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).