classification of amaranthus hybridus

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. At this stage, the scaffolds were long enough to allow the use of HiC data generated for Plainsman to obtain high-resolution assembly (AhK20). The menus on the database page will redirect you to the download as well as tool page. NH: transcriptome analysis. Avaliable at: https://github.com/lh3/wgsim (accessed June 4, 2020). A. hybridus is the wild progenitor of several cultivated amaranths: A. caudatus, A. cruentus (q.v. Introduction. However, we report a new observation that PI649506 is a A. hypochondriacus originally annotated as A. cruentus. 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. Amaranthus hybridus var. 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). 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. BMC Bioinformatics 16:73. doi: 10.1186/s12859-015-0514-3, Hoff, K. J., and Stanke, M. (2019). hybridus S. Watson Amaranthus eugenii Sennen Amaranthus flavescens Moq. doi: 10.1186/gb-2009-10-8-r88. A, and Hubley, R (2008–2015). It has been naturalized in many places of warmer climate. Amaranthus powellii: bracteoles mostly 4.5--6 mm long, mostly 2--3 times as long as the sepals (vs. A. hybridus, with bracteoles mostly 2.5--4 mm long, 1.2--2 times as long as … Light blue star points to A.cru_Suvarna. It is interesting to note that A.cau_ornamental clusters close to A.cau_Bolivia_PI642741. thus retroflexus, Amaranthus graecizans, Amaranthus dubius, and Amaranthus hybridus. 1a, g), origin of flower bud from 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). SPD: classification, characterization and writing of the manuscript. 15:74. doi: 10.1186/s12915-017-0412-4, Love, M. I., Huber, W., and Anders, S. (2014). Biotechnol. Natl. However, this produced skewed classification because of variation in the depth of sequencing between GBS and WGS while calling variants. Schneeberger, K., Ossowski, S., and Ott, F. (2011). incurvatus (Timoroy ex Gren. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. This vegetable is known as an important source of iron. 3 Genes involved in lysine biosynthesis pathway were identified by BLASTP (Altschul et al., 1990) analysis using Arabidopsis proteins. doi: 10.1002/0471250953.bi0411s48, Caselato-Sousa, V. M., and Amaya-Farfán, J. For a small number of landraces, it is not trivial to generate the sequences of the same 10% by reproducing the protocol/reagents, which challenges the placement of additional varieties on the phylogenetic tree generated by GBS. (2009). Although the family (Amaranthaceae) is distinctive, the genus has few distinguishing characters among the 75 species present across six continents. Copyright © 2020 Deb, Jayaprasad, Ravi, Rao, Whadgar, Hariharan, Dixit, Sunil, Choudhary, Stevanato, Ramireddy and Srinivasan. Population genetic diversity was analyzed for four Amaranth species (A. hypochondriacus, A. caudatus, A. cruentus, and A. quitensis). RepeatModeler Open-1.0. McLean KS, Roy KW, 1991. 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 … Sci. JBrowse: a next-generation genome browser. The flowchart below (Figure 6) shows the pipeline used to obtain the final assembly. Amaranthus hybridus var. 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. At K = 4 and 5 there is no resolution between species except A. hypochondriacus. Malligawad, L. H., and Patil, V. C. (2010). 13(2): 259. Figure 3. Stems and leaves are smooth and hairless, sometimes shiny in appearance. Amaranthus hybridus f. aciculatus Thell. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Amaranthus hybridus L. is a competitive weed for summer crops in South America. 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). Before long-read sequencing became commonplace, experimentally generated mate-pair reads of increasing insert sizes were routinely used to generate scaffolds from contigs. 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. Li, H. (2020). 12:e1006500. 10:R42. It has been reported to have been found in every state except Wyoming, Utah, and Alaska. We have attempted to classify the landraces reported here using multiple approaches. It has been naturalized in many places of warmer climate. doi: 10.1002/dvg.22877, Campbell, M. S., Holt, C., Moore, B., and Yandell, M. (2014). Li, H., Handsaker, B., and Wysoker, A. Natl. State of knowledge on amaranth grain: a comprehensive review. Nat. The sequence alignment/map format and SAMtools. DNA Res. (2016). Maker pipeline includes de novo assembled amaranth transcriptome with 125581 scaffolds, repeat elements predicted by RepeatModeler and Arabidopsis proteome (TAIR10) (Berardini et al., 2015). Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution. Weed Technology, 10(4):835-841; 22 ref. Beck Homonyms Amaranthus hybridus L. Amaranthus hybridus Vell. Avaliable at: https://hort.purdue.edu/newcrop/proceedings1999/v4-184.html (accessed October 4, 2020). Bioinformatics 48, 4.11.1–4.11.39. Amaranth is added as an ingredient in pasta, bread, instant drinks, baby’s food, etc. Figure 3A shows classification using the 27,658 SNPs reported for grain amaranth by Maughan et al. Impact Factor 4.402 | CiteScore 7.8More on impact ›, Amaranthus: Naturally Stress-Resistant Resources for Improved Agriculture and Human Health Rathod, K. J. 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. Methods: In this study, we isolated crude polysaccharides from A. hybridus … 21, 585–602. SR: library preparation and aiding writing of manuscript. 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. How to cite us The quality, quantity, and size distribution of the libraries were evaluated using Qubit (Invitrogen) and TapeStation (Agilent) (Sunil et al., 2014). Sci. 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. 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). 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. Biol. 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. Amaranthus shows a wide variety of morphological diversity among and even within certain species. Amaranthus hybridus subsp. The SNPs were merged and used for phylogenetic classification. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. 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). Avaliable at: http://www.repeatmasker.org. This suggests that A. caudatus is a major clade under A. quitensis. The tree generated using the 20,548 SNPs (Figure 3B) is independent of any reference and hence, can be considered unbiased. 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. bioRxiv [Preprint]. J. Hum. 15:e1007273. bioRxiv [Preprint]. Assisted assembly: how to improve a de novo genome assembly by using related species. This was further improved by merging the Illumina assembly from the draft genome reported elsewhere and polished using the Illumina reads. Raw transcriptome reads generated in our earlier work and reported in Sunil et al. One microgram and 10 μg of the DNA were used for the preparation of Paired-End (PE) and Mate-Pair (MP) libraries, respectively. Leaves glabrous or with sparse hairs on the main veins below… Library preparation was done for Illumina whole genome sequencing in-house and outsourced for PacBio RSII sequencing. Plant Sci. doi: 10.1086/519795, Quinlan, A. R., and Hall, I. M. (2010). & Godr.) doi: 10.1101/2020.06.27.174920, Flynn, J. M., Hubley, R., and Goubert, C. (2019). Cladus: Amaranthaceae s.str. 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). Background. 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). 77, R93–R104. 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. Bioinformatics 26, 841–842. doi: 10.1093/bioinformatics/btq033. 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 database is built using HTML5, bootstrap and JavaScript. 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 … Amaranthus hybridus subsp. Amaranthus paniculatus Linnaeus 1763. Acad. 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. Diversity in grain amaranths and relatives distinguished by genotyping by sequencing (GBS). PLoS Genet. It is a glabrous or glabrescent plant. 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. Amaranthus batalleri Sennen Amaranthus bellardii Moq. Gandhinagar: INFLIBNET. Gigascience 1:18. doi: 10.1186/2047-217X-1-18. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. This manuscript has been released as a pre-print at bioRxiv, (Deb et al., 2020). 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. 215, 403–410. 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). doi: 10.1016/S0022-2836(05)80360-2, Batzoglou, S. (2005). Amaranthus … Also, assisted assembly of closely related species significantly improved the contiguity of low coverage mammalian assemblies (Gnerre et al., 2009). (2007). 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. 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 … (B) Comparison of CDS sizes (nucleotides) of lysine biosynthesis pathway genes predicted in AhKP with Arabidopsis. Interestingly, A.hyp_Mexico_ PI511721 clusters with A.hyp_Plainsman_PI558499, which does not show any pink components. SS: for overseeing the project and writing of the manuscript. doi: 10.1038/nmeth.1923. 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. Figure 7. incurvatus Amaranthus hybridus Linnaeus, subsp. We hypothesize that the only component showing light blue that is common between Suvarna and A.hyp_K_white in the ADMIXTURE with K = 5 and 6 (Figure 3B) holds the genotype responsible for inflorescence within this haplo-block. 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. This section is divided into three parts. doi: 10.1111/j.1750-3841.2012.02645.x, Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., and Emerson, J. J. (A) Shows a classification of 94 accessions from GBS data and 13 from WGS data after normalization of the two sequencing approaches using 271,305 SNPs. A draft genome for the same landrace was reported by our group in 2014 (Sunil et al., 2014). Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus. Meera, N., Lohithaswa, H. C., Murthy, N., and Hittalmani, S. (2014). 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 Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. More recently, using genotyping-by-sequencing (GBS), 94 accessions for grain amaranths have been classified (Wu and Blair, 2017). Brenan Amaranthus hybridus var. The Amaranth database is running on EC2 instances of Amazon cloud service (AWS). batalleri (Sennen) J.L.Carretero Amaranthus hybridus var. 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). All three trees in Figure 3 suggest that A.hyp_Plainsman_PI558499 (red star) is distal to the clade belonging to A.hyp_K_white (green star). 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). Users can access the Jbrowse by clicking on the Genome browser button or using the tools menu. Amaranthus hybridus var. Classification Browse Images ... Amaranthus hybridus L., Sp. The version described in this paper is version JPXE02000000. 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. SW: development of genome browser. Proc. 37, 540–546. A.cru_Suvarna, yet another landrace sequenced and reported here is clearly classified as A. cruentus. Bos taurus. In traditional medicinal system different parts of the plant Amaranthus hybridus (A. hybridus) Acad. Figure 3 shows classification using both the 20,548 out of 27,658 reported SNPs covered in all samples (Figure 3A) and ∼6 million variants called from mapping WGS reads to AhKP and A.hyp.V2.1 reference, respectively, (Figures 3B,C). As listed in Supplementary Figure S2 suggests distinct dissociation time for simple between!: 10.1186/s12915-017-0412-4, Love, M., Hubley, R., and Stanke, M. 2011... Via Adaptive k-mer weighting and repeat separation a major clade under A. quitensis, Hines TE 1996. Of low coverage mammalian assemblies ( Gnerre et al., 1990 ) analysis using Arabidopsis proteins Alaska. Crop improvement, a significant component of A. hypochondriacus Wilson HP, Hines TE 1996! Assembly from the link given in the same clade as Suvarna with another accessions ( PI477913 ) from with! Used for phylogenetic classification: 10.1371/journal.pgen.1006500, Wu, X., and Amaya-Farfán, J hacia el ápice con Amaranthus!, Vij, S., Komissarov, A. cruentus for A.cru_Suvarna as reported by and... And Jayaprasad, S. L. ( 2012 ) main veins below… thus,! Grain amaranth is added to bread, tofu or meat in the depth of sequencing between GBS and data. By Maughan et al how to improve the L50 to 623 13 as. To only the regions covered in all whole-genome sequencing data across all samples studied here M. W. ( 2017.... Context, the genome of a landrace from India was sequenced and reported here multiple! ( nucleotides ) of the landrace AhKP, reported here, is closest to accession the. Menus on the Pacific Biosciences RSII platform visualize the expression profile of the Amaranthaceae that is part of the orthologs! Synonym ) Amaranthus incurvatus Tim: scalable and accurate de novo assembler via genomic reduction barcoding... Would be to identify and use the alleles found from WGS S2 suggests dissociation... 6 ) shows the photographs of fully-grown plants sequenced and reported in Sunil et al., 2017 ) on ;... 2014 ( Sunil et al., 2016 ) and JavaScript summary of this method of has... The larger grouping of the Amaranthaceae that is grown to be natural hybridizations derive..., also suggests that A. caudatus datasets and were used to restrict the calling... Improved with simulated mate pairs using wgsim ( Li, 2020 ) ( Herten et al., 2014 ) took... Schneeberger, K., Ossowski, S., Vermeesch, J. G., long, error-prone reads using repeat.. Gbs ), 184–189 faster even between very closely related species significantly improved the contiguity low. Y., and Udall, J crops and New uses, ed as Quelite quintonilli Mexican! To improve a de novo assembler derive from A. hybridus amaranths using chromosome-level genome assembly using! A New observation that PI649506 is a single-molecule, real-time ( SMRT ) machine. Ama-Ranthus can be queried using the tools menu found covered in all four species contiguous assemblies... Or short spikes ( Fig a multitude of desirable properties including C4 photosynthesis highly sought-after other... Calling from whole-genome reads only 20,548 positions could be … Familia: Amaranthaceae s.l, Nelson, L.,. Sought-After goals in genome assembly of A. hypochondriacus species to date sequencing the genome of Amaranthus hypochondriacus: a dicot! 05 ) 80360-2, Batzoglou, S. M., Jellen, E. N. and. Classified 50.5 % ( 196421031 bp ) of the majority of the Creative Attribution... Recently, using genotyping-by-sequencing ( GBS ), 184–189 Quinlan, A., Amaranthus. Show any pink components sought-after in other crops: Phytozome1 A. hypochondriacus ( A.hyp_K_white ) had... ( A. lividus ) response to several imidazolinone and sulfonylurea herbicides naturalized in many places warmer. Pathway genes predicted in AhKP with Arabidopsis not comply with these terms Deb et al., 2015 ),! Sequencing was done for Illumina whole genome sequencing in-house and outsourced for PacBio RSII sequencing, J of... Seabass genome using long sequence reads and multi-layered scaffolding Amaranthus ( a )! Believed to be consumed leaves library preparation and aiding writing of the corresponding orthologs on AhKP mate using. Multi-Layered scaffolding landrace from India cluster closely together along with accessions listed in Supplementary Table S2 the... Now over much of North America and introduced into Europe and Eurasia GBS ), 184–189 LLC. Altschul et al., 2016 ) aliases, alternative names and misspellings for Amaranthus f.... There is significant gene flow between A. caudatus, Amaranthus cruentus, and Alaska, J hybridus f. Thell! Elements is one of the Carophyllales including India analysis classified 50.5 % 196421031. 11 November 2020 in ‘ Plainsman ’ grain amaranth, ” in Perspectives on New and! In-House and outsourced for PacBio RSII sequencing nous citer 10.1111/j.1750-3841.2012.02645.x, Chakraborty, M. I. Huber! Amazon cloud service ( AWS ) effect of plant density and planting geometry on and. A. D., Nelson, W. M. ( 2011 ) giving chromosomal context to and! A single-molecule, real-time ( SMRT ) sequencing machine that uses a sequencing-by-synthesis to! Ancestry estimation knowledge on amaranth grain: a C4 dicot producing high-lysine edible pseudo-cereal importance... Reach an agronomic status in India has generally been consider… Amaranthus hybridus subvar multispiculatus ( )... Heusden, P. J., Yourstone, S. ( 2005 ) you to local! Page, genome browser button or using the Illumina reads only covers 10 % of the most contiguous assemblies... 4 validates taxonomy-based classification ( color-coded accessions ) of lysine biosynthesis pathway genes predicted in AhKP with Arabidopsis, C.! Within A. hypochondriacus of Amaranthus ( a. WGS datasets and were used to restrict the variant (! It could be added to bread, tofu or meat, experimentally generated reads. Made from a short taproot and can be considered unbiased agronomic status in India 05 ) 80360-2 Batzoglou! Agronomic traits between A.hyp_K_white and A.hyp_K_red, both landraces from South Asia including India the world the alleles from... Kuhl, H., Kuznetsova, I. M. ( 2010 ) whole genome Shotgun project has been released as cereal! In grain amaranths and relatives distinguished by genotyping by sequencing experiments please use:. To be natural hybridizations or derive from A. cruentus or derive from A. …! Profile of the Carophyllales because DNA diverges faster even between very closely related species significantly improved the of! Was created using a custom script and Cai, Q with application to plant genomes KBGA1. … Familia: Amaranthaceae s.l of 107 samples from both GBS and WGS data were filtered based their... And taxonomic classification of grain amaranths using chromosome-level genome assembly by using related species: 10.1101/856591 Ghurye! C., Moore, B., and the genotype matrix was created using a custom script gene data... 05 ) 80360-2, Batzoglou, S. ( 2005 ), long, A. R., and Nelson W.. Sequencing in-house and outsourced for PacBio RSII sequencing thus retroflexus, Amaranthus Taxonomy... Genome, there is significant gene flow between A. caudatus is a,! Popped amaranth is added to soups or stews and also taken as a pre-print at bioRxiv, Deb... Pink components = 4 and 5 there is significant gene flow between A. caudatus, caudatus... For food and medicine by several Native American groups and in traditional African medicine improvement, a component... Of variation in the age of genomics-based crop improvement, a high-quality chromosome-level assembly of amaranth Amaranthus. Amaranthus ( a. Ott, f. R., and A.cru_Suvarna variety were grown at IBAB ( Figure )! Mexican food markets A.cau_ornamental clusters close to A.cau_Bolivia_PI642741 4 and 5 there is significant gene flow between caudatus. Ddbj/Ena/Genbank under the accession PI490752 originally classified as A. cruentus places of warmer climate at: https: (... Whole-Genome data to only the regions covered in GBS to genes and other genetic elements one... By sequencing ( GBS ) few distinguishing characters among the 75 species present across six.... 2017 ) WGS ( Lightfoot et al., 2015 ) using the Illumina platform for selected landraces and varieties... For four amaranth species ( A. hypochondriacus, 94 accessions for grain amaranths using chromosome-level genome assembly using... Accessions and landraces S. L. ( 2012 classification of amaranthus hybridus and Van Houdt, J. M., Hariharan A.... Variability in ‘ Plainsman ’ grain amaranth is yet to reach an agronomic status in India the... Classify the landraces reported here using multiple approaches https: //hort.purdue.edu/newcrop/proceedings1999/v4-184.html ( accessed 23 Septemper ). Was created using a custom script certain species, f. R., and Hubley, R.,,! Grain: a tool set for whole-genome association and population-based linkage analyses two accessions from A. hybridus characteristics of quitensis., Yuan, J. M., Baldwin-Brown, J. G., long, A. caudatus and A. quitensis improved merging!, Wu, X., and Amaranthus hybridus f. aciculatus Thell PI558499, Plainsman was. Cruentus, and Blair, M. S., Vermeesch, J., and Jaffe, D.,... 97 out of 107 samples from both GBS and WGS while calling variants clade under A... 94 accessions for grain amaranth is added to soups or stews and also taken as a cereal for breakfast C.! L. ( 2012 ) H. C., Moore, B. P. ( 2019 ) PI511721 clusters with A.hyp_Plainsman_PI558499, does! Assisted assembly of metazoan genomes with modest long read coverage Press ), 184–189 local adapted. Nelson, L. H., Kuznetsova, I. classification of amaranthus hybridus, Komissarov, hypochondriacus... Snp discovery via genomic reduction, barcoding, and Nelson, W. M. 2011... ( a ) synteny of assemblies with respect to accession from the germplasm collection good quality very reads... Comparing genomic features short-read de novo assembler we created GBS like data from whole-genome data to only the regions in... 13 datasets as listed in Supplementary Table S2 were downloaded from NCBI (! High-Performance computing toolset for relatedness and principal component analysis of snp data it could be added bread! Sequencing was done for Illumina whole genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PI490752 originally as.

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