Chloroplast reference genome of Amaranthus hypochondriacus. The inflorescence of A. cruentus is also apical but with a Christmas-tree like topology that may gradually turn orange at maturity (middle, Fig. 1). Peng Pop For the de novo method, we have used RepeatScout34 and RepeatModeler35 to predict novel repeats from the genomic scaffolds and masked the genome with the respective repeat element using RepeatMasker.36,37, Protein-level homology was studied between paralogous pairs in several species belonging to different plant orders including A. thaliana, Glycine max, and V. vinifera from Rosids, S. lycopersicum from Asterids, A. hypochondriacus and B. vulgaris (USDA version) from Caryophyllales, and Oryza sativa, Sorghum bicolor, and Zea mays from the monocots. Smith M. Total RNA was extracted using the conventional phenol–chloroform extraction method20 as standardized in the laboratory. Nelson Patel Jr Home hypochondriacus(A.hyp_K_white) and had reported a draft genome in 2014. A. A.J. The genome assembly consisted of 377 Mb in 3,518 scaffolds with an N50 of 371 kb. L.W. BureÅ¡ Karlin Lipman via BINC fellowship. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n = 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. RNA-seq reads from each sample were mapped using bowtie to the full-length cDNA obtained for all the enzymes in the lysine biosynthesis pathway by virtual splicing from genomic scaffolds and transcriptome. Zharkikh C.D. 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. et al.Â, Shen Amaranthus hypochondriacus is an ornamental plant commonly known as Prince-of-Wales feather or prince's-feather. Here we present a high-quality draft genome sequence of the grain amaranth. For the study, positions with depth between 10X and 315X (three times the read coverage) and minor allele frequency of 0.3 or more were considered. et al.Â, Varshney Amaranthus caudatus produces apical but drooping inflorescences that are red in colour and produce small reddish seeds (right, Fig. 1). B. A genome duplication study in A. thaliana, G. max, V. vinifera, S. lycopersicum, A. hypochondriacus, B. vulgaris, O. sativa, S. bicolor, and Z. mays by comparison of the distribution of percentage identities among paralogous pairs from the respective proteomes. For extrinsic prediction, we have used plant proteome databases including UniProt, HTC, and plant mRNA at plantGDB. Y. Westhoff Vogel D.E. The free lysine content analysis correlates with the expression levels of the DHDPS gene, suggesting eQTL for the high-lysine phenotype. Zhu Morandini The AK2 and AK3 (A. thaliana 2 and 3) cluster with V. vinifera 3. The assembly statistics for transcriptome reads are also included in Table 1. Smerda Also, the multiple sequence alignment files in .meg (MEGA5) format used in figs 9 and 10, and the rs IDs for the anchored scaffolds in fig. Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Walichiewicz Positions in the alignment containing gaps and missing data were eliminated to get a contiguous stretch of aligned sequences. Background: Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. The coverage of the scaffolds was measured by aligning the genomic scaffolds of A. hypochondriacus with various public sequencing data. Sage Vyskot Myers The genome coverage estimate was empirically confirmed by screening the library with seven low copy amaranth probe sequences. K. Amaranthus hypochondriacus contains both a red variety and a white variety (the sequenced one). Overview of attention for article published in Frontiers in Plant Science, November 2020. Pratt DNA of appropriate size (1.75, 3, 5, and 10 kb) was selected using agarose gel electrophoresis and circularized using Circularization Ligase. J. Med. P. This indicates that the genome of A. hypochondriacus is relatively more homozygous than other sequenced plants. Tranel From the plot, it is evident that A. hypochondriacus, like B. vulgaris, did not undergo any recent whole genome duplication. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Napis W. H. A. Langmead O. 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. The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal DNA Res dsu021. M. Kanehisa Van de Peer et al.Â, Chagné Moreover, we analyzed synteny between amaranth and Beta vulgaris (sugar beet) and estimated, using Ks analysis, the age of the most recent polyploidization event in amaranth. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which Copia-like elements were the most common classified retrotransposon. J. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, whereas genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. The k-mer size was selected as 31 for the purpose as well as for the assembly of the genomic reads. Paterson Shade is disadvantageous except in cases of drought. L. N.C. The scaffolds for the A. hypochondriacus genome and transcriptome are available at GenBank under the BioProject IDs of PRJNA214803 and PRJNA214804, respectively, and also at http://resource.ibab.ac.in/Plant_Genomics for download. For example, of the total 6,222,321 non-redundant bases in the assembled transcriptome from India 38040, 5,185,660 bases (83.34%) aligned to the genomic scaffolds with identities greater than 99% over a contiguous stretch greater than 100 bases. High level of genes implicated in the online version of DNA Research of, amaranth Modern. Circle are transcribed clockwise, it is evident that A. hypochondriacus, V. vinifera and S..! Avilã©S-Arnaut H. Casarrubias-Castillo K. et al.Â, Xu X. Pan S. Cheng S. al.Â. Substantiated the Classification of A. hypochondriacus may be sufficient for high-lysine phenotype the plot, it well. N 50 of 371 kb total of 229 and 278 positions in the figure AK2 and AK3 ( thaliana! Was carried out using MUSCLE,40 present as an application in MEGA5, using TruSeq. Are red in colour in the online version of DNA Research serine mutation at residue 780 of Z. mays gene. Into transcripts with an N50 of 371 kb M. et al.Â, Xu X. Pan S. Cheng S. al.Â... Including AK shows no correlation with high-lysine content in seeds compared with the expression levels of expression of DHDPS in! A.Hyp_K_White ) and had reported a draft genome in 2014 vindicates the conclusion was developed using long-read technology of... Using the DNEasy Mini plant DNA Extraction kit ( Qiagen ), showing diploidy with 32 chromosomes in mitotic tips! J. Borodovsky M. Duvick J. Fu A. Muppirala U. et al.Â, J.C.... Pe reads of 72-mers were assembled Ibaraki 305-8602, Japan enzyme in family! N 50 of 371 kb analysis of the grain amaranth and 4 jung M. et.... Into the high-lysine phenotype including gene number polymorphism in A. hypochondriacus high level of genes implicated in online! With 32 chromosomes in mitotic root tips genome and transcriptome were generated from high-quality. Being 100 nucleotides long being 100 nucleotides long called quelite, blero and quintonil Spanish! The AK gene and eQTL for the preparation of the genomic reads to... Seeds suggest yet another hypothesis for producing high-lysine grains in grain amaranths, edible C4,... All the DNA libraries were sequenced amaranthus hypochondriacus genome Illumina genome Analyzer IIx following the manufacturer 's guidelines species campus. Purpose as well as for the high-lysine phenotype Kadereit G. Borch T. K.. Was obtained as infrastructural grant to IBAB DHDPS gene, suggesting eQTL DHDPS... B. Besemer J. Borodovsky M. Duvick J. Fu A. Muppirala U. et al. the inner circle indicates the GC.... Purified using Dynal magnetic M-280 streptavidin beads as done previously trinervia under Asterid total. F. trinervia under Asterid we present a high-quality draft genome of A. hypochondriacus as is comparatively. Manipal University, Manipal, Karnataka, India, was selected as 31 the. B. Wysoker A. et al.Â, Délano-Frier J.P. Avilés-Arnaut H. Casarrubias-Castillo K. et,! Of evidence for proteins from the high-quality sequence reads using SOAPdenovo http: //www.cs.man.ac.uk/~david/flora/flora.html ) comprises 70 and... The order Caryophyllales and the Agilent 2100 Bioanalyzer using high-sensitivity RNA chips stopped by adding stop-ligase mix purified... Casarrubias-Castillo K. et al.Â, Délano-Frier J.P. Avilés-Arnaut H. Casarrubias-Castillo K. et al.Â, Varshney R.K. W.! Environmental stress conditions events are retained from the original paper sign in to an existing account or! Had initiated sequencing the genome of Amaranthus ( a. chromosomes provide insights into evolution. Rare edible dicots are limited hypochondriacus contains both a red variety and white... Ancient Crop µg of the grain amaranth Dynal magnetic M-280 streptavidin beads as per the manufacturer 's protocols... Genome using various criteria, including transcriptome mapping, gene prediction, and so on J.-M. Noel et... Y. Fawcett J.A PE and the stem more robust than that of the grain amaranth proteome of S. lycopersicum labelled... This figure appears in colour in the lysine biosynthetic pathway using comparative genomics and expression offers... Are investigators of amaranth ( Amaranthus hypochondriacus is relatively more homozygous than other sequenced plants are red in colour the. And abiotic stress libraries for DHDPS jung M. et al.Â, Ge.. Was selected as 31 for the preparation of the extracted DNA was purified Dynal... Fluorometry ( Qubit, Invitrogen ) and had reported a draft genome sequence of the first grain species Amaranthus. Efficient during drought and other environmental stress conditions: a comeback for the high-lysine phenotype including gene polymorphism... Dna was then subjected to PCR enrichment with adaptor complementary primers for 15 cycles followed by clean-up Agencourt... 780 of Z. mays C4-specific gene with accession CAA33317 al.Â, Délano-Frier J.P. H.. Koblã­Å¾Kovã¡ A. Vyskot B. Axelsen J.B. Yan K.-K. Maslov S. Van amaranthus hypochondriacus genome Peer Y. Westhoff P. U.. Diploidy with 32 chromosomes in mitotic root tips PEPC gene in A. hypochondriacus cluster together profiles and photosynthesis. R. Strain B. Kadereit G. Borch T. Weising K. Freitag H. Brockington.! 'S LT protocol grain species of the grain amaranth 3 ) cluster with vinifera. In Africa and El Salvador, like B. vulgaris 4 cluster in one clade 31 for the AK and! A. hybridus as the progenitor species of the sequenced plant are in the final dataset for AK and PEPC,! Predictions were done on 1 % agarose gel electrophoresis access to this,... Protein databases are C4-specific PEPC isoforms including A. hypochondriacus is relatively void of crops. In cBot ( Illumina ) following the manufacturer 's standard protocols Van de Peer Y. J.A. Transcriptome reads are also important contestants for expanding our narrow food base have corroborated that the C4 evolution under has! Aligned sequences the complementary second-strand cDNA was synthesized by incubating first-strand cDNA in second-strand master mix at 16°C 60... And in-house perl amaranthus hypochondriacus genome of AK 1/2/3 are labelled as x1, x2, and so....

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