BMC Bioinformatics 16:73. doi: 10.1186/s12859-015-0514-3, Hoff, K. J., and Stanke, M. (2019). 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). Reference-assisted chromosome assembly. 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. 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. P: Species Amaranthus lineatus R. Br. Besides, the seed sizes shown in Figure 2F also validate classification for Suvarna as A. cruentus with relatively bigger seed size. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., et al. (B) Genetic admixture analysis of A. hypochondriacus, A. caudatus, A. cruentus, and A. quitensis. Users can access the Jbrowse by clicking on the Genome browser button or using the tools menu. Amaranthus … However, we report a new observation that PI649506 is a A. hypochondriacus originally annotated as A. cruentus. Amaranthus batalleri Sennen Amaranthus bellardii Moq. A near-chromosome level genome assembly of Anopheles stephensi. The two predicted libraries of repeat elements were merged together and repeat masking was done using RepeatMasker version 4.1.0 (Smit and Hubley, 2008–2015). A., Van Heusden, P., et al. Fast gapped-read alignment with Bowtie 2. Here, we present the most contiguous draft assemblies of these three species to date. doi: 10.1093/bioinformatics/btq033. The two assemblies obtained were then merged together using Quickmerge (Chakraborty et al., 2016). (2017). 19, 1630–1638. Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly Amaranthus cruentus. A. hybridus with accession of PI605351 clusters in the same clade as Suvarna with another accessions (PI477913) from A. cruentus. ex Gren. 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. 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. We generated WGS data with coverage of ∼50–150X using the Illumina platform for selected landraces and ornamental varieties. 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 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. (2016). hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. For genomics-based crop improvement of local landraces, it is critical to classify these with respect to accession from the germplasm collection. 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. BMC Bioinformatics 5:59. doi: 10.1186/1471-2105-5-59, Langmead, B., and Salzberg, S. L. (2012). thus retroflexus, Amaranthus graecizans, Amaranthus dubius, and Amaranthus hybridus. A whole-genome assembly of the domestic cow. The average insert size was around 200 bp for PE libraries and 1.75, 3, 5, and 10 kb for four MP libraries. doi: 10.1101/856591, Ghurye, J., Rhie, A., and Walenz, B. P. (2019). 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). Amaranthus spinosus is an Annual herb with multi-branched, smooth, herbaceous annual growing to 2 ft. This is because DNA diverges faster even between very closely related species. Although easily controlled and not particularly competitive, it is recognized as a harmful weed of North American crops. 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: 10.1101/2020.06.27.174920, Flynn, J. M., Hubley, R., and Goubert, C. (2019). (2017). 1950. batalleri (Sennen) J.L.Carretero (synonym) Amaranthus hybridus subvar multispiculatus (Sennen) J.L.Carretero (synonym) Amaranthus incurvatus Tim. 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). Manley BS, Wilson HP, Hines TE, 1996. More recently, using genotyping-by-sequencing (GBS), 94 accessions for grain amaranths have been classified (Wu and Blair, 2017). Food Sci. Abstract. hypocondriacus (2009). 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). 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. Nat. Since GBS only covers 10% of the genome, there is a need to normalize the variants from WGS data for comparison. Front Plant Sci. Amaranth is added as an ingredient in pasta, bread, instant drinks, baby’s food, etc. Amaranthus shows a wide variety of morphological diversity among and even within certain species. DNA was sheared using Adaptive Focused Acoustic technology (Covaris, Inc.) to generate fragments of desired insert size. erythrostachys de Candolle, Prodr. Plant Sci., 11 November 2020 Amaranthus hybridus L. is a competitive weed for summer crops in South America. 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. 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 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). Beck Homonyms Amaranthus hybridus L. Amaranthus hybridus Vell. Amaranthus paniculatus Linnaeus 1763. (B) Comparison of CDS sizes (nucleotides) of lysine biosynthesis pathway genes predicted in AhKP with Arabidopsis. doi: 10.1093/nar/gkr123, Sunil, M., Hariharan, A. K., and Nayak, S. (2014). Genome Biol. Received: 20 August 2020; Accepted: 12 October 2020;Published: 11 November 2020. Maker pipeline includes de novo assembled amaranth transcriptome with 125581 scaffolds, repeat elements predicted by RepeatModeler and Arabidopsis proteome (TAIR10) (Berardini et al., 2015). Also, assisted assembly of closely related species significantly improved the contiguity of low coverage mammalian assemblies (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. 21, 585–602. 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). A brief comparison of major agronomic traits between A.hyp_K_white and Plainsman (Supplementary Figure S1) is shown in Supplementary Table S3. 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). Vegetable Ama-ranthus can be easily distinguished by inflorescence features like mostly or exclusively axillary glomerules or short spikes (Fig. McLean KS, Roy KW, 1991. This was further improved by merging the Illumina assembly from the draft genome reported elsewhere and polished using the Illumina reads. 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. J. Janick (Alexandria, VA: ASHS Press), 184–189. 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. 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. Amaranthus hybridus var. A draft genome for the same landrace was reported by our group in 2014 (Sunil et al., 2014). Amaranthus hybridus was originally a pioneer plant in eastern North America. 15:74. doi: 10.1186/s12915-017-0412-4, Love, M. I., Huber, W., and Anders, S. (2014). Plant Breed. Besides, a C0t analysis shown in Supplementary Figure S2 suggests distinct dissociation time for simple repeat between these two accessions. Of these only 20,548 positions could be found covered in all whole-genome sequencing data across all samples studied here. 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. Brief Bioinformatics 6, 6–22. doi: 10.1093/dnares/dsu021, Sunil, M., Hariharan, N., Dixit, S., Choudhary, B., and Srinivasan, S. (2017). Familia: Amaranthaceae s.l. At K = 6 other unique components within A. hypochondriacus gets resolved. Preview Abstract or chapter one below Format: PDF and MS Word (DOC) pages = … Hojas acuminadas o agudas hacia el ápice con … (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. 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). ER: forinitiating translational work and validating transcripts. doi: 10.1073/pnas.1220349110, Kolmogorov, M., Yuan, J., Lin, Y., and Pevzner, P. A. SD: DNA isolation and repeat analysis. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact … doi: 10.1016/S0022-2836(05)80360-2, Batzoglou, S. (2005). Amaranthus is part of the Amaranthaceae that is part of the larger grouping of the Carophyllales. At this stage, the scaffolds were long enough to allow the use of HiC data generated for Plainsman to obtain high-resolution assembly (AhK20). While the genomes of hundreds of organisms at the draft stage allow deciphering the majority of the proteomes, draft genomes lack chromosomal context under which they evolve and transcribe, which is necessary for a full understanding of biology. 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). 77, R93–R104. 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). It is also found in many provinces of Canada, and in parts of Mexico, the West Indies, Central America, and South America. 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). Amaranthus hybridus grows from a short taproot and can be up to 2.5 m in height. The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal. Plant Genome 2, 260–270. (2013). doi: 10.1371/journal.pone.0180528, Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. Genes involved in lysine biosynthesis pathway were identified by BLASTP (Altschul et al., 1990) analysis using Arabidopsis proteins. Although the family (Amaranthaceae) is distinctive, the genus has few distinguishing characters among the 75 species present across six continents. 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. Am. No use, distribution or reproduction is permitted which does not comply with these terms. It took about 500 years after the Columbian exchange and intense efforts by the United States before this grain received the much-deserved global attention. View all (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. 44:e147. bioRxiv [Preprint]. 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. 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. 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). (2015). Figure 2. (2015). 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]. (2012). Plainsman reference: Phytozome1 A. hypochondriacus genome V.2.1(A.hyp.V.2.1) (Lightfoot et al., 2017) GBS: Blair et al. Gigascience 1:18. doi: 10.1186/2047-217X-1-18. Weed Technology, 10(4):835-841; 22 ref. However, at K = 6 there is resolution in components for all four species with green for A. hypochondriacus, dark blue for A. cruentus and major yellow representing components of A. caudatus and A. quitensis. Amaranthus catechu Moq. Figure 3. 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. VASCAN was last updated on 2020-09-04; Comment nous citer. From the mapped reads, variants were called using samtools (v1.9) mpileup (Li et al., 2009) and bcftools (v1.9) (Li et al., 2009). 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. In this case, one could use synteny between species at protein levels to build chromosomes. (2009). Integrating Hi-C links with assembly graphs for chromosome-scale assembly. The clusters were generated in cBot and paired-end sequenced on Illumina HiSeq 2500 platform. 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). Figure 6. Figure 4. Nucleic Acids Res. J. This is also obvious from the stem solidness as reported by Malligawad and Patil (2010) and as shown in Figure 2E. The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information. Interestingly, this germplasm includes seeds from many amaranth landraces from South Asia including India. Possible aliases, alternative names and misspellings for Amaranthus hybridus. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. doi: 10.1002/0471250953.bi0411s48, Caselato-Sousa, V. M., and Amaya-Farfán, J. It is among the species consumed as Quelite quintonilli in Mexican food markets. This suggests that A. caudatus is a major clade under A. quitensis. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. 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. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Figure 5. The accession PI490752 originally classified as A. hypochondriacus now classifies under A. quitensis. This database is made from a framework provided by Meghagen LLC. 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. 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 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. Workflow used in the assembly of AhKP. Amaranthus hybridus, commonly called green amaranth,[2] slim amaranth,[3] smooth amaranth, smooth pigweed, or red amaranth, is a species of annual flowering plant. Here, to understand/translate the high-lysine phenotype and to validate the gene structure obtained from our annotation efforts, the transcriptomes have been mapped to AhKP reference and the expression profiles of the predicted genes have been generated across the developmental stages. RepeatModeler Open-1.0. 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). J. doi: 10.1101/2020.04.27.063040, Deb, S., Suvrath, J., Ravi, S., Whadgar, S., Hariharan, N., Sunil, M., et al. PLoS Genet. 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). 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. 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). SPD: classification, characterization and writing of the manuscript. Li, H. (2020). BC: for overseeing the experimental component of the project. State of knowledge on amaranth grain: a comprehensive review. Natl. 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. 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. (2009). Background: Amaranthus hybridus L. is an annual, erect or less commonly ascending herb that is a member of the Amaranthaceae family. BASIONYM: Amaranthus incurvatus Grenier & Godron 1846. It is a weedy species found now over much of North America and introduced into Europe and Eurasia. (synonym) Raw transcriptome reads generated in our earlier work and reported in Sunil et al. doi: 10.3835/plantgenome2009.08.0022. 14, 155–167. (2009). JBrowse: a next-generation genome browser. Subfamilia: Amaranthoideae Genus: Amaranthus Species: Amaranthus quitensis The menus on the database page will redirect you to the download as well as tool page. 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). SR: library preparation and aiding writing of manuscript. Amaranth flour could be mixed with wheat flour to make bread or other foods. The flowchart below (Figure 6) shows the pipeline used to obtain the final assembly. 990. Amaranthus hybridus f. aciculatus Thell. Figure 7. Amaranthus hecticus Willd. Farm 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. 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 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. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. doi: 10.1073/pnas.1107739108, Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J., and Holmes, I. H. (2009). Guillen-Portal, F. R., Baltensperger, D. D., Nelson, L. A., and D’Croz-Mason, N. (1999). 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). Library preparation was done for Illumina whole genome sequencing in-house and outsourced for PacBio RSII sequencing. However, this produced skewed classification because of variation in the depth of sequencing between GBS and WGS while calling variants. Lh3/Wgsim. PLoS Comput. doi: 10.1093/nar/gkw654, Chida, A. R., Ravi, S., and Jayaprasad, S. (2020). J. Gene finding in novel genomes. 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). The seed could be … 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 … SNAP (Korf, 2004) and Augustus were also used to predict gene models and used in the subsequent rounds of MAKER (Campbell et al., 2014). Rathod, K. J. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Amaranthus hybridus … At K = 4 and 5 there is no resolution between species except A. hypochondriacus. doi: 10.1186/gb-2009-10-8-r88. Bioinformatics 26, 841–842. The database is built using HTML5, bootstrap and JavaScript. ), A. hypochondriacus (q.v.). Here, a chromosome level assembly (AhKP) of a landrace, A.hyp_K_white, under contiguous cultivation in India for over several centuries is reported.

classification of amaranthus hybridus

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