosome-level assembly can be generated at a reasonable cost. While a large number of landraces, adapted to local environments for small scale cultivation exist, their origins and relations to the large germplasm, collection at GRIN-Global are not established. Whole-genome sequencing from a few landraces and ornamental varieties generated in-house and several other accessions from public sources are clustered using 20,548 SNPs out of the 27,658 SNPs reported for grain amaranths (Figure 3A). 5, 511–516. doi: 10.1371/journal.pcbi.1007273, Gnerre, S., Lander, E. S., Lindblad-Toh, K., and Jaffe, D. B. (2016). Light blue star points to A.cru_Suvarna. Also, the browser can be queried using the accessions of Arabidopsis to visualize the expression profile of the corresponding orthologs on AhKP. J. hybridus S. Watson Amaranthus eugenii Sennen Amaranthus flavescens Moq. SNP discovery via genomic reduction, barcoding, and 454-pyrosequencing in amaranth. Further, we generated synteny of the AhK20 against A.hyp.V.2.1 using Symap (Soderlund et al., 2011) based on which AhK20 was improved to the final AhKP assembly. Figure 1A shows the synteny of the scaffolds from the assembly AhK20 on A.hyp.V.2.1 and Figures 1B–D show synteny of AhKP on to A.hyp.V.2.1 (Lightfoot et al., 2017) in various representations. All the accessions from A. quitensis and A. caudatus clusters together in a single clade with two branches of A. quitensis enclosing A. caudatus, which is also reported using only GBS data using A.hyp.V.2.1 as reference (Lightfoot et al., 2017). At K = 4, a significant component of A. quitensis is found in all four species. 11:579529. doi: 10.3389/fpls.2020.579529. It could be added to soups or stews and also taken as a cereal for breakfast. Besides, the seed sizes shown in Figure 2F also validate classification for Suvarna as A. cruentus with relatively bigger seed size. 2017 (Wu and Blair, 2017) WGS (Lightfoot et al., 2017)2. Since then, the chromosome-level genome of a different cultivar with an accession of PI558499 (Plainsman), has been deciphered using state-of-the-art technologies including Bionano, HiC, and long PacBio reads (Lightfoot et al., 2017). Subfamilia: Amaranthoideae Genus: Amaranthus Species: Amaranthus quitensis More recently, the plummeting cost of sequencing has democratized the application of genomics technologies not only to non-model crops but has extended its reach to individual landraces with direct benefit to local farmers. We believe that this is the first demonstration of generating a cost-effective de novo assembly for a landrace utilizing low coverage PacBio reads in conjunction with the genome and HiC data from another accession. Further, the biotinylated, adapter-ligated immobilized DNA were enriched by PCR. For genomics-based crop improvement of local landraces, it is critical to classify these with respect to accession from the germplasm collection. Figure 2 shows the photographs of fully-grown plants sequenced and reported here. Amaranthus hybridus subsp. Suvarna (R 104-1 -1), a pureline released by University of Agricultural Sciences (UAS), Bangalore-1992 from the material “Rodale Plus” received from Rodale Institute (Rathod, 2017) has previously been classified as A. hypochondriacus in Meera et al., 2014. doi: 10.1093/bioinformatics/bts606, Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., et al. This landrace was selected for its aggressive growth, and its yield compared to a few other landraces including one with red inflorescence cultivated in India. Amaranthus hybridus is an erect annual plant with a stem that can be much-branched to nearly free of branches; it usually grows 30 - 200cm tall, occasionally to 250cm 270 Title We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact … “Variability in ‘Plainsman’ grain amaranth,” in Perspectives on New Crops and New Uses, ed. 14, 155–167. 1961. 1753. The variants were filtered using bcftools (Li et al., 2009) with the criteria of QUAL (quality) greater than 10 and DP (read depth) greater than 3 and INDELs were also removed. (2012). doi: 10.1016/S0022-2836(05)80360-2, Batzoglou, S. (2005). Raw transcriptome reads generated in our earlier work and reported in Sunil et al. Amaranthus hybridus var. Classification Browse Images ... Amaranthus hybridus L., Sp. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., et al. Grain amaranth, also known as Ramdana (The God’s grain) or Rajgira or Rajeera, has been in continuous cultivation at least since last century in India. These plants are grown as ornamentals or for their grain, they do not exist in the wild, and are not weeds. Nat. Gandhinagar: INFLIBNET. Repeat elements for the Plainsman and the A.hyp_K_white variety of A. hypochondriacus assemblies were predicted using RepeatModeler version 2.0.1 (Flynn et al., 2019) along with LTR discovery. incurvatus Amaranthus hybridus Linnaeus, subsp. In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. VASCAN was last updated on 2020-09-04; Comment nous citer. doi: 10.1186/gb-2009-10-4-r42, Keywords: grain amaranths plainsman, A. hypochondriacus, A. cruentus, A. caudatus, genotyping by sequencing, whole genome sequencing, global-germplasm resources information network (GRIN), Citation: Deb S, Jayaprasad S, Ravi S, Rao KR, Whadgar S, Hariharan N, Dixit S, Sunil M, Choudhary B, Stevanato P, Ramireddy E and Srinivasan S (2020) Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. doi: 10.1371/journal.pone.0180528, Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. Amaranthus hybridus Taxonomy ID: 3565 (for references in articles please use NCBI:txid3565) current name. doi: 10.1086/519795, Quinlan, A. R., and Hall, I. M. (2010). doi: 10.1002/0471250953.bi0411s48, Caselato-Sousa, V. M., and Amaya-Farfán, J. Amaranthus hybridus L. is an annual, erect or less commonly ascending herb that is a member of the Amaranthaceae family (Akubugwo et al., 2007; Das, 2016).This plant is often used as a vegetable to treat intestinal bleeding, diarrhea and excessive menstruation (Olusola & Anslem, 2010).The Amaranthus … Workflow used in the assembly of AhKP. BMC Bioinformatics 16:73. doi: 10.1186/s12859-015-0514-3, Hoff, K. J., and Stanke, M. (2019). Amaranthus paniculatus Linnaeus 1763. More recently, using genotyping-by-sequencing (GBS), 94 accessions for grain amaranths have been classified (Wu and Blair, 2017). ex Gren. Amaranthus hybridus was originally a pioneer plant in eastern North America. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Further DESeq2 (Love et al., 2014) was used to get normalized read counts of all the predicted genes using the MAKER (Campbell et al., 2014) gene annotation pipeline. The largest genus, Amaranthus, contains about 70 species of herbs, including the ornamentals love-lies-bleeding, prince’s feather (A. hybridus), and Joseph’s coat (A. tricolor). It has been reported to have been found in every state except Wyoming, Utah, and Alaska. The authors wish to acknowledge GKVK for providing us with seeds for Suvarna and Dr. Xingbo Wu of Dr. Blair’s lab for providing us with raw GBS data from 94 accession. Annotation using the MAKER (Campbell et al., 2014) annotation pipeline predicted 18,858 gene models which has been validated for the 12 genes from lysine biosynthesis pathway by comparing it to Arabidopsis gene model as shown in Figure 5. J. Janick (Alexandria, VA: ASHS Press), 184–189. Front. In this case, one could use synteny between species at protein levels to build chromosomes. MS: PacBio data, developmental transcriptome and taxonomic classification of landraces. It is also found in many provinces of Canada, and in parts of Mexico, the West Indies, Central America, and South America. In this article, we intend to unravel the molecular mechanisms by which an A. hybridus population from Argentina has become resistant to extraordinarily high levels of glyphosate. In yet another report, 16 out of 60 chromosomes of the Tibetan antelope were reconstructed from draft assemblies using its homology to cattle (Kim et al., 2013). Bioinformatics 26, 841–842. Also, A.hyp_K_white is closest to A.hyp_Nepal_PI619259 and A.hyp_India_PI481125 with A.hyp_K_red relatively distal from A.hyp_K_white. The plant was used for food and medicine by several Native American groups and in traditional African medicine. Front. Common Name(s): Smooth Amaranth, Slim Amaranth, Slender Pigweed, Slender Pigweed - Green Form, Slender Pigweed - Red Form, Green Amaranth, Green Pigweed, Pigweed, Smooth Pigweed Amaranth flour could be mixed with wheat flour to make bread or other foods. Although the family (Amaranthaceae) is distinctive, the genus has few distinguishing characters among the 75 species present across six continents. Table 1 shows the assembly statistics. (A) Phylogenetic tree using the 20,548 SNPs reported for grain amaranths (green: A. hypochondriacus, blue: A. caudatus, and purple: A. cruentus, dashed arrows: ornamental, solid arrows: landraces with green star for A.hyp_K_white and red star for A.hyp_Plainsman variety, (B) Classification using 5,545,132 SNPs from the mapping of short reads onto AhKP as reference, (C) Classification using 6,383,490 SNPs from the mapping of short reads to A.hyp.V2.1 as reference. (2012). 37, 540–546. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. The seed could be … (2015). Proc. Guillen-Portal, F. R., Baltensperger, D. D., Nelson, L. A., and D’Croz-Mason, N. (1999). (2013). Bioinformatics 65:e57. We also downloaded WGS data from NCBI for seven other accessions including A.cau_Bolivia_PI642741, A.cru_Mexico_PI 477913, A.hyp_India_PI481125, A.hyp_Plainsman_PI558499, A.hyp_Nepal_PI619259, A.hyp_Pakistan_PI540446, A.hyp_ Mexico_PI511731, and A.hyb_Greece_PI605351. (A) Representative images from the institute’s field for the varieties A.hyp_K_white (B) A.hyp_K_red (C) A.cau_ornamental (love-lies-bleeding) (D) A.cru_ornamental (Autumn touch) (E) A.cru_Suvarna with white inflorescence grown at the institute campus and elsewhere for taxonomic classification (F) color-coded error graph of seed size for each variety. The evolution of herbicide‐resistant weeds is one of the most important concerns of global agriculture. We then selected K =4–6 as the optimal number subpopulation “K” based on the lowest cross-validation (c.v) error value plot as reported by ADMIXTURE(v1.3) where we see a dip in the c.v value at K = 4 and 6 (Supplementary Figure S4). Bioinformatics 25, 2078–2079. Amaranthus hypocondriacus Linnaeus 1753. (2017). 39:e68. The SNPs were merged and used for phylogenetic classification. 8:1960. doi: 10.3389/fpls.2017.01960, Zheng, X., Levine, D., Shen, J., Gogarten, S. M., Laurie, C., and Weir, B. S. (2012). Beck Homonyms Amaranthus hybridus L. Amaranthus hybridus Vell. The successful integration of WGS and GBS data attempted here, is apparent from the clustering of variants from WGS and GBS data for the same accession together as marked with red arrow in Figure 4A. doi: 10.1093/bioinformatics/btq033. doi: 10.1101/2020.04.27.063040, Deb, S., Suvrath, J., Ravi, S., Whadgar, S., Hariharan, N., Sunil, M., et al. It is extremely variable, and many other Amaranthus species are believed to be natural hybridizations or derive from A. hybridus. The tree in Figure 4A is very similar to that reported in Wu and Blair (2017) with 10,688 SNPs from accessions using GBS technology. Of these only 20,548 positions could be found covered in all whole-genome sequencing data across all samples studied here. A separate VCF file was made for all the 13 datasets as listed in Supplementary Table S2 with the respective alleles at these positions. (2020). 19, 1630–1638. Brief Bioinformatics 6, 6–22. Brenan Amaranthus hybridus var. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Stems and leaves are smooth and hairless, sometimes shiny in appearance. Plant Genome 2, 260–270. The landrace A.hyp_K_white is currently being used to identify mutations in targeted loci for a given desirable phenotype from a germplasm collection using eco-TILLING and to discover novel mutations that result in desirable traits like determinate growth, enhanced seed yield, seed lysine content and oil content using TILLING-based approaches. The raw PacBio data was assembled using Canu (Koren et al., 2017) and Flye (Kolmogorov et al., 2019) independently. The variants from WGS data from all the plants in Figure 2 were compared with those from the Plainsman accession and a handful of other accessions from public resources including A. hypochondriacus, Amaranthus caudatus, Amaranthus cruentus, and Amaranthus hybridus (Lightfoot et al., 2017). Grain amaranth is yet to reach an agronomic status in India. KRR: assembly and analysis of other landraces. This was further improved by merging the Illumina assembly from our previously reported draft genome of the same landrace A.hyp_K_white (Sunil et al., 2014), to get a contig-level assembly with an L50 of 593 (AhK593). chlorostachys (Willd.) PLoS One 12:e0180528. Abstract—The hybridus species complex of the genus Amaranthus is a group of weedy and cultivated plants from the New World that are considered difficult to identify. SD: DNA isolation and repeat analysis. Only 20,548 SNPs were commonly covered in all 13 WGS datasets and were used during classification. 77, R93–R104. One microgram and 10 μg of the DNA were used for the preparation of Paired-End (PE) and Mate-Pair (MP) libraries, respectively. This assembly was improved using HiC data from Painsman (Lightfoot et al., 2017) to obtain an assembly with a L50 of 99 (column 3, Table 1). 15:550. doi: 10.1186/s13059-014-0550-8, Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., et al. In this report, Suvarna is undoubtedly classified as A. cruentus based on 20,548 reported SNPs and roughly 6 million variants covered in WGS data (Figure 3). doi: 10.1111/j.1750-3841.2012.02645.x, Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., and Emerson, J. J. GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments. SPD: classification, characterization and writing of the manuscript. The database consists of a landing page, genome browser and NCBI BLAST (Altschul et al., 1990) tool. The mapped files were processed using samtools (Li et al., 2009) and raw read count was counted for all predicted genes using bedtools multiBamCov (Quinlan and Hall, 2010). Users can access the Jbrowse by clicking on the Genome browser button or using the tools menu. In fact, using independent mapping data and conserved synteny between the cattle and human genomes, 91% of the cattle genome was placed onto 30 chromosomes (Zimin et al., 2009). Such an approach can simply be extended for reference-guided improvement of draft genomes of a plant using simulated mate pairs of varying insert sizes from an existing assembly of a different variety/cultivar of the same species. Also, assisted assembly of closely related species significantly improved the contiguity of low coverage mammalian assemblies (Gnerre et al., 2009). These two assemblies were then merged using Quickmerge (Chakraborty et al., 2016) to improve the L50 to 623. J. McLean KS, Roy KW, 1991. bioRxiv [Preprint]. Whole-genome PacBio sequencing was done by Molecular Biology and Genomic Core, Washington University using P5/C3 chemistry on the Pacific Biosciences RSII platform. Stems angled or with longitudinal lines or ridges, green or brown, leaves alternate, broadly lance late to ovate, discolors, conspicuously veined beneath, up to 7 cm long, 4 cm wide. It is a weedy species found now over much of North America and introduced into Europe and Eurasia. Diversity in grain amaranths and relatives distinguished by genotyping by sequencing (GBS). It is interesting to note that A.cau_ornamental clusters close to A.cau_Bolivia_PI642741. This high-quality assembly has now allowed placement of about one hundred accessions from the germplasm on a phylogenetic tree (Wu and Blair, 2017) allowing for both establishing genotype-to-phenotype relationships and to place various landraces with very distinct phenotype on the tree for further characterization. Also, morphological features like stem solidness and total height at maturity as mentioned by Malligawad and Patil (2010) and seed size (Figure 2F) supports this classification. A detailed summary of this method of normalization has been explained in Figure 7. Scaffolds from AhK20 are further stitched based on synteny to A.hyp.V.2.1 (Lightfoot et al., 2017) to get the final chromosome-level assembly AhKP for the accession A.hyp_K_white. In this context, the draft assembly of a landrace from India was sequenced and reported (Sunil et al., 2014). Amaranthus hybridus, commonly called smooth amaranth, smooth pigweed, red amaranth, or slim amaranth, is a species of annual flowering plant.It is a weedy species found now over much of North America and … No use, distribution or reproduction is permitted which does not comply with these terms. U.S.A. 110, 1785–1790. Giving chromosomal context to genes and other genetic elements is one of the most sought-after goals in genome assembly. erythrostachys de Candolle, Prodr. Genet. & Godr. One way to do this would be to identify and use the alleles found from GBS data with the respective alleles found from WGS. We also improved AhK593 using simulated mate pairs from the reference genome of the Plainsman accession (Lightfoot et al., 2017), to build scaffolds of contigs from AhK593 to an L50 of 56 (AhK56) and subsequently using raw HiC data of the Plainsman accession from public sources to obtain a scaffold-level assembly with an L50 of 20 (AhK20) using SALSA (Ghurye et al., 2019). doi: 10.1002/cpbi.57, Kim, J., Larkin, D. M., and Cai, Q. Similarly, the malarial strain, Plasmodium falciparum HB3, was improved using the reference of P. falciparum 3D7 combined with an assisted assembly approach that significantly improved the contiguity of the former (Gnerre et al., 2009). However, natural selection puts sufficient selection pressure on protein sequences for maintaining functional contiguity required during evolution. It has been naturalized in many places of warmer climate. Tools, such as SOAPdenovo, use the known insert size between the mate-pair reads to connect contigs into longer scaffolds by filling the gaps with unidentified nucleotides (Ns) (Luo et al., 2012). Amaranthus hybridus can be consumed in various ways, namely made vegetables, directly consumed when raw, or made into … This was further improved by merging the Illumina assembly from the draft genome reported elsewhere and polished using the Illumina reads. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Amaranthus hybridus was originally a pioneer plant in eastern North America. It is among the species consumed as Quelite quintonilli in Mexican food markets. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. The editor and reviewers' affiliations are the latest provided on their Loop research profiles and may not reflect their situation at the time of review. The authors wish to recognize lab infrastructure support from DST, computing infrastructure by GoK and DBT for support to SPD via JRF under the project BT/PR23613/BPA/118/354/2017 titled “Non-transgenic crop improvement of grain amaranths (A. hypochondriacus) for determinate growth, enhanced seed yield and oil by establishment of TILLING by sequencing platform.”, The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2020.579529/full#supplementary-material, Alexander, D. H., and Lange, K. (2011). Figure 3. Also, the read depth considered during variant calling was restricted using samtools mpileup to 10 to match the depth of GBS data (Li et al., 2009). Natl. Figure 5. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. In a review article, synteny has been used to filter, organize and process local similarities between genome sequences of related organisms to build a coherent global chromosomal context (Batzoglou, 2005). ), A. hypochondriacus (q.v.). However, we report a new observation that PI649506 is a A. hypochondriacus originally annotated as A. cruentus. Amaranthus hybridus … Meera, N., Lohithaswa, H. C., Murthy, N., and Hittalmani, S. (2014). Amaranthus hybridus L. is a competitive weed for summer crops in South America.In this article, we intend to unravel the molecular mechanisms by which an A. hybridus population from Argentina has become … The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Articles, Campo Experimental Valle de México, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Mexico, Centro de Investigaciones y Estudios Avanzados, Instituto Politécnico Nacional de México (CINVESTAV), Mexico, Michoacana University of San Nicolás de Hidalgo, Mexico.