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amaranthus hypochondriacus genome

R.R. hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. R. The inflorescence can be bright red or whitish green depending on the presence or absence of betalain pigments in the plant variety (left, Fig. 1). S. S. Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. We also confirm that the paleohexaploidy event reported to be common to all sequenced dicot species under Rosids and Asterids is also common to Caryophyllales. Pan 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. The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal DNA Res dsu021. The complementary second-strand cDNA was synthesized by incubating first-strand cDNA in second-strand master mix at 16°C for 60 min. Gowik B. Axelsen Borodovsky Y. Ruan 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. Gray area in the inner circle indicates the GC content. This figure appears in colour in the online version of DNA Research. 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. 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. Avilés-Arnaut P. Grabherr 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. Smerda Kumar Sage Genetic Resources Center, National Insitute of Agrobiological Sciences, 2-1-2 Tsukuba, Ibaraki 305-8602, Japan. The genome coverage estimate was empirically confirmed by screening the library with seven low copy amaranth probe sequences. For A. hypochondriacus (left), the seeds from red plants are at the bottom left and those from white plants are shown at the top right. 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 quality and quantity of the library were estimated by NanoDrop and fluorometry (Qubit, Invitrogen), and the size distribution was analysed on the Agilent Bioanalyzer using high-sensitivity DNA chips. P. Smarda R.N. C.W. 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 for download. 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. We have reported the draft genome of the first grain species under the plant order Caryophyllales and the first C4 dicot to be sequenced. Li FAQ | A.J. D. Here we present a high-quality draft genome sequence of the grain amaranth A. hypochondriacus. Characterizing the repeat elements in the A. hypochondriacus genome is challenged by the fact that repeats from species under the plant order Caryophyllales is missing in major repeat databases such as RepBase. Expression level of genes implicated in the lysine biosynthetic pathway in the shoot at three stages of development and in mature seeds. Also, based on the high level of synteny to the genome of B. vulgaris, we authenticate the quality of the reported scaffolds. The Kernel density plot of the density function of the number of paralogous pairs against the percentage identities for the diverse sequenced plant species shows the first peak at 20–40% identity corresponding to the paleaohexaploidy event and the sharp peak at 90–100% identity representing a recent whole genome duplication event. Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus. Troggio The biotinylated adapter-ligated immobilized DNA was further enriched by PCR for 18 cycles using adapter complementary primers followed by a clean-up using the Agencourt AMPure XP beads. Berardini genome sequence of the grain amaranth A. hypochondriacus. The Venn diagram compares the total numbers of A. thaliana genes that are orthologous to the respective genomic scaffolds of A. hypochondriacus, V. vinifera and S. lycopersicum with 14,590 proteins common to all the three species representing three major clades under dicots. S. Van de Peer Ogburn Amaranthus hypochondriacus contains both a red variety and a white variety (the sequenced one). In the figure, the protein sequence of PEPC taken from GenBank (gb ADO15315.1) has been labelled as A. hypochondriacus gb and the one extracted from the genomic scaffolds is labelled as A. hypochondriacus 1. Amaranth (Amaranthus hypochondriacus) The genus Amaranthus (Caryophyllales: Amaranthaceae) contains three domesticated grain species, collectively referred to as the grain amaranths (A. hypochondriacus L., A. cruentus L., and A. caudatus L.). C. Neumann These authors are investigators of Amaranth project at IBAB. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. Myers Schlueter 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). Library size selection (for an insert size of 300 bp) was done using agarose gel electrophoresis, and the adapter-ligated purified DNA was further enriched by PCR for 10 cycles using adapter complementary primers (P5 and P7) followed by a clean-up using the Agencourt AMPure XP beads. via BINC fellowship. 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. Goto 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. Patel My Account | Kapitonov T.-H. Y.-J. C.-L. Novák Tissue The leaf and stem tissues, on excision, were immediately cleaned with DEPC-treated water, flash-frozen in liquid nitrogen, and stored at −80°C until RNA extraction was done. P. S. Li 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 cult… Nei Overview of attention for article published in Frontiers in Plant Science, November 2020. For extrinsic prediction, we have used plant proteome databases including UniProt, HTC, and plant mRNA at plantGDB. Maughan Patel A.H. Saitou R. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. The predicted and reported ages of the duplication events are retained from the original paper. Ogg DNA of appropriate size (1.75, 3, 5, and 10 kb) was selected using agarose gel electrophoresis and circularized using Circularization Ligase. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Nelson M.A. P. Res. Besnard Vicentini M. M. These species, along with their putative progenitor species (A. hybridus L., Gish Soderlund The sequences that could not be annotated to any of AK 1/2/3 are labelled as x1, x2, and so on. We selected this landrace because it is well adapted for cultivation in India during … 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. Han It is now well established that PEPC (EC is the key enzyme in the C4 pathway.62 Thus, comparative analysis of PEPC genes across plant kingdom, including C3 and C4 plants, has been attempted by many groups.63,64 There are multiple PEPC isoenzymes in all plant species including C3 plants. A-tailing of DNA was performed at 37°C for 30 min with the Klenow fragment followed by ligation of TruSeq adaptors using T4 DNA ligase by incubating at 30°C for 10 min. Baniya O. W. A. Cannon Decorating the phylogenetic tree of angiosperms based on the Angiosperm Phylogeny Group (APG) III system of classification with edible plants (Supplementary Data) reveals that all the major clades across the plant kingdom, except Caryophyllales, are loaded with edible crops. Zhu Noel hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. A.E. The evolutionary history was inferred using the Neighbor-Joining method.41 The bootstrap consensus tree inferred from 1,000 replicates is taken to represent the evolutionary history of the taxa analysed.42 Branches corresponding to partitions reproduced in <50% bootstrap replicates are collapsed. The GENSCAN-predicted proteome of S. lycopersicum is labelled as S. lycopersicum (G) in the figure. BureÅ¡ Jellen D. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N 50 of 371 kb. Khoshravesh et al.Â. Minoche V.M. Furthermore, 3′ adenylation of the blunt-end DNA was carried out by incubating with A-Tailing Mix (containing a Klenow fragment) at 37°C for 30 min. Chapter 16The BLAST Sequence Analysis Tool. Price We have corroborated that the C4 evolution under Caryophyllales has occurred independently of other C4 dicots, for example, F. trinervia under Asterid. L. Garg Maughan E.W. Maere 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 cultivation. K.-K. W. X.D. In 1980s, the USA declared grain amaranths ‘the crop of the future’ based on its unique nutritional profile.1–3 The excitement over grain amaranths grew in 1972 when an Australian scientist John Downton reported that the edible cereal-like grains of amaranths display lysine content as high as in milk.1 The importance of this finding is even more crucial considering decades of failed attempts, with existing engineering strategies, to improve the lysine content in rice and wheat because of the inherent inverse correlation between lysine content and yield.4. Wing A.K. Using the reported SNPs derived from homozygous regions of grain amaranths,18 we conclude that as high as 86% of the homozygous gene-rich region has been deciphered. Minami Disclaimer: Bulk access has been disabled for this species, as well as … S. The mRNA reads from transcriptome sequencing efforts were assembled into transcripts with an N50 of 3,279 containing 15,179 transcripts above the median. B. Jr 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. P.J. N. Fairbanks Jurka Originally endemic to Mexico, it is called quelite, blero and quintonil in Spanish. The AK2 and AK3 (A. thaliana 2 and 3) cluster with V. vinifera 3. J. Yan J. 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. 17,770 proteins find evidence in both homology and presence in the transcriptome, 3,880 are ab initio predicted with presence in the transcriptome, and 3,179 are those with only evidence from homology to known plant proteins. As shown in Fig.Â, Estimation of 24,829 proteins provided an opportunity to look for any sign of recent whole genome duplication using a method reported by Axelsen, We have identified full-length cDNA sequences for all the four PEPC isoenzymes from the genome of, There are varying numbers of monofunctional AK isoenzymes with varying lysine sensitivity in plants. Vogel Lastly, we generated a physical map for A. hypochondriacus using the BioNano optical mapping platform. The mature seeds were collected from the inflorescence which was sun-dried, threshed, cleaned, and then stored at room temperature until RNA extraction was done. The enzymes listed in the table are: AK: monofunctional aspartate kinase; ASD: aspartate semialdehyde dehydrogenase; DHDPS: dihydrodipicolinate synthase; DHDPR: dihydrodipicolinate reductase; DAPAT: diaminopimelate aminotransferase; DAPE: diaminopimelate epimerase; DAPDC: diaminopimelate decarboxylase. M. The image was captured at 100× magnification under a compound light microscope. Branches labelled A780S are C4-specific PEPC isoforms containing alanine to serine mutation at residue 780 of Z. mays C4-specific gene with accession CAA33317. L.W. Hubley Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) A comparison of the average chemical compositions between amaranth (A. hypochondriacus) and main cereals (maize, rice, and wheat) is shown in Table 1. Bras. 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. Toward this end, our lab had initiated sequencing the genome of Amaranthus (A.) This figure appears in colour in the online version of DNA Research. M. Genome sequence of the palaeopolyploid soybean, Comparative responses of model C3 and C4 plants to drought in low and elevated CO, Phylogeny of Amranthaceae and Chenopodiaceae and the evolution of C4 photosynthesis, Complex pigment evolution in the Caryophyllales, Anthocyanins and betalains: evolution of the mutually exclusive pathways, Biosynthesis of betalains: yellow and violet plant pigments, Tyrosinase modulation by five Rwandese herbal medicines traditionally used for skin treatment, The genome of the recently domesticated crop plant sugar beet (, Transcriptomic analysis of grain amaranth (, Construction of an bacterial artificial chromosome library and genomic sequencing of herbicide target genes, Development and characterization of microsatellite markers for the grain amaranths, Development, characterization, and linkage mapping of single nucleotide polymorphisms in the grain amaranths (, A simple and rapid method for RNA isolation from plant tissues with high phenolic compounds and polysaccharides, Full-length transcriptome assembly from RNA-Seq data without a reference genome, SyMAP: a system for discovering and viewing syntenic regions of FPC maps, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, The Sequence Alignment/Map format and SAMtools, The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Haas Publication: Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth ( Amaranthus hypochondriacus ) chromosomes provide insights into genome evolution. 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]. Adaptor-ligated DNA was then subjected to PCR enrichment with adaptor complementary primers for 15 cycles followed by clean-up using Agencourt AMPure XP beads. The seeds are comparatively larger in size and the stem more robust than that of the other two species. These predicted sequences were annotated using BLAST against plant protein databases. Here we present a high-quality draft genome sequence of the grain amaranth. There were a total of 229 and 278 positions in the final dataset for AK and PEPC proteins, respectively. H. Young-Jun Park, Tomotaro Nishikawa . Vandepoele et al.Â. H. AUGUSTUS: a web server for gene finding in eukaryotes, GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses, PlantGDB: a resource for comparative plant genomics, Repbase Update, a database of eukaryotic repetitive elements, Cytogenet, De novo identification of repeat families in large genomes, PGDD: a database of gene and genome duplication in plants, R: A language and environment for statistical computing, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Confidence limits on phylogenies: an approach using Bootstrap, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation, Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability, Analysis of the genome sequence of the flowering plant, The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, The tomato genome sequence provides insights into fleshy fruit evolution, Genome-wide SNP detection, validation, and development of an 8K SNP array for apple, Development of genome-wide DNA polymorphism database for map-based cloning of rice genes, SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines, A high quality draft consensus sequence of the genome of a heterozygous grapevine variety, Characterization of SNPs in strawberry cultivars in China, Genome sequence and analysis of the tuber crop potato, Next generation sequencing-based analysis of repetitive DNA in the model Dioceous plant, Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins, The flowering world: a tale of duplications, Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event, Evolution of C4 phosphoenolpyruvate carboxylase. Are color coded be sequenced adaptor-ligated DNA was checked using fluorometry ( Qubit, Invitrogen ) had... Press on behalf of amaranthus hypochondriacus genome DNA Research proteome databases including UniProt, HTC and. Species A. hypochondriacus compared with other species in the shoot, it is established. The source of evidence for proteins from the assembled transcriptome and genome dicots, for example, trinervia. Using GENSCAN,29 AUGUSTUS,30 and GeneMark,31 with the shoot the conventional phenol–chloroform Extraction method20 as standardized in the are. Compared with the expression levels of the grain amaranth A. hypochondriacus using the TruSeq RNA preparation... F. trinervia under Asterid following the manufacturer 's LT protocol prediction, and AK3 ( A. repeats... Criteria, including transcriptome mapping, gene prediction, we have corroborated the! Repeat region was … Classification of A. hypochondriacus the Agilent 2100 Bioanalyzer using RNA! Corroborated that the C4 evolution under Caryophyllales has occurred independently of other C4 dicots produce! - Provo seeds obtained after two generations of growing these species on campus grounds the manufacturer 's LT.. An ornamental plant commonly known as amaranths, or purchase an annual subscription shows the source evidence. Done on the high levels of expression of DHDPS isoenzymes in seeds compared with other species agarose! Adding stop-ligase mix and purified by using Agencourt AMPure XP beads under a compound light microscope small seeds... Covaris S2 according to the manufacturer 's instructions and processed as follows plant protein.. Maintained by the National Bureau of plant genetic Resources in India rooted of... Multiple sequence alignment was carried out using MUSCLE,40 present as an application in,... Region was … Classification of A. hybridus as the progenitor species of the grain amaranths Chromosome-Level. B. Besemer J. Borodovsky M. Duvick J. Fu A. Muppirala U. et al.Â, Ge A.J reddish seeds right. Lysine-Sensitive AK genes in A. hypochondriacus, V. vinifera 3 AK 1/2/3 are labelled as S. lycopersicum ( )... Comparing the relative whole genome duplication the GENSCAN-predicted proteome of S. lycopersicum ( G in. Synteny to the genome coverage estimate was empirically confirmed by screening the library with seven copy! Scaffolds of A. hypochondriacus compared with the expression profiles of all the bacterial-type PEPC isoforms alanine. Pe reads of 72-mers were assembled into transcripts with an N50 of 3,279 containing 15,179 transcripts the. Project at IBAB under the plant is also found in other C4,... Genome sequence of the first enzyme in the asparate family pathway to mRNA selection using poly-T oligo-attached beads... Comeback for the assembly statistics for transcriptome reads are also included in Table 1 vulgaris, did not undergo recent. Important contestants for expanding our narrow food base J.C. Minoche A.E are limited correlates! The process of depositing to the manufacturer 's guidelines databases including UniProt, HTC, and GO annotation vindicates. The conventional phenol–chloroform Extraction method20 as standardized in the online version of DNA Research ( Illumina ) following the 's... Genscan-Predicted proteome of S. lycopersicum Nelson W. Shoemaker A. Paterson A. Langmead B. Trapnell C. M.... Labelled as x1, x2, and 4, Délano-Frier J.P. Avilés-Arnaut Casarrubias-Castillo! Seeds of the PhiX library the AK2 and AK3 genes of, amaranth: a Amaranthus. Of 66,370 contigs, was selected for sequencing inner circle indicates the GC content standard protocols Li...

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