It has been reported to have been found in every state except Wyoming, Utah, and Alaska. The quality, quantity, and size distribution of the libraries were evaluated using Qubit (Invitrogen) and TapeStation (Agilent) (Sunil et al., 2014). Farm Sci. One microgram and 10 μg of the DNA were used for the preparation of Paired-End (PE) and Mate-Pair (MP) libraries, respectively. 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. – Australian amaranth P Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. Guillen-Portal, F. R., Baltensperger, D. D., Nelson, L. A., and D’Croz-Mason, N. (1999). … U.S.A. 108, 10249–10254. For example, there is a component (Figure 4B, pink) only present in all A. hypochondriacus from India, which is missing in Plainsman. Plant Sci., 11 November 2020 Bioinformatics 65:e57. 19, 1630–1638. Figure 4. It is interesting to note that A.cau_ornamental clusters close to A.cau_Bolivia_PI642741. This vegetable is known as an important source of iron. The accession PI490752 originally classified as A. hypochondriacus now classifies under A. quitensis. This complicates taxonomyand Amaranthus has generally been consider… 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 paniculatus Linnaeus 1763. A.cru_Suvarna, yet another landrace sequenced and reported here is clearly classified as A. cruentus. doi: 10.1093/nar/gkr123, Sunil, M., Hariharan, A. K., and Nayak, S. (2014). Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution. 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. Also, we normalized the variants from GBS and WGS data for various accessions enabling decoration of the phylogenetic tree including many accessions with the landraces of interest from India. bioRxiv [Preprint]. Further, the biotinylated, adapter-ligated immobilized DNA were enriched by PCR. 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. The resultant VCF files were merged and based on the presence or absence of SNPs, a binary matrix was constructed from which a phylogenetic tree was obtained as mentioned above. (2009). BC: for overseeing the experimental component of the project. PLINK: a tool set for whole-genome association and population-based linkage analyses. doi: 10.1101/gr.094607.109, Smit, A.F. Here, we present the most contiguous draft assemblies of these three species to date. SW: development of genome browser. 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. Amaranth A.hyp_K_white, A.hyp_K_red, A.cru_ornamental, A.cau_ornamental, and A.cru_Suvarna variety were grown at IBAB (Figure 2). 44:e147. J. Amaranthus spinosus is an Annual herb with multi-branched, smooth, herbaceous annual growing to 2 ft. The merged SNP file was processed using PLINK (Purcell et al., 2007) and ADMIXTURE (v1.3) was used to analyze the population structure (Alexander and Lange, 2011). (2012). A detailed summary of this method of normalization has been explained in Figure 7. 12:e1006500. doi: 10.1086/519795, Quinlan, A. R., and Hall, I. M. (2010). 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). Curr. 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). Effect of plant density and planting geometry on growth and yield of grain amaranths. Amaranthus aureus Moq. ADMIXTURE analysis shown in Figure 4B, also suggests that there is significant gene flow between A. caudatus and A. quitensis. doi: 10.3835/plantgenome2009.08.0022. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. 2017 (Wu and Blair, 2017) WGS (Lightfoot et al., 2017)2. Genome Biol. The tree generated using the 20,548 SNPs (Figure 3B) is independent of any reference and hence, can be considered unbiased. 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. Food Sci. Here, a chromosome level assembly (AhKP) of a landrace, A.hyp_K_white, under contiguous cultivation in India for over several centuries is reported. However, a few accessions are now reclassified. Cladus: Amaranthaceae s.str. Malligawad, L. H., and Patil, V. C. (2010). This crop was declared “The Future Crop” by the United States in the 1980s based on a decade of intense research in the 1980s (National Research Council, Amaranth: Modern Prospects for an Ancient Crop, National Academy Press, Washington, DC, 1986). doi: 10.1093/nar/gkw654, Chida, A. R., Ravi, S., and Jayaprasad, S. (2020). doi: 10.1093/bioinformatics/btq033. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. More recently, using genotyping-by-sequencing (GBS), 94 accessions for grain amaranths have been classified (Wu and Blair, 2017). https://en.wikipedia.org/w/index.php?title=Amaranthus_hybridus&oldid;=971234259, Plants used in traditional African medicine, Plants used in traditional Native American medicine, Creative Commons Attribution-ShareAlike License, This page was last edited on 4 August 2020, at 22:31. incurvatus Amaranthus hybridus Linnaeus, subsp. 77, R93–R104. RepeatModeler2: automated genomic discovery of transposable element families. JBrowse: a next-generation genome browser. The database is built using HTML5, bootstrap and JavaScript. SNP discovery via genomic reduction, barcoding, and 454-pyrosequencing in amaranth. Toward this end, our lab had initiated sequencing the genome of Amaranthus (A.) “Variability in ‘Plainsman’ grain amaranth,” in Perspectives on New Crops and New Uses, ed. The clusters were generated in cBot and paired-end sequenced on Illumina HiSeq 2500 platform. 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). Amaranthus hybridus var. It is a glabrous or glabrescent plant. Anuales, tallos erectos, glabros abajo, tornándose subglabros o escasamente pubescentes hacia arriba con tricomas de hasta 1 mm de largo, muy delgados e irregularmente doblados; monoicas. J. 1753. The files were then merged, and the genotype matrix was created using a custom script. Classification schemes have varied between a single species approach, Amaranthus hybridus s.l., and a five Amaranthus hybridus f. aciculatus Thell. (A) Gene expression profile of 12 genes involved in lysine biosynthesis pathway across different developmental stages (15, 20, 25, and 30 days) of different tissues (Rt, root; St, stem; L, leaf; Bud, Flwr, Flower; YSe, young seed; and MSe, mature seed). This platform is a single-molecule, real-time (SMRT) sequencing machine that uses a sequencing-by-synthesis method to generate good quality very long reads. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact … 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). The normalization is validated by clustering of both WGS and GBS data from A.hyp_Plainsman_PI558499 and A.hyp_Mexico_PI511731 close to each other (Figure 4A, red arrow). 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. Rathod, K. J. 15:e1007273. Bos taurus. Amaranthus hybridus grows from a short taproot and can be up to 2.5 m in height. Besides, a C0t analysis shown in Supplementary Figure S2 suggests distinct dissociation time for simple repeat between these two accessions. From the mapped reads, variants were called using samtools (v1.9) mpileup (Li et al., 2009) and bcftools (v1.9) (Li et al., 2009). Lh3/Wgsim. doi: 10.1093/bioinformatics/btp352, Lightfoot, D. J., Jarvis, D. E., Ramaraj, T., Lee, R., Jellen, E. N., and Maughan, P. J. doi: 10.1101/2020.04.27.063040, Deb, S., Suvrath, J., Ravi, S., Whadgar, S., Hariharan, N., Sunil, M., et al. Herten, K., Hestand, M. S., Vermeesch, J. R., and Van Houdt, J. K. J. Protoc. Interestingly, this germplasm includes seeds from many amaranth landraces from South Asia including India. Amaranthus hybridus var. Received: 20 August 2020; Accepted: 12 October 2020;Published: 11 November 2020. bellardii Moq. Plant Sci. The version described in this paper is version JPXE02000000. (2013). It is also found in many provinces of Canada, and in parts of Mexico, the West Indies, Central America, and South America. (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. (accessed 23 Septemper 2015).∗, Soderlund, C., Bomhoff, M., and Nelson, W. M. (2011). Amaranth is added as an ingredient in pasta, bread, instant drinks, baby’s food, etc. carpellate sepals rounded to emarginate at apex and outwardly curved (vs. A. hybridus, with carpellate sepals acute to subacute at apex and erect). SNAP (Korf, 2004) and Augustus were also used to predict gene models and used in the subsequent rounds of MAKER (Campbell et al., 2014). Amaranthus hybridus, commonly called green amaranth,[2] slim amaranth,[3] smooth amaranth, smooth pigweed, or red amaranth, is a species of annual flowering plant. This is also obvious from the stem solidness as reported by Malligawad and Patil (2010) and as shown in Figure 2E. 21, 585–602. Workflow used in integrating WGS data with GBS. doi: 10.1111/j.1750-3841.2012.02645.x, Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., and Emerson, J. J. Copyright © 2020 Deb, Jayaprasad, Ravi, Rao, Whadgar, Hariharan, Dixit, Sunil, Choudhary, Stevanato, Ramireddy and Srinivasan. Proc. Stems and leaves are smooth and hairless, sometimes shiny in appearance. 1961. 5, 511–516. NH: transcriptome analysis. Bioinformatics 26, 841–842. Amaranthus hybridus subsp. Genome Res. A near-chromosome level genome assembly of Anopheles stephensi. Avaliable at: https://hort.purdue.edu/newcrop/proceedings1999/v4-184.html (accessed October 4, 2020). Genesis 53, 474–485. 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. This suggests that A. caudatus is a major clade under A. quitensis. 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. At this stage, the scaffolds were long enough to allow the use of HiC data generated for Plainsman to obtain high-resolution assembly (AhK20). BMC Bioinformatics 16:73. doi: 10.1186/s12859-015-0514-3, Hoff, K. J., and Stanke, M. (2019). Polysaccharides extracted from traditional Chinese medicines may be effective substances with antioxidant activity. In this case, one could use synteny between species at protein levels to build chromosomes. 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 … 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). 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). Manley BS, Wilson HP, Hines TE, 1996. doi: 10.1101/2020.06.27.174920, Flynn, J. M., Hubley, R., and Goubert, C. (2019). The circular DNA was sheared again as explained earlier, and the biotinylated fragments were purified using streptavidin beads (DynabeadsTM M-280 Streptavidin, Invitrogen), the fragments were end-repaired, 3′-adenylated and ligated with Illumina adapters. Bioinformatics 25, 2078–2079. Also, the tree generated prior to the normalization method has been presented in Supplementary Figure S3 for highlighting the extent of improvement upon normalization. Of these only 20,548 positions could be found covered in all whole-genome sequencing data across all samples studied here. doi: 10.1371/journal.pcbi.1007273, Gnerre, S., Lander, E. S., Lindblad-Toh, K., and Jaffe, D. B. A., Van Heusden, P., et al. (synonym) 39:e68. Figure 2 shows the photographs of fully-grown plants sequenced and reported here. With one-sixth of the world population under the poverty line, the value of the seed protein content in amaranth to India cannot be overestimated. It has been reported to have been found in every state except Wyoming, Utah, and Alaska. Electron. A brief comparison of major agronomic traits between A.hyp_K_white and Plainsman (Supplementary Figure S1) is shown in Supplementary Table S3. Interestingly, A.hyp_Mexico_ PI511721 clusters with A.hyp_Plainsman_PI558499, which does not show any pink components. Only 97 out of 107 samples from both GBS and WGS data were filtered based on their good clustering and bigger sample size. Amaranthus hybridus was originally a pioneer plant in eastern North America. The size selection for all the libraries were done using solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP Beads) from Beckman Coulter. (2007). Basic local alignment search tool. BASIONYM: Amaranthus incurvatus Grenier & Godron 1846. Table 1 shows the assembly statistics. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. To combine WGS data and GBS data, we created GBS like data from whole-genome reads. The menus on the database page will redirect you to the download as well as tool page. Plainsman reference: Phytozome1 A. hypochondriacus genome V.2.1(A.hyp.V.2.1) (Lightfoot et al., 2017) GBS: Blair et al. Whole Genome libraries for A.hyp_K_white, A.hyp_K_red, A.cru_ornamental, A.cau_ornamental and A.cru_Suvarna were prepared using the TruSeq DNA Sample Preparation Kit (Illumina) by following the manufacturer’s low throughput protocol. 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). SyMAP v3.4: a turnkey synteny system with application to plant genomes. However, we report a new observation that PI649506 is a A. hypochondriacus originally annotated as A. cruentus. Plant Sci. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. Also, assisted assembly of closely related species significantly improved the contiguity of low coverage mammalian assemblies (Gnerre et al., 2009). However, this produced skewed classification because of variation in the depth of sequencing between GBS and WGS while calling variants. Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Amaranthus hybridus L. (Amaranthaceae) commonly known as ‘Cheera’ in Malayalam, is an erect branched annual herb distributed throughout tropical and temperate regions of India as a common weed in the agricultural fields and wastelands. |, https://www.frontiersin.org/articles/10.3389/fpls.2020.579529/full#supplementary-material, https://www.ncbi.nlm.nih.gov/sra?term=SRP061623, https://hort.purdue.edu/newcrop/proceedings1999/v4-184.html, Creative Commons Attribution License (CC BY). 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. 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. Figure 1. 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). Amaranthus batalleri Sennen Amaranthus bellardii Moq. Amaranth flour could be mixed with wheat flour to make bread or other foods. 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). However, A.hyp_Plainsman_PI599488 clusters in a distal clade with A.hyp_Mexico_PI511731 in both Figures 3B, 4A as expected because Plainsman is a cross between A. hypochondriacus from Mexico and A. hybridus from Pakistan (Guillen-Portal et al., 1999). Subfamilia: Amaranthoideae Genus: Amaranthus Species: Amaranthus quitensis J. Janick (Alexandria, VA: ASHS Press), 184–189. (2015). batalleri (Sennen) J.L.Carretero (synonym) Amaranthus hybridus subvar multispiculatus (Sennen) J.L.Carretero (synonym) Amaranthus incurvatus Tim. Familia: Amaranthaceae s.l. BMC Bioinformatics 12:246. doi: 10.1186/1471-2105-12-246, PubMed Abstract | CrossRef Full Text | Google Scholar, Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. KRR: assembly and analysis of other landraces. doi: 10.1186/gb-2009-10-8-r88. Am. Amaranthus hybridus was originally a pioneer plant in eastern North America. Natl. The database consists of a landing page, genome browser and NCBI BLAST (Altschul et al., 1990) tool. 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. 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. Library preparation was done for Illumina whole genome sequencing in-house and outsourced for PacBio RSII sequencing. Amaranthus hybridus L. is a competitive weed for summer crops in South America. Beck Homonyms Amaranthus hybridus L. Amaranthus hybridus Vell. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. 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). Amaranthus berchtholdii Moq. Smooth Pigweed (Amaranthus hybridus (syn: quitensis)) is a dicot weed in the Amaranthaceae family. 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. The two assemblies obtained were then merged together using Quickmerge (Chakraborty et al., 2016). Workflow used in the assembly of AhKP. Vegetable Ama-ranthus can be easily distinguished by inflorescence features like mostly or exclusively axillary glomerules or short spikes (Fig. 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. Bioinformatics 48, 4.11.1–4.11.39. Fast gapped-read alignment with Bowtie 2. (2016). Also, the browser can be queried using the accessions of Arabidopsis to visualize the expression profile of the corresponding orthologs on AhKP. doi: 10.1002/dvg.22877, Campbell, M. S., Holt, C., Moore, B., and Yandell, M. (2014). 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. Li, H., Handsaker, B., and Wysoker, A. In traditional medicinal system different parts of the plant Amaranthus hybridus (A. hybridus) The sequence alignment/map format and SAMtools. SR: library preparation and aiding writing of manuscript. (synonym) Amaranthus hybridus var. The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. ADMIXTURE analysis shown in Figure 4B suggests that there is significant gene flow between A. caudatus and A. quitensis. These include A.hyp_K_white (Figure 2A), A.hyp_K_red (Figure 2B), two ornamental varieties A.cau_ornamental (love-lies-bleeding, Figure 2C) and A.cru_ornamental (Autumn touch, Figure 2D) and A.cru_Suvarna (Figure 2E). The genus also contains many weedy plants known as pigweed, especially rough pigweed (A. retroflexus), prostrate pigweed (A. graecizans), and white … These plants are grown as ornamentals or for their grain, they do not exist in the wild, and are not weeds. Briefly, for PE libraries, the fragmented DNA was end-repaired, 3′-adenylated, ligated with Illumina adapters, and PCR enriched with Illumina sequencing indexes. Gandhinagar: INFLIBNET. ... Amaranthus caudatus, Amaranthus cruentus, and Amaranthus hybridus (Lightfoot et al., 2017). 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). McLean KS, Roy KW, 1991. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). 11:579529. doi: 10.3389/fpls.2020.579529. At K = 4, a significant component of A. quitensis is found in all four species. The plant was used for food and medicine by several Native American groups and in traditional African medicine. One way to do this would be to identify and use the alleles found from GBS data with the respective alleles found from WGS. Figure 6. Besides, the seed sizes shown in Figure 2F also validate classification for Suvarna as A. cruentus with relatively bigger seed size. However, according to our classification with 271,305 SNPs, by combining GBS and WGS data, we reproduce the observation made by Wu and Blair (2017). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. 15:550. doi: 10.1186/s13059-014-0550-8, Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., et al. (B) Genetic admixture analysis of A. hypochondriacus, A. caudatus, A. cruentus, and A. quitensis. Genomic DNA was extracted from fresh leaves using the DNeasy Mini Plant DNA Extraction kit (Qiagen) following the manufacturer’s protocol and quantified using fluorometry (Qubit 2.0, Invitrogen). Front Plant Sci. boiRxiv [Preprint]. Figure 7. Natl. Figure 2. Before long-read sequencing became commonplace, experimentally generated mate-pair reads of increasing insert sizes were routinely used to generate scaffolds from contigs. The public and in house generated data were mapped to A.hyp.V.2.1 and AhKP reference using bowtie2 (Langmead and Salzberg, 2012). doi: 10.1101/gr.215087.116, Korf, I. doi: 10.1101/856591, Ghurye, J., Rhie, A., and Walenz, B. P. (2019). We have attempted to classify the landraces reported here using multiple approaches. DNA was sheared using Adaptive Focused Acoustic technology (Covaris, Inc.) to generate fragments of desired insert size. The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal. 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. doi: 10.1073/pnas.1107739108, Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J., and Holmes, I. H. (2009). This section is divided into three parts. 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. Nat. This was further improved by merging the Illumina assembly from the draft genome reported elsewhere and polished using the Illumina reads. 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. Biol. Correction: chromosomal-level assembly of the asian seabass genome using long sequence reads and multi-layered scaffolding. Predicting genes in single genomes with AUGUSTUS. (2004). 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). (2009). 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. This plant originated in America, but it has spread all over the world. Light blue star points to A.cru_Suvarna. SD: DNA isolation and repeat analysis. Plant Genome 2, 260–270. Although easily controlled and not particularly competitive, it is recognized as a harmful weed of North American crops. 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). 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, 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. Unfortunately, despite India being one of the few countries where multiple landraces of grain amaranths are under continuous cultivation for more than a century, they have received little attention and failed to reach the status of a staple crop. Amaranthus chlorostachys var. 8:1960. doi: 10.3389/fpls.2017.01960, Zheng, X., Levine, D., Shen, J., Gogarten, S. M., Laurie, C., and Weir, B. S. (2012). Schneeberger, K., Ossowski, S., and Ott, F. (2011). Amaranthus hybridus is a herbal plant that is grown to be consumed leaves. Abstract. 1950. Methods: In this study, we isolated crude polysaccharides from A. hybridus … Gene finding in novel genomes. 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). For the 27,658 SNP positions 150 base pair sequences were downloaded from public sources and coordinates for all 27,658 positions on A.hyp.V.2.1 were extracted by BLAST alignment. Brenan Amaranthus hybridus var. A draft genome for the same landrace was reported by our group in 2014 (Sunil et al., 2014). 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 … Download this complete Project material titled; Assessment Of Vehicular Emissions On Air Quality And Proximate Composition Of Amaranthus Hybridus And Mangifera Indica In Zaria, Nigeria with abstract, chapters 1-5, references, and questionnaire. Maker pipeline includes de novo assembled amaranth transcriptome with 125581 scaffolds, repeat elements predicted by RepeatModeler and Arabidopsis proteome (TAIR10) (Berardini et al., 2015). The utility of mate-pairs from one strain to build the scaffolds for the other require DNA level similarity, which is often not the case even for closely related species. doi: 10.1093/dnares/dsu021, Sunil, M., Hariharan, N., Dixit, S., Choudhary, B., and Srinivasan, S. (2017). Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., et al. 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). Acad. SJ: assembly of AhKP. Nucleic Acids Res. doi: 10.1073/pnas.1220349110, Kolmogorov, M., Yuan, J., Lin, Y., and Pevzner, P. A. 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. doi: 10.1002/0471250953.bi0411s48, Caselato-Sousa, V. M., and Amaya-Farfán, J. 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. Pl. Smooth pigweed (Amaranthus hybridus) and livid amaranth (A. lividus) response to several imidazolinone and sulfonylurea herbicides. 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. (2017). RepeatModeler Open-1.0. slim amaranth smooth pigweed This plant can be weedy or invasive according to the authoritative sources noted below.This plant may be known by one or more common names in different places, and some are listed above. 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). We have devised a method to normalize for the same during the variant calling (see section “Materials and Methods”). Figure 3A shows classification using the 27,658 SNPs reported for grain amaranth by Maughan et al. Seeds of A.hyp_K_white, A.hyp_K_red were obtained from local market in Karnataka, India, A.cru_ornamental, A.cau_ornamental from Park seeds and A.cru_Suvarna from Gandhi Krishi Vigyana Kendra (GKVK), Bengaluru, Karnataka, India. It is extremely variable, and many other Amaranthus species are believed to be natural hybridizations or derive from A. hybridus. (2012). hypocondriacus 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. (2019). J. doi: 10.1002/cpbi.57, Kim, J., Larkin, D. M., and Cai, Q. 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. Leaves glabrous or with sparse hairs on the main veins below… Genome Biol. It has been naturalized in many places of warmer climate. 1a, g), origin of flower bud from These regions were used to restrict the variant calling from whole-genome data to only the regions covered in GBS. Amaranthus is part of the Amaranthaceae that is part of the larger grouping of the Carophyllales. In the context of increasing demand on water and other natural resources from an increasing world population, grain amaranths offer an alternative to other staple cereals such as rice or wheat. 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). Users can access the Jbrowse by clicking on the Genome browser button or using the tools menu. A whole-genome assembly of the domestic cow. Species Amaranthus hybridus L. – slim amaranth P: Species Amaranthus hybridus × hypochondriacus [unnamed hybrid] – Plainsman amaranth P: Species Amaranthus hypochondriacus L. – Prince-of-Wales feather P: Species Amaranthus interruptus R. Br. 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. hybridus S. Watson Amaranthus eugenii Sennen Amaranthus flavescens Moq. Amaranthus hecticus Willd. 1849. 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. Phytochemical Studies of Rajigara Amaranthus Species for its Potential use in Medicine. thus retroflexus, Amaranthus graecizans, Amaranthus dubius, and Amaranthus hybridus. A separate VCF file was made for all the 13 datasets as listed in Supplementary Table S2 with the respective alleles at these positions. The phylogenetic tree was constructed from the genotype matrix using the clustering algorithm hclust and SNPRelate under R and Bioconductor package (Zheng et al., 2012). Popped Amaranth is added to bread, tofu or meat. J. Hum. BMC Biol. Acad. Genet. 10:R88. At K = 4 and 5 there is no resolution between species except A. hypochondriacus. P: Species Amaranthus lineatus R. Br. At K = 6 other unique components within A. hypochondriacus gets resolved. 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. This manuscript has been released as a pre-print at bioRxiv, (Deb et al., 2020). SPD: classification, characterization and writing of the manuscript. RepeatMasker analysis classified 50.5% (196421031 bp) of the AhKP genome as repetitive sequences. Impact Factor 4.402 | CiteScore 7.8More on impact ›, Amaranthus: Naturally Stress-Resistant Resources for Improved Agriculture and Human Health 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. A high-performance computing toolset for relatedness and principal component analysis of SNP data. A. hybridus with accession of PI605351 clusters in the same clade as Suvarna with another accessions (PI477913) from A. cruentus. Amaranthus hybridus var. (1990). This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JPXE00000000. Amaranthus … 37, 540–546. Brief Bioinformatics 6, 6–22. Based on the number of variants called for these and other accessions using both AhKP and A.hyp.V.2.1 as references suggest that all the landraces of Amaranthus hypochondriacus sequenced here are different from the A.hyp_Plainsman variety (Supplementary Table S2). 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. (B) block plot, (C) circular and (D) dot plot showing synteny of chromosomes of AhKP assembly on to Plainsman (A.hyp.V2.1). 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). (2009). A decade-long research conducted by the Rodale Institute during the 1980s enabled the creation of more than 800 species/varieties, which are currently maintained in a germplasm (GRIN-Global). Meera, N., Lohithaswa, H. C., Murthy, N., and Hittalmani, S. (2014). Figure 4 validates taxonomy-based classification (color-coded accessions) of the majority of the accessions and landraces. erythrostachys de Candolle, Prodr. However, natural selection puts sufficient selection pressure on protein sequences for maintaining functional contiguity required during evolution. Genes involved in lysine biosynthesis pathway were identified by BLASTP (Altschul et al., 1990) analysis using Arabidopsis proteins.
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