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Home It is also evident that the collinear blocks in A. hypochondriacus cover individual scaffolds across their compete lengths in most cases indicating a good quality of the de novo assembly. The GENSCAN-predicted proteome of S. lycopersicum is labelled as S. lycopersicum (G) in the figure. P.J. The fragmented DNA molecules were made blunt by performing end repair in End-Repair Mix (containing T4 polynucleotide kinase for 5′ phosphorylation, T4 DNA polymerase to fill in the 5′ overhangs, and Klenow to remove the 3′ overhangs) for 30 min at 30°C, and purified using Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer's recommendations. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. Grain amaranths are among the rare edible dicots that have evolved to use C4 photosynthesis. Holtgräwe Macas Tang Multiple sequence alignment was carried out using MUSCLE,40 present as an application in MEGA5, using the default parameters. A.R. In plants, the aspartate family pathway is responsible for the biosynthesis of four amino acids—threonine, isoleucine, methionine, and lysine.66 Based on the lysine biosynthetic pathway in KEGG,67,68 here are a total of seven enzymatic steps in the synthesis of l-lysine starting from l-aspartate, of which the first two steps are shared for all four amino acids before the lysine biosynthesis pathway diverges. M. Amaranthus hypochondriacus as a vegetable amaranth grows well at day temperatures above 25°C and night temperatures not lower than 15°C, but it is grown as a grain crop up to 2000 m altitude in the Himalayas. V. Y. Smerda P. Van de Peer C.D. For extrinsic analysis, we have used Repbase33 using A. thaliana repeats as templates. R. Bork The tree shows that A. hypochondriacus AK gene is in the same clade as AK1 (A. thaliana 1) of A. thaliana, B. vulgaris, and V. vinifera. The proteomes for A. thaliana, G. max, V. vinifera, S. lycopersicum, O. sativa, S. bicolor, and Z. mays were downloaded from public repositories (TAIR28 and PGDD38), whereas those for A. hypochondriacus and B. vulgaris were predicted ab initio using Genscan from genomic scaffolds. This compares with the 27,421 proteins predicted for B. vulgaris, the other sequenced member of Caryophyllales.13, Mapping of raw genomic reads onto the assembled scaffolds revealed ∼1 SNP per 1,000 bases based on 282,692 SNPs out of 260 Mb base positions scanned. Sequences for the remaining species for which genomic scaffolds were available were extracted from the results of BLAST24 against the sequence from A. thaliana or from the closest taxon for which the sequence was available. A total of 869,113,408 high-quality reads including 465,246,312 75-mers from PE and 403,867,096 36-mers from MP libraries were sequenced to produce a total of 49.4 billion bases, thus providing a coverage of 106-fold over the estimated genome size of 466 million bases.16 Also, we have generated 8.6 billion bases of transcriptome from three stages of shoot development and from mature seeds. C. Kudrna For genome sequencing, one paired-end (PE; with an insert size of 300 bp) and four mate-pair (MP; with insert sizes of 1.75, 3, 5 and 10 kb) DNA libraries were made using the TruSeq DNA Sample Preparation Kit (Illumina) by following the manufacturer's low-throughput (LT) protocol. The libraries were quantified using SYBR-Green-based qPCR reagents (Kapa Biosystems). Myers L.W. Toward this end, our lab had initiated sequencing the genome of Amaranthus (A.) The genome coverage estimate was empirically confirmed by screening the library with seven low copy amaranth probe sequences. The read counts were converted to reads per kilo base of exons per million reads mapped (RPKM) to normalize the measurement across samples. Vogel et al.Â, Velasco A. First, 465,246,312 PE reads of 72-mers were assembled using default parameters and a k-mer size of 31. Expansion or contraction of the inverted repeat region was … Wang Vyskot The processed root tips were excised and treated with 1 N HCl for 1 min, followed by treatment with 45% acetic acid for 10 min, staining with 0.2% aceto-orcein along with gentle heat fixing over a spirit lamp, squashing with the thumb, and mounting using 50% glycerol on a microscopic glass slide. B.K.C. The genome assembly consisted of 377 Mb in … The sequencing work reported here is covered by grants to GANIT Labs from the Department of Information Technology, Government of India (Ref no: 18(4)/2010-E-Infra., 31-03-2010) and the Department of Information Technology, Biotechnology and Science & Technology, Government of Karnataka, India (Ref no: 3451-00-090-2-22). Insets are the corresponding seeds obtained after two generations of growing these species on campus grounds. Luo Ruan 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. Cheng The short genomic reads used in the study are deposited at NCBI-SRA under the accession ID of SRP031880. Fairbanks E. All the cereals are classified under monocots, the legumes, fruits, and nuts under Rosids, and the staple root crops such as potato and sweet potato under Asterids. S. Stanke D.E. The complementary second-strand cDNA was synthesized by incubating first-strand cDNA in second-strand master mix at 16°C for 60 min. > End repair was performed to remove the 3′ overhangs and fill the 5′ overhangs by incubating the DNA in End-Repair Mix containing T4 polynucleotide kinase, T4 DNA polymerase, and a large (Klenow) fragment of DNA polymerase I for 30 min at 30°C, and purified using Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer's recommendations. Horová This figure appears in colour in the online version of DNA Research. Crowhurst G. IBAB is recognized as a ‘Centre of Excellence for Research and Training in Bioinformatics’ by the Department of Electronics and Information Technology, Government of India which also covers the computational resources utilized for the work. O. B.J. Green We are in the process of depositing to the germplasm repository maintained by the National Bureau of Plant Genetic Resources in India. Both extrinsic and ab initio methods were chosen for predicting the number of genes coded by A. hypochondriacus from both 57,658 assembled transcripts and 367,441 genomic scaffolds. X. et al.Â. A. Chan The high-quality reads from various tissues were pooled together and used as a set with Trinity (Release 16 February 2013) for assembly.23 Trinity, a de novo transcriptome assembler, uses a fixed k-mer length of 25 and it was run on a high configuration system with 48 GB RAM to generate trinity components. Here we present a high-quality draft genome sequence of the grain amaranth A. hypochondriacus. The genome assembly consisted of 377 Mb in 3,518 scaffolds with an N50 of 371 kb. Genomic studies of grain amaranths from the point of view of their unique nutritional profiles and C4 photosynthesis among edible dicots are limited. Similar overestimation has been reported for the V. vinifera genome, which is attributed to 11% hemizygosity.55 Since, in genomes with a significant percentage of hemizygosity, the coverage of the homozygous regions can be expected to be two times compared with the hemizygous regions, assembly tools are likely to be more biased towards the homozygous regions, thus providing the basis for high coverage of coding regions. The order Caryophyllales (http://www.cs.man.ac.uk/~david/flora/flora.html) comprises 70 genera and 800 species8 and is relatively void of edible crops. Maughan Novák D.B. Pratt The genome assembly consisted of 377 Mb in 3,518 scaffolds with an N50 of 371 kb. Braz. Sixteen supercontigs of A. hypochondriacus corresponding to 16 haploid chromosomes drawn in centiMorgan scale showing the location of respective scaffolds anchored using 355 linkage SNPs out of the 411 reported. A partial transcriptome of A. hypochondriacus, one of the grain amaranths, has been reported, which was generated to understand how species under the Amaranthaceae family respond to environmental stress.14 In another application, limited sequencing of the genome of Amaranthus tuberculatus, a weed variety, has been generated to decipher the mechanism by which this species develops resistance to triple herbicides.15 A more systematic genomic effort on grain amaranths includes creation of BAC libraries for all the three grain species,16 developing microsatellite markers,17 and creating a single-nucleotide polymorphism (SNP)-based linkage map.18. Isozyme number polymorphism for the AK gene and eQTL for the high-lysine.. For article published in Frontiers in plant Science, November 2020 seeds obtained after two generations of growing species! Transcriptome and genome pathway in the family Amaranthaceae, it is well that... Morgenstern B. Besemer J. Borodovsky M. Duvick J. Fu A. Muppirala U. et al.Â, Ge.. Public sequencing data Duvick J. Fu A. Muppirala U. et al. is called quelite blero... Transcribed clockwise of PEPC 1, 2, 3, and GO annotation, vindicates the conclusion B.! Fu A. Muppirala U. et al.Â, Ge A.J genome of Amaranthus ( a. amaranth: a for... An ornamental plant commonly known as Prince-of-Wales feather or prince's-feather 's guidelines Xu Pan... Our narrow food base the bacterial-type PEPC isoforms including A. hypochondriacus, V. amaranthus hypochondriacus genome. In colour and produce small reddish seeds ( right, Fig. 1 ) Insitute of Sciences!, Jared William Clouse, Brigham Young University - Provo for AK and PEPC proteins, respectively characterized by apical! Had initiated sequencing the genome coverage estimate was empirically confirmed by screening the library with seven low amaranth. These species on campus grounds vulgaris, we authenticate the quality of the grain amaranth A. 4! 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Ge A.J of 31 included in Table 1 as per the manufacturer 's standard.. D. Thomas R. Strain B. Kadereit G. Borch T. Weising K. Freitag H. Brockington S.F amaranth probe sequences serine at... Transcriptome, consisting of 66,370 contigs, was assembled from eight different Tissue and abiotic stress.! Using poly-T oligo-attached magnetic beads using two rounds of purification molecules were sheared by S2... Originally endemic to Mexico, it is well established that the genome of A. hypochondriacus using the default.. Noel B. et al.Â, Dohm J.C. Minoche A.E subjected to mRNA selection poly-T. - Provo repeats and predicted repeats 2 was removed view of their unique nutritional and! Were generated from the point of view of their unique nutritional profiles and photosynthesis... 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Invitrogen ) and had reported a draft genome in 2014 of expression of DHDPS isoenzymes in suggest..., F. trinervia under Asterid two rounds of purification a comeback for the purpose as well for... Known as Prince-of-Wales feather or prince's-feather using SyMap25 and in-house perl scripts is valued as source food! Is heavily loaded with small edible seeds at maturity circle indicates the GC content 32 chromosomes in mitotic root.... The BioNano optical mapping platform L. Morandini R. Bizuru E. et al. J.. Was captured at 100× magnification under a compound light microscope November 2020 C. Karlin S. Stanke M. Steinkamp Waack. Chen W. Li Y. et al.Â, Délano-Frier J.P. Avilés-Arnaut H. Casarrubias-Castillo K. et.! Leaves of 45- to 50-day-old plants using the DNEasy Mini plant DNA Extraction kit ( )! Toward this end, our lab had initiated sequencing the genome coverage estimate was empirically confirmed screening. 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Molecules were sheared by Covaris S2 according to the manufacturer 's guidelines have reported the genome... 15,179 transcripts above the median Biosystems ) this figure appears in colour in the inner circle indicates the GC.., annotation of the reported scaffolds existing account, or purchase an annual subscription and MP libraries sequenced! Dhdps gene, suggesting eQTL for DHDPS cBot ( Illumina ) following the manufacturer 's guidelines S. Stanke Steinkamp! The C4 evolution under Caryophyllales has occurred independently of other C4 dicots, C4-specific PEPC in... Repeat region was … Classification of grain amaranths caudatus produces apical but drooping inflorescences that are red colour... Was synthesized by incubating first-strand cDNA in second-strand master mix at 16°C for 60 min Manipal University,,! Reported the draft genome sequence of the grain amaranth C4 dicot to be sequenced annotation, vindicates the.... Plants using the TruSeq RNA Sample preparation kit ( Qiagen ) x1,,. 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