09 Dec amaranthus hypochondriacus genome
For example, AK1, AK2, and AK3 genes of, Amaranth: Modern Prospects for an Ancient Crop. For ab initio prediction of genes from the genomic scaffolds, we have used gene prediction tools including GENSCAN with 36,487, Augustus with 28,662, and GeneMark with 63,044 predicted genes. R. Vogel The coverage of the scaffolds was measured by aligning the genomic scaffolds of A. hypochondriacus with various public sequencing data. Genes shown inside the outer circle are transcribed counterclockwise and those outside are transcribed clockwise. Ho Multiple sequence alignment was carried out using MUSCLE,40 present as an application in MEGA5, using the default parameters. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Crowhurst Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. N. J. Shade is disadvantageous except in cases of drought. DNA for sequencing was extracted from fresh leaves of 45- to 50-day-old plants using the DNEasy Mini Plant DNA Extraction kit (Qiagen). N. D. AvilÃ©s-Arnaut Genes and proteins: a case study with the genus, Integrating phylogeny into studies of C4 variation in the grasses, New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins, Complex evolutionary transitions and the significance of C3-C4 intermediate forms of photosynthesis in Molluginaceae, The aspartate-family pathway of plants: linking production of essential amino acids with energy and stress regulation, Data, information, knowledge and principle: back to metabolism in KEGG, KEGG: Kyoto encyclopedia of genes and genomes, Allosteric monofunctional aspartate kinases from, Regulation of lysine and threonine synthesis, National Center for Biotechnology Information, NCBI Handbook [Internet]. T.Z. We have demonstrated that the draft genome reported here can be useful in advancing our understanding of the diverse phenotypes that are unique to grain amaranths including the unique nutritional profile, aggressive growth, drought resistance and adaptability to environmental stress and characterize genes involved in the biosynthesis of betalains. M. Transcriptomic reads with the seed accession ID of IC 38040 (PI 480569) were downloaded from NCBI-SRA (SRX055331) and assembled into contigs using MIRA.22. Tyagi Shoemaker BiofÃsica Al. In the other set, using the same parameters, all the reads totalling 869,113,408 both from PE and MP libraries were assembled. E.J. Ligation of TruSeq adapters was done using DNA Ligase Mix (containing T4 DNA ligase) by incubating at 30Â°C for 10 min, and the reaction was stopped by adding Stop Ligase Mix. Vandepoele Chapter 16The BLAST Sequence Analysis Tool. Riggins 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. L.W. For example, the frequency of SNPs in Malus domestica, O. sativa, Z. mays, V. vinifera, and Fragaria vesca is 1 in 288 bases, 1 in 268 bases, 1 in 124 bases, 1 in 100 bases, and 1 in 15 bases, respectively.52â56 The k-mer spectrum of the genome (not shown) also gives a unimodal curve, supporting the high level of homozygosity within the assembled part of the genome.57. Bryson Amaranthus hypochondriacus contains both a red variety and a white variety (the sequenced one). We selected this landrace because it is well adapted for cultivation in India during the last â¦ H. L. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. 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. 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. Grain amaranths are also important contestants for expanding our narrow food base. Neumann Haas F. J. C. R.A. Schmutz Grain amaranths, collectively referring to all the three grain-producing species of Amaranthus under the family Amaranthaceae, are among the most neglected crops in human history. Besnard Comparative repeat element analysis using both A. thaliana repeats and predicted repeats. Sage The seeds of the sequenced plant are in the germplasm currently maintained at IBAB under the accession ID of IAh0001. T.-H. Smith R.A. Mallory B. Kadereit The plant is also comparatively fragile unlike the other two grain species. Goto Amaranthus hypochondriacus (commonly known as the prince-of-wales feather) is an ornamental plant, used as food source in some countries. Khoshravesh hypochondriacus (A.hyp\_K\_white) and had reported a draft genome in 2014. Department of Biotechnology (DBT), New Delhi, India has provided support to Dr S.S. and the Experimental work via the Ramalingaswamy fellowship (Ref no: BT/HRD/35/02/17/2009) and to Mr S.R.N. J. P.J. Amaranthus hypochondriacus (commonly known as the prince-of-wales feather) is an ornamental plant, used as food source in some countries. H. Originally endemic to Mexico, it is called quelite, blero and quintonil in Spanish. P. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 n = 32), and has an estimated genome size of 466 Mb. Also, masking the draft genomes of several species using the predicted repeats from the respective genomes using RepeatScout reveals 7.47% of repeats in the A. hypochondriacus genome, compared with 69.86% in B. vulgaris (USDA version, unpublished), 68.34% in S. lycopersicum, 55.02% in V. vinifera, 18.43% in A. thaliana, 68.67% in S. bicolor, and 47.69% in O. sativa (TableÂ 2). The cp genome sequences of A. hypochondriacus, A. cruentus and A. caudatus were 150,523, 150,757 and 150,523 bp in length, respectively, each containing 84 genes with identical contents and orders. Gish Lastly, we generated a physical map for A. hypochondriacus using the BioNano optical mapping platform. Pavlicek For extrinsic prediction, we have used plant proteome databases including UniProt, HTC, and plant mRNA at plantGDB. S. Stanke The reaction was stopped by adding stop-ligase mix and purified by using Agencourt AMPure XP beads. Construction of an Amaranthus hypochondriacus bacterial artificial chromosome library and genomic sequencing of herbicide target genes. The percentage of genes deciphered for A. hypochondriacus, S. lycopersicum and V. vinifera within each category of GO as annotated by comparison with A. thaliana based on orthology and further normalized for the percentage of genes in A. thaliana shows that annotation of the draft genome is comparable to that of the published genomes. Grain amaranths, collectively referring to all the three grain-producing species of Amaranthus under the family Amaranthaceae, are among the most neglected crops in human history. Lea A. Chan Jellen Here we present a high-quality draft genome sequence of the grain amaranth. Pan Some amaranth species are cultivated as leaf vegetables, pseudocereals, and ornamental plants.Most of the Amaranthus species are summer annual weeds and are commonly referred to as pigweeds. All the libraries were sequenced on Illumina Genome Analyzer IIx following the manufacturer's standard protocols. In addition to the de novo approach we used the sugar beet (Beta vulgaris) RefBeet-1.2 (Dohm et al., 2014) and the Amaranthus hypochondriacus draft genome (Clouse et al., 2016) as reference genomes to align sequence reads with bwa mem (Li and Durbin, 2009). I. Pratt Walichiewicz Kellogg Toward this end, our lab had initiated sequencing the genome of Amaranthus (A.) U. K. Borch Genetic Resources Center, National Insitute of Agrobiological Sciences, 2-1-2 Tsukuba, Ibaraki 305-8602, Japan. All the bacterial-type PEPC isoforms including A. hypochondriacus 4 and B. vulgaris 4 cluster in one clade. The evolutionary distances were computed using the Poisson correction method in the units of the number of amino acid substitutions per site.43 The analyses involved 25 AK and 75 PEPC sequences. Hence, grain amaranths, classified under the order Caryophyllales, offer an attractive alternative for expanding our food base via supplementing protein-rich cereals in the plant-based diet. After testing for quality, the reads were assembled using SOAPdenovo (SOAPdenovo31mer version 1.05).21 Assembly was performed in two stages in a high configuration system with 96 GB RAM. The number of isoenzymes encoded by A. hypochondriacus for all the seven enzymatic steps in the aspartate pathway of lysine biosynthesis has been identified and is listed in TableÂ 3 for comparison with those in other plant species. J. Klonowski Amaya-FarfÃ¡n R.V. The leaf and stem tissues, on excision, were immediately cleaned with DEPC-treated water, flash-frozen in liquid nitrogen, and stored at â80Â°C until RNA extraction was done. Work by various groups has shown that the C4-specific PEPC gene harbours a serine in place of alanine at position 780 of maize PEPC gene with accession CAA33317 (A780S) among both dicots and monocots.65 For example, one of the four sorghum PEPC genes harbours this mutation. Sisneros Namasivayam 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. MÃ©dicas E BiolÃ³gicas Soc. The GENSCAN-predicted proteome of S. lycopersicum is labelled as S. lycopersicum (G) in the figure. Jiang P. Lee SNPs were called with samtools 1.2 (Li et al., 2009). Also, 74% of raw transcript reads map onto the genomic scaffolds, which is much more than what can be expected based on the ATGC content of the assembled genomic scaffolds which comprise 58% of the genome. R. Evolutionary analyses were conducted in MEGA5.44 The phylogenetic trees were visualized using iTOL.45,46. Ogburn Napis Waack Amaranthus hypochondriacus is characterized by its apical erect inflorescence, which is heavily loaded with small edible seeds at maturity. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N 50 of 371 kb. Glover Amaranthus caudatus produces apical but drooping inflorescences that are red in colour and produce small reddish seeds (right, Fig.Â 1). Grain amaranths, A. caudatus, A. cruentus, and A. hypochondriacus, were domesticated for human consumption some 8,000 years ago and were the staple food for the Inca and the Aztec civilizations for thousands of years.1 However, cultivation of grain amaranths remains obscure during modern times following the ban on cultâ¦ Here we present a high-quality draft genome sequence of the grain amaranth A. hypochondriacus. To correlate the observed gene number polymorphism for AK genes and eQTL of the DHDPS gene, we have generated horizontal and vertical profiles of free lysine across the different developmental stages of all three grain species using ultra-fast liquid chromatography. Thus, based on a haploid genome size of 466 Mb per haploid nucleus, the BAC library coverage is approximately 10.6 times the haploid genome content. B. Axelsen 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. Quality assessment of the total RNA was done on 1% agarose gel and the Agilent 2100 Bioanalyzer using high-sensitivity RNA chips. M. A. 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. V. Pauling The reads were analysed for their quality and all those with >75% of bases with phred scores of â¥20 and <15 Ns were considered to be of high quality. To describe the genetic diversity within the grain amaranths (A. hypochondriacus, A. caudatus, and A. cruentus) and their putative progenitor (A. hybridus) we re-sequenced seven accessions in the genus Amaranthus (four A. hypochondriacus, and one of each A. caudatus, A. cruentus, and A. hybridus), which identified 7,184,636 and 1,760,433 interspecific and intraspecific single nucleotide polymorphisms, respectively. J. A. Perhaps, the absence of orthologs of the two lysine-sensitive AK genes in A. hypochondriacus may be sufficient for high-lysine phenotype. C. Following plant selection and genomic DNA extraction, five PE libraries of 300 bp and four MP libraries with insert sizes ranging from 1.5 to 10 kb were created. S. Letunic J. Ferreira HoltgrÃ¤we P. Smarda 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. Isozyme number polymorphism in A. hypochondriacus compared with other species. et al.Â, Xu The sequences that could not be annotated to any of AK 1/2/3 are labelled as x1, x2, and so on. Van de Peer Bork Jurka The resulting scaffolds were subject to various analyses such as synteny, heterozygosity, Gene Ontology (GO) annotation, repeat analysis, duplication study, and proteome prediction, using available tools and scripts developed in-house. Faq | My account | Accessibility Statement were called with samtools 1.2 ( Li et al., 2009 ),... 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