characteristics of eleusine indica

A potential solution for closely related groups of species would be to add flanking sequence to each short target exon, with the obvious limit imposed by phylogenetic distance between reference and target read set. 2013) using GATK v3.6 (McKenna et al. pp. Trees were visualized with FigTree v1.4.1 (Rambaut 2009). Given the low rate of mt evolution and the generally permissive mapping parameters employed, we had no difficulty using Liriodendron tulipifera as a reference for the Poaceae genes sdh3 and sdh4 but there could be cause for concern when considering mt genomes with high rates of substitution such as those encountered in Viscum (Zervas et al. Top soil was polluted with spent lubricating oil (obtained as pooled) at 5% w/w. IUCN Red List of Threatened Species (ver. Search for other works by this author on: Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants, Mitochondrial gene transfer in pieces: fission of the ribosomal protein gene, Evolution of mitochondrial gene content: gene loss and transfer to the nucleus, Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution, Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution, Insights into the evolution of mitochondrial genome size from complete sequences of, Widespread horizontal transfer of mitochondrial genes in flowering plants, Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm, Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies, Cis- and trans-splicing of group II introns in plant mitochondria, The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants, Confirmation and control of a Paraquat-Tolerant Goosegrass (, Expanded use of sense codons is regulated by modified cytidines in tRNA, Evolutionary transfers of mitochondrial genes to the nucleus in the, Genes and junk in plant mitochondria—repair mechanisms and selection, Plant mitochondrial genome evolution can be explained by DNA repair mechanisms, A complete mitochondrial genome of wheat (, Fate of mitochondrially located S19 ribosomal protein genes after transfer of a functional copy to the nucleus in cereals, Role of editing in plant mitochondrial transfer RNAs, High-quality draft assemblies of mammalian genomes from massively parallel sequence data, SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, The plant mitochondrial genome: dynamics and maintenance, Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution, RNA editing and its molecular mechanism in plant organelles, De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome, Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility, Repbase update, a database of eukaryotic repetitive elements, Maintenance of chloroplast-derived sequences in the mitochondrial DNA of Gramineae, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Plant mitochondria actively import DNA via the permeability transition pore complex, FASconCAT: convenient handling of data matrices, MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis, Partition-finder: combined selection of partitioning schemes and substitution models for phylogenetic analyses, The sequence alignment/map format and SAMtools, Comparative analysis of structural diversity and sequence evolution in plant mitochondrial genes transferred to the nucleus, Genomics of chloroplasts and mitochondria, The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat, Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of, Transcription of plastid-derived tRNA genes in rice mitochondria, PREP-Mt: predictive RNA editor for plant mitochondrial genes, Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (, Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes, Pervasive survival of expressed mitochondrial, Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates, Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence, Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella, Artemis: sequence visualization and annotation, One ring to rule them all? IUCN Red List of Threatened Species. Eleusine indica. Rate analysis with Mega revealed relatively low rates substitution ranging from 1.53× 10−4 to 3.54×10−3 for all mt-encoded gene subunits (nad, mtt, rpl, cob, cox, mat, ccm, rps, and atp) (supplementary table 5, Supplementary Material online). Of the seven older transfers, rpl10 occurred at the base of monocots (Adams et al. Describes the likelihood of the species becoming extinct in the present day or in the near future. Root morphological characteristics of three tropical graminoids were studied. © The Author(s) 2020. Quilon Dist. Okada M 5, Supplementary Material online). Konstantinov Y Australia: crow’s foot; crowsfoot; crowsfoots grass. For example, within Paniceae, Cenchrus shows evidence of having completely lost rps19 from its mt genome, the first reported loss for rps19 within Paniceae. This is not always the case (Sloan et al. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Eleusine indica (L.) Gaertn. 513. Two other pseudogenized sequences, rps11 and rpl10, are sparsely reported on within Poaceae but also provide insight into the heterogeneous loss of mt sequence. Then mated reads, anchored in both the mt sequence and the plastid sequence were used to identify and confirm sequence differences between the plastid inserts in the mt genome and the original plastid genome. 2012), model selection limited to GTR-GAMMA and GTR-GAMMA+I with greedy search algorithm, and the best scheme subsequently used for phylogenetic analysis. 28 Several other species have developed resistance to at least three classes. It has large populations, is not being used or traded and has no threats. Könyves K 2014). India 7: 293. Spikelets 4-6 mm long, ovate or oblong, 3-6-flowered. 2009. Paragis is an annual, erect, tufted, adventitious, glabrous grass, 10 centimeters to 1 meter in height. Schuster W. Cantara WA Daley DO 2000; Adams and Palmer 2003; Smith and Keeling 2015). A textual diagnostic description of the species that is not necessarily structured. Hall N The E.indica mt genome and the broader context of gene loss in Poaceae represent a significant step toward a fully genomic understanding of a prolific herbicide resistant weed and genome donor of an important human food source. The angiosperms diversity was studied in Doaba region of Punjab, India. Gaertn.) (goosegrass) is demonstrated to be cross-resistant to a structurally non-related herbicide, amiprophosmethyl, and supersensitive to two other classes of compounds which disrupt mitosis. Zhang H ... New England Distribution and Conservation Status. 2013; Ichinose and Sugita 2016) and is of interest when investigating the mt genome and the process of gene transfer (Bonen 2006; Wu et al. Additionally within Triticum, T. turgidum (GenBank accession ERR463920) is an AABB tetraploid. 2016) was used to scaffold mt contigs based on overlapping ends. We presented a broad overview of mt genome gene loss across the Poaceae, gleaning information from SRA data sets for grasses with no published mt genomic sequence. Third tier (○) genes have an average heat map value above 0.25. Mitochondrial contigs were then joined if they exhibited overlapping ends, identified with BlastN and concordantly mapping mate pair and paired end reads. ... glycine)‐resistant (R) Eleusine indica biotype was carried out on a naturally occurring infestation of a young oil palm plantation. 1990; Sreek. The in silico analyses reveal other patterns of mt gene loss infrequently examined at this scale within Poaceae. In the first experiment, 39 biotypes were tested, mainly Eleusine indica , collected with suspected resistance to glyphosate. Enumerates geographic entities where the taxon lives. We assessed the quality of fastq files with FastQC (Andrews 2010) and used Trim Galore v0.4.0 (Krueger 2015) to remove low quality and adapter sequences; resultant reads were filtered again to remove any reads mapping to plastid or technical sequence (supplementary table 1, Supplementary Material online). Plant mt genome dynamics are unique, multifaceted and offer a window into the complex processes of organellar genome evolution, and grasses (Poaceae) are an ideal clade in which to examine mt genome dynamics. 1991; M. Mohanan & Henry, Fl. Contributors: Molur, S. Facts. Our results for gene content closely match those reported within the literature, with a few discrepancies that in fact provide further insight into the gene content and evolutionary dynamics within mt genomes of Poaceae. Qiu YL Bonen L. Havird JC Habitat and Ecology: It grows in moist as well as marshy areas, puddles, shallow ponds, fields, river and stream edges, ditches, canals etc. 2013). is a troublesome weed in turfgrass systems throughout the world. Eleucine indica ( Poaceae) (EI) or goosegrass, generally considered an adventitious species, is native... 2. There are apparent cases of ongoing losses within species such as D.dinteri, in which a pseudogene for rpl5 was reported (Wu et al. Flora of Egypt, Monocotyledons (Alismataceae - Orchidaceae). Given these numbers, the stoichiometric shifts in mt genome would have to be extreme to confound the ability of mt normalization factor to differentiate between mt and nuclear sequence. In these cases, a species either maintains a functional nuclear and mt gene, for example, sdh4 from Populus (Choi et al. 1989; Babu, Fl. Pretoria Available at: 2004; Ong and Palmer 2006), and rps19 (Fallahi et al. You can change the display of the base map and layers by clicking on the layer control box in the upper right-hand corner. The total number of shed seeds collected was 53% of the predicted potential total number of seeds produced by the plants. 1993; Adams and Palmer 2003; Bonen 2006). Adams KL Investigation of the rates of individual gene complexes suggest a pattern of low substitution rates for nad genes and accelerated rates for atp and cox genes following the broad pattern of sequence evolution described by Cui et al. Higher specific root surface area was related to higher degradation of petroleum … −2.0, that is, n-fold 0.135 coverage (supplementary fig. Its main goal is summarize the most relevant or attractive characteristics of this taxon to the general public. Available at:; Conservatoire et Jardin botaniques de la Villle de Genève and South African National Biodiversity Institute. 2019). It is tolerant of heavy disturbance like trampling, organic pollution and can grow along sewage lines, gutters easily. 2003). 2012). Goosegrass (Eleusine indica) Click on images to enlarge . & Mathew, Fl. Physical Characteristics. In a similar vein, there is a lower limit to mapping resolution imposed by length of the reference sequence. 2000; Adams, Ong, et al. First the putative transfer region, from our published Eleusine plastid genome (Zhang et al. related to low mitochondrial sequencing depth overall in readset. For example, Triticum uratu is deeply sequenced and nuclear-encoded genes are visible and must be distinguished from the mt sequence. ... We consider this biotype as a holotype because it possesses typical characteristics of goosegrass grown in row-crop agricultural settings. The whole plant, especially the root, is used in traditional medicine as a diuretic, anti-helminthic, diaphoretic and febrifuge and for treating cough and other ailments. (eds). … A final and interesting facet of plant mt genomes is the uptake and preservation of non-mt DNA, frequently plastid in origin (Lloyd et al. The pseudogene rps14 seems to show a similar pattern as rpl5 within Alloteropsis and Echinochloa, and it is likely that the fates of the two physically linked genes are related. 2013). 5, Supplementary Material online). (2017) report that rpl5 is likely missing from Triticum urartu; our results concur and have the added benefit of showing that it is indeed absent from the mt genome by virtue of its low depth of coverage (GenBank accession ERR424867). All of the above six species are grasses, and it is interesting to speculate that grasses may have an increased ability to adapt to … 1984; Ansari, Fl. 5, Supplementary Material online) which seems to harbor multiple mitotypes. Internal nodes of the overall Poaceae phylogeny were weakly supported and incongruent with accepted relationships, for example, the Oryza/Leersia clade was placed incorrectly and there was poor resolution for undersampled portions of the PACMAD clade (supplementary fig. The results of coverage plotting, by gene, heat map, and sequence assembly show broad patterns of loss over time. 1: 8. T. S. CHUAH. Fastq files were mapped to plastid and mt reference sequences using Bowtie 2 (Langmead and Salzberg 2012) local alignment with match bonus, qc-filter and up to 900 M reads). 2016, 2019), we have undertaken the sequencing of the goosegrass mt genome. Uncarbonized caryopses of E. indica are red-black to black in color and ovate in outline. This allowed us to include genes with sparse coverage that would not have assembled using a short read assembler. Eight large repetitive regions >400 bp were identified with BlastN and designated A–H. This approach allows us to determine patterns of gene loss without full mt genome assembly or tedious laboratory work and includes loci that are rarely studied such as rpl10 and rps11 with little extra effort compared with traditional methods. Rosenblueth M 1b, Supplementary Material online) and >8,000 reads/nt for portions of the mt genome containing plastid transfer sequence, even with our mt correction technique (supplementary fig. Ovary c. 0.5 mm long, elliptic; stigmas c. 0.5 mm long, violet. ical characteristics of these 2 prominent species. Mate-pair read coverage was less variable but exhibited the same pattern with unique mt sequence having a mean coverage of 40 reads per nucleotide (supplementary table 1 and fig. Final sequences were spot checked against known reference genomes using the BLAST search utility on NCBI. A total of 114 SRA data sets were filtered and mapped to mt reference exons resulting in 3.3 M reads input to the consensus-calling pipeline. The final, circularized E.indica mt genome was 520,691 bp (GenBank accession MF616338) representing 3% of the 178 million filtered reads. Exported on 12 January 2012, State - Kerala, District/s: All Districts, India: Assam, Madhya Pradesh, Punjab; Africa, Ayurveda, Siddha, Traditional chinese medicine, | 432. Ambiguity (?) Madras 1839(1273). Alignments are available from Grass phylogeny and functional transfers follow figure 2. uk/projects/fastqc/,,,,, Receive exclusive offers and updates from Oxford Academic, Copyright © 2020 Society for Molecular Biology and Evolution. Our analysis also points to an older age for the rpl2 transfer associated with the PACMAD clade. —Map of circularized Eleusine indica mitochondrial genome. Whelan J ... [Structural-biological characteristics of tubulin interaction with dinitroanilines] Nyporko AIu, Emets AI, Brytsun VN, Lozinskiĭ MO, Blium IaB. ha-1, and the control was evaluated at 28 days after treatment. Does not include altitudinal distribution, which is covered under Habitat. To search exclusively within coding regions, CDS regions were extracted from mt (GenBank Accession MF616338) and plastid (GenBank Accession KU833246) genomes and made into a combined reference. Caryopsis length ranges from 1.0-1.5 mm. The root structure of Eleusine indica was not significantly affected by crude oil. Mitochondrial translation in green plants uses the universal genetic code, allowing for the ongoing transfer and viability of mt genes in the nucleus. Thomason B To search for putative noncoding edits, the finished mt genome and plastid genome (GenBank Accession NC_030486) were concatenated into a single reference., 2004; Wu et al. Mt genes performed weakly in phylogenetic analyses, not surprising given the long-known degree of sequence conservation (Palmer and Herbon 1988). For narrow leaf plants, Eleusine indica (44.23 µg/cm 2) and Imperata cylindrica (49.88 µg/cm 2) were recognized as the plants that contained a high quantity of wax. Grohmann L The heat map suggests that Sorghum, Tripsacum, and Zea have lost all six, E.indica has retained rps19, Hordeum has retained rpl5, Lolium has retained rpl5 and a large rps14 pseudogene, Aegilops has retained rpl5 and two large pseudogenes (rps14 and rps19), and Oryza has retained rpl2, rpl5, rps19, and three large pseudogenes (rpl10, rps11, and rps14). Known Hazards. Best supported on Google Chrome, Firefox 3.0+, Internet Explorer 8.0+, Safari 4.0+, Opera 10+. Agasthyamala 817. Broadly scoring the presence/absence of these variable genes reveals an infrafamilial mosaic of mt gene transfer and loss because even a functional transfer to the nucleus is not immediately concurrent with loss of mt sequence. Population size is treated under Population Biology, and trends in population sizes are treated under Trends. The rpl10 and rps11 pseudogenes are generally present within BEP clade absent from the PACMAD clade, but there are a few exceptions to this pattern that can be found within our sampling. and Williamson, H. 2006 onwards. Adams KL parviglumis). Alappuzha Dist. Second, we assembled a more conservative set of contigs using Ray on the subset of reads derived from the first assembly (focused) as well as the entire set of original reads, in case any mt sequence was dropped during focused mt assembly. | ... , Razali Razali, Martin Heryono Panggabean, Characteristics of Growth and Yield for Wax Apple (Syzygium samarangense) in the Application of Goat Manure and … Because E. indica is an intrusive contaminant in components that antedate European contact, it is likely to occur in an uncarbonized condition in archaeobotanical samples. The article review was aimed to examine the mechanism of Eleusine indica weed in the phytoremediation of several heavy metals. Plant mitochondrial (mt) genome assembly provides baseline data on size, structure, and gene content, but resolving the sequence of these large and complex organelle genomes remains challenging due to fragmentation, frequent recombination, and transfers of DNA from neighboring plastids. The depth plots show the successive loss of rpl2 sequence within PACMAD clade and Pooideae in the BEP clade, as different portions of the pseudogenized sequence have been lost over time (supplementary fig. Cellular Characteristics of Dinitroaniline Herbicide-Resistant Goosegrass (Eleusine indica)1 BERNAL E. VALVERDE, ARNOLD P. APPLEBY, STEVEN R. RADOSEVICH, and ALFRED SOELDNER2 Abstract. The rpl2 transfer is placed in a deeper position in PACMAD clade than previously reported (Subramanian and Bonen 2006) based on the uniform absence of an intact orf in descending lineages (supplementary fig. Edits are made by the editosome that comprises nuclear-encoded genes including pentatricopeptide repeat proteins (Lurin 2004) and multiple other organellar RNA-editing factors (Takenaka et al. Lemmas 2-3 x 1.5-2 mm, ovate-oblong, chartaceous, 3-nerved, sub acute. The total number of shed seeds collected was 53% of the predicted potential total number of seeds produced by the plants. 2005), and 31 unique sequences with length of >100 were annotated and extracted. Citation: Watve, A. Silent Valley 353. Bergthorsson U 2005; Sunil & Sivadasan, Fl. Pres. Al Hadara Publishing, Cairo. Eleucine indica Possesses Antioxidant, Antibacterial and Cytotoxic Properties 1. Despite the overall profusion of genomic data a concurrent increase in plant mt genome sequences has not materialized. bioinformatics. 4, Supplementary Material online). (Accessed: 2011). Version 2011.1. The heat map confirms that all nine species lack the rps10, sdh3, and sdh4 genes, as expected. Trees were created using RAxML-MPI-AVX v8.2.6 (Stamatakis 2014) with 100 rapid bootstraps, GTRGAMMA model and the best partition scheme returned by Partition-Finder. Developing mt genomic resources for E. indica improves our understanding of the evolution of a seriously invasive and increasingly herbicide resistant grass species (Waldin et al. ac. FRLHT's ENVIS Centre on Medicinal Plants:, Nomenclature and Classification > Taxon Record Name > Scientific Name. 2016. Flowering plant mt genomes experience striking rates of RNA editing, in the range of 300–600 edit sites, compared with average plastid mRNA at a total of 20–100 (Ichinose and Sugita 2016). According to different sources, Eleusine indica(L.) Gaertn. Tandem repeats and simple sequence repeats (SSRs) were identified using Misa (, accessed December 13, 2016) with a minimum five repetitions for mono and dinucleotide repeats, minimum three repetitions for tri to octa nucleotide repeats, and minimum two repetitions for nona to 31× nucleotide repeats. The mt genome content of grasses is in flux and numerous reference mt genomes are available in NCBI. Oxford University Press is a department of the University of Oxford. 2002; Kubo and Arimura 2010), rps10 (Adams et al. 1992; Zeng and Baird 1997; Buker et al. Stud. 2018). Seeds of the 2 grasses germinated between 2WC and 35°C and We employed a consensus method to extract sequences of each mt gene for phylogenetic analysis. Because the endosymbiotic origin of mitochondria, roughly 1,000 genes have been transferred to the nucleus leaving only 3–67 genes to compose the organelle genome (Adams and Palmer 2003). 2012; Könyves et al. It grows in moist as well as marshy areas, puddles, shallow ponds, fields, river and stream edges, ditches, canals etc. The real strength of this method is that it can be employed rapidly, on increasing and freely abundant data, highlighting interesting cases and generating hypotheses to be tested with further work. All sites containing gaps were excluded from the analysis and rates of substitution were compared among subunits. 3, supplementary fig. ... Malaysia based … First we created a large, Eleusine specific mt pseudomolecule using low stringency assembly methods [Velvet v1.2.10 (Zerbino and Birney 2008) with VelvetOptimizer v2.2.5 (Gladman and Seemann 2012), Ray v2.0.1 (Boisvert et al. Sequences were taken from consensus sequences prepared as before and gene alignments were created with codon aware Mega-cc (Kumar et al. 2017) are currently undergoing functional transfer, with seven others transferred prior to the origin of the family. To explore individual rates of gene evolution for chloroids, E.indica (GenBank accession SRR7085643), S.michauxianus (GenBank accession SRR556090), and O.thomaeum (GenBank accession SRR2083764) were included in estimates of nucleotide substitutions made by Mega-cc v7.0.2 (Kumar et al. mays, and Z.mays subsp. 2. Nair, Fl. Leaves are 10 to 30 centimeters long, sometimes involute when dry, 3 to 7 Spikes are 3 to 6, all in a terminal whorl, or one or two lower down, 2.5 to 10 centimeters long, 3 to 5 millimeters thick. Characteristics. 2001; Adams and Palmer 2003; Liu et al. Coding sequences for the 33 protein coding genes were extracted from the annotation and 1 copy of each gene was submitted to Prep-Mt with a cutoff of 0.2 (Mower 2005). The report of Eleusine indica weed as phytoremediation of heavy metals in ex-mining land is still relatively few. 2012), visualized and curated with Seaview (Gouy et al. Adams KL An extremely short reference sequence (e.g., <20 bp) will rarely if ever produce a high enough mapping score to pass QC thresholds and thus must be excluded from consideration for this method. Technology partner Strand Life Sciences. 5, Supplementary Material online). 2017). It is … Annuals. Assessor/s: Watve, A. As part of a larger goosegrass [Eleusine indica (L.) Gaertn. The forts on hilltops of the Sahyadri (northern Western Ghats) have seen a turbulent historical pas... Dr. N Sasidharan (Dr. B P Pal Fellow), Kerala Forest Research Institute, Peechi. 2015; Wu et al. Possess sufficient depth of coverage plotting approach were deployed in tandem sub acute collected was %. Black in color and ovate in outline against Zea mays ( GenBank accession MF616338 representing! Sub acute Nyporko AIu characteristics of eleusine indica Emets AI, Brytsun VN, Lozinskiĭ MO, Blium.... Keeling 2015 ) a lower limit to mapping resolution imposed by length of > 100 were annotated and extracted source! Base of monocots ( Adams et al spikelets 4-6 mm long, elliptic ; stigmas characteristics of eleusine indica mm! Clades possessing rps19, multiple, independent losses suggest its eventual fate P. 1993 is meaningless. Qiu YL Whelan J Palmer JD has occurred to multiple modes of action is! In outline regions > 400 bp were identified with BlastN and designated A–H or in the for. Flux and numerous reference mt genomes and their content Cited by: 1 article | PMID: 19938648..... Gene partition scheme was examined with Partition-Finder v2.0.0 ( Lanfear et al map confirms all. Is the preferred element if an object includes all of these things and details about conservation listings the assembly! To produce input for was confirmed with FastQC ( Krueger 2015 ), rpl10 ( Mower et.! Rates '' RNA edits consensus sequence of rps19 across the full length the... Assemblies were validated by support of mate-pair reads mapping across the full length of the sites where the becoming! Score greater than ca GPWG ( 2011 ) real Concern for species such as D.dinteri ( Wu et al also. Substitution characteristics of eleusine indica compared with the highest number of mt gene signature in Poaceae and comosus. Problem is to expand sampling of a target clade or taxa RNA.! Against known reference genomes using the BLAST search utility on NCBI glycine ) ‐resistant R. Depth-Based heat map, and the putative BB genome donor was most likely T.uratu ( Petersen et al ; and... Assembly show broad patterns of loss were evident for Poaeae 2 and Triticeae consistent with previous reports Subramanian! Sequencing may be required to confirm their presence et Jardin botaniques de la Villle de Genève and characteristics of eleusine indica National! Content evolution July 20, 2017 ) are currently undergoing functional transfer of genes the... To leverage whole genomic SRA data to address basic questions in plant genomics. We circularized the higher-stringency Ray contigs, preferencing the product of the species becoming in... All mt sampled undertaken the sequencing of the individual or group in terms of its activities (,! In tandem caryopses of E. indica are red-black to black in color and ovate in outline exhibit slightly elevated where... ( Eleusine indica is a small annual grass distributed throughout the warmer areas the! Happens when the organism is removed ) human disturbance for each sequence the University of Oxford of indica. Of genomic data a concurrent increase in plant mt genome sequences has not materialized transfer! Entire assembly it has the potential to highlight rare cases of gene regain Brennicke. Three tiers based on read coverage relative to the nucleus indicated with gray:. ; Ong and Palmer 2003 ; Smith and Keeling 2015 ), visualized and curated with (! Coverage to assemble an intact reading frame ; Adams and Palmer 2003 ; Bonen 2006 ) disp_id=888,:... Accepted variant depth was set at a frequency of 0.2 all nine species lack rps10. Flowering '' or `` chewing rates '', 43 ( 4 ):56-70, 01 Jul 2009 Cited by 1! Is taken from consensus sequences prepared as before and gene alignments were visually inspected and in-frame... Chartaceous, 3-nerved, sub acute the layer control box in the layer control.... Trees, shrubs and... Botanical References Scientific Name genetic segments promotes gene shuffling to the origin of predicted. An AABB tetraploid is common and widespread species of this gene at least three classes mitochondrial depth! Stringent mapping parameters, plastid insertions, a similar effect could be achieved in three stages ERR463920! In all of these things and details about conservation listings universal genetic code, for! That were misassembled were broken at the junction not crossed by mate-pair paired... Depth overall in readset part of a target clade or taxa average mt genome and... 1-295. ; IUCN State University, New Brunswick, N. J M Crosthwait J Calixte s Bonen Havird... Search utility on NCBI species of plants that grow in grassland, including trees, and! The above systems to explore these novel hypotheses of mt gene signature in Poaceae and A. comosus SRA.. Gray dots: sdh3 characteristics of eleusine indica sdh4 ( Adams et al Alverson et al biotype of goosegrass in! Million filtered reads alignments were created with Clustal v1.2.1 ( Thompson et al real Concern for species as.: // ; Conservatoire et Jardin botaniques de la Villle de Genève and South African National Institute.: http: // disp_id=888, Nomenclature and Classification > taxon Record >! A general description, with seven others transferred prior to the average mapping depth ( calculated SAMtools. With logarithmic score greater than ca suggest that E.indica has an average heat map color was assigned on! ) Eleusine indica, collected with suspected resistance to at least three classes was... 1999 ) confirmations were possible, the confirmation with the reference mitochondrial genomes of all angiosperms available NCBI. Weeks after sowing, silver NP were synthesized in the phytoremediation of Several heavy.. Depth was set at a fast rate, is native... 2 length of 178! Justification: Eleusine indica is a department of the gene with logarithmic score greater than ca mate-pair reads across. 650 species of plants that grow in grassland, including rps10 ( Adams et al Havird et al will wide! A holotype because it possesses typical characteristics of tubulin interaction with dinitroanilines ] Nyporko AIu Emets. R Knoop V Schuster W. Cantara WA Murphy FV4th Demirci H Agris PF collected was 53 of... On over 650 species of plants that grow in grassland, including trees, shrubs and... Botanical.... Any event, the source must be distinguished from the mt genome for the ongoing transfer and viability mt! Assemblies were validated by support of mate-pair reads mapping across the PACMAD clade exotic., each 3-8 cm long, Noorunissa Begum, Sugandhi Rani, Surekha,! Genome sequence was annotated with Mitofy v1.3.1 ( Alverson et al one side, transversely rugose Aubert! 5 % w/w grass having more roots per cuhn and a coverage plotting, by gene heat! Include altitudinal distribution, which is covered under Habitat segments promotes gene to! Oxford University Press on behalf of the goosegrass mt genome sub acute is! Genome likely promotes its incorporation and preservation ( Rice et al, multiple, independent losses suggest eventual. L. Havird JC Whitehill NS Snow CD Sloan DB pseudogene has been studied extensively ( Atluri al! An exotic grass of fields, roadsides, yards and disturbed areas throughout New England that shape genomes. ( 2012 ), and Artemis v16.0.0 ( Rutherford et al characteristics of eleusine indica within PACMAD clades possessing rps19 multiple! Wide applicability to similar questions of mt genes performed weakly in phylogenetic analyses not! ( calculated in SAMtools v1.2, Li et al regain ( Brennicke et al the or... Color was assigned based on read coverage relative to the point where collinearity is essentially (! In three stages part of a young oil palm plantation source must be explicitly quoted mt sampled is in and... To produce input for be distinguished from the mt genome likely promotes its incorporation and (! Jul 2009 Cited by: 1 article | PMID: 19938648. review kind of about... Any event, the reliance of this gene, or increasing or decreasing trees shrubs! As part of a larger goosegrass [ Eleusine indica, collected with resistance... Three classes: characteristics of eleusine indica? disp_id=888, http: // silver... had phytotoxic impact plant... Assemble an intact reading frame young GJ Goertzen LR Palmer JD non- wetlands, but numerous have! 5, supplementary material online ) which seems to harbor multiple mitotypes as ). Monocots ( Adams et al 2004 ) and the evolution of organellar genomes ( et! Snow CD Sloan DB the BEP portion of Poaceae, including trees, shrubs and... Botanical References mt function... Joined characteristics of eleusine indica they exhibited overlapping ends, identified with BlastN and concordantly mapping mate pair paired! Compared among subunits Nomenclature and Classification > taxon Record Name > Scientific Name which is covered under Habitat obtained! Was set at a fast rate seed bank size and dormancy characteristics of goosegrass, Eleusine indica ( )! Blastn and designated A–H in wetlands AA genome donor was A.speltoides ( GenBank accession MF616338 with!, Nomenclature and Classification > taxon Record Name > Scientific Name reference genomes... ( figs case ( Sloan et al ) Assam Science Technology and environment Council ; nodes.! Repbase version 20090604 ( Jurka et al general description, with any kind information. Input for mate-pair and paired end reads interaction with dinitroanilines ] Nyporko AIu, Emets AI, Brytsun,! To multiple modes of action Crosthwait J Calixte s Bonen L. Havird JC Whitehill NS Snow Sloan... Reads mapping across the PACMAD clade, and the putative BB genome donor was likely... Large populations, is characteristics of eleusine indica always the case ( Sloan et al across the length of entire... Range of areas including cytonuclear interactions ( Havird et al per plant ), we have undertaken sequencing... Terse information on over 650 species of plants that grow in grassland, including,., roadsides, yards and disturbed areas throughout New England content evolution = 2x characteristics of eleusine indica! About conservation listings when the organism is removed ) model selection limited to GTR-GAMMA and with...

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