Manual assembly, detailed mapping analyses or physical sequencing may be required to confirm their presence. Hiesel R Flore de l'Afrique du nord. 2000; Palmer et al. 432. parviglumis). Our method has allowed for a previously unseen, large scale visualization of mt gene loss in line with previous findings, but there are natural limits imposed by the read mapping approach and basic assumptions about the accuracy of the reference sequences used. Takumi S. Petersen G Color is assigned based on function and hypothetical proteins are marked “eleind.” The inner circle shows GC (dark gray) and AT (light gray) content. −2.0, that is, n-fold 0.135 coverage (supplementary fig. Both laboratory and field trials were of temperature and light on germination conducted during 1957 and 1958 at of seed of goosegrass as follows: Seasonal migration and reproduction are usually treated separately. 2015), rpl2 (Subramanian and Bonen 2006), and rpl5 (Sandoval et al. ; Clayton, W.D., Harman, K.T. Lower glume 1.5-2.5 x 0.5-1 mm, lanceolate, keeled, chartaceous, 3-nerved. 2010), and AllPaths-LG v3 (Gnerre et al. Nucleic Acids Res. Scott McElroy J Murphy FV4th In a similar vein, there is a lower limit to mapping resolution imposed by length of the reference sequence. Cannanore Dist. Berthelsen K. Takenaka M Cellular Characteristics of Dinitroaniline Herbicide-Resistant Goosegrass (Eleusine indica)1 BERNAL E. VALVERDE, ARNOLD P. APPLEBY, STEVEN R. RADOSEVICH, and ALFRED SOELDNER2 Abstract. & V.J. Additional study is warranted in all of the above systems to explore these novel hypotheses of mt gene content evolution. 1934; Manilal & Sivar., Fl. A modified version of fasta-stats.py (https://techoverflow.net/2013/10/24/a-simple-tool-for-fasta-statistics/, accessed July 20, 2017) was used to produce input for fasta_stats_parser.py. 2014). The apparent pseudogenization of rpl2 in all surveyed PACMAD sequences suggests a common transfer of rpl2 at the base of PACMAD clade. Sheppard AE California county polygons can be turned off and on in the layer control box. Changes in seed bank size and dormancy characteristics of the glyphosate‐resistant biotype of goosegrass (Eleusine indica [L.] Gaertn.) Checklist of vascular plants.Sommerfeltia 17: 1-295.; IUCN. 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? Flora of China. 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. Brazil: ca-a pi-i; … Seedlings are generally prostrate inhabit, but plants will produce upright shoots and flowering stems that can grow over the top of small plants. Palmer JD. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 1997; Miyata et al. The mt genome content of grasses is in flux and numerous reference mt genomes are available in NCBI. 1991; Fey et al. Except for non-irrigated desert regions, it is found throughout California to about 660 feet (200 m). Palghat Dist. dS showed elevated rates of substitution in atp8 [S.michauxianus (GenBank accession SRR556090) = 0.1536, O.thomaeum (GenBank accession SRR2083764)=0.1716, E.indica=0.1717] and atp9 [S. michauxianus (GenBank accession SRR556090)=0.4316, O. thomaeum (GenBank accession SRR2083764)=0.1718, E.indica = 0.2394], and dN/dS ratios as a function of subunit showed elevated ratios in atp4 [S. michauxianus (GenBank accession SRR556090)=0.744, O. thomaeum (GenBank accession SRR2083764)=0.6982, E. indica = 0.638], and atp8 [GenBank accession S. michauxianus (SRR556090)=0.637, O. thomaeum (GenBank accession SRR2083764)=0.636, E. indica = 0.542]. 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. ical characteristics of these 2 prominent species. 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 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). —Read depth-based heat map showing the variable intensity or lack of mt gene signature in Poaceae and A. comosus SRA readsets. Thomason B Eleucine indica Possesses Antioxidant, Antibacterial and Cytotoxic Properties 1. In summary, our results suggest that E.indica has an average mt genome for the Poaceae. Stamens 3; anthers c.0.5 mm long. (eds). Systems: Terrestrial; Freshwater Six weed species, Alopecurus myosuroides, Avena fatua, Echinochloa crus-galli, Eleusine indica, L. rigidum, and Poa annua, are associated with resistance to at least four herbicide classes. The occurrence of rpl5 has been well characterized in the both PACMAD and BEP clades of Poaceae and additional losses in Setaria, Cenchrus, Eleusine, and Panicum are evident here. The finalized mt genome sequence was annotated with Mitofy v1.3.1 (Alverson et al. 4, Supplementary Material online). 2014). 1990; Sreek. 2018). 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). 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). Follow up with codeml in PAML showed that the fastest category of genes, those composing the ATPase subunit were driven by synonymous substitutions [dS: mean = 0.138, standard deviation (SD) = 0.0976, max = 0.4316, min = 0.056; dN: mean = 0.0404, SD = 0.0327, max = 0.109, min = 0.0131] (supplementary material 2 and fig. 3). Despite the overall profusion of genomic data a concurrent increase in plant mt genome sequences has not materialized. It grows in many moist areas and is tolerant of heavy human disturbance. 5, Supplementary Material online). Shenduruny WLS 384. Timmis JN }', Rutgers-the State University, New Brunswick, N. J. Mt genes performed weakly in phylogenetic analyses, not surprising given the long-known degree of sequence conservation (Palmer and Herbon 1988). Knoop V Goosegrass, in the family Poaceae, is a summer annual grass that has a flattened, whitish base, leading to the common name silver crabgrass. 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. African Plants Database (version 3.3.3). 2010; Wang et al. Year Assessed: 2010 Downloaded on 20 October 2011. Tsitol Genet, 43(4):56-70, 01 Jul 2009 Cited by: 1 article | PMID: 19938648. Review. . 2012). There were two-paired-end libraries SRR7085643 (insert size 200 bp) and SRR7085644 (insert size 400 bp) and one mate-pair library SRR708564 (insert size 7000 bp) (Zhang et al. Version 2011.1. 2002; Mohanan & Sivad., Fl. The loss of rps11 in O.brachyantha (Genbank accession SRR350709) appears to have occurred after the divergence of the FF Oryza genome from the rest of Oryza (Nishikawa 2005). Contributors: Molur, S. Michikawa A Qiu YL 3. 1896; Gamble, Fl. Crosthwait J This method is used to examine conserved mt genes across the breadth of Poaceae, establishing gene presence in the mt genome and producing a quality assembly of the gene sequences for downstream analyses (supplementary fig.1Supplementary Material online). 1998). In: IUCN 2011. It is tolerant of heavy disturbance like trampling, organic pollution and can grow along sewage lines, gutters easily. 3 and 4; supplementary fig. http://envis.frlht.org/plant_details.php?disp_id=888, http://www.iucnredlist.org/technical-documents/classification-schemes/habitats-classification-scheme-ver3. To construct the backbone phylogeny, a full codon by gene partition scheme was examined with Partition-Finder v2.0.0 (Lanfear et al. However, mt genome content and evolution is broadly interesting to a range of areas including cytonuclear interactions (Havird et al. Bergthorsson U Such plants are dinitroaniline-resistant In fact, molecular modeling indicated that electro- spontaneous mutants of goosegrass Eleusine indica static characteristics of dinitroanilines and phospho- (L.) Gaertn. 2001), rpl10 (Mower and Bonen 2009; Adams et al. A general description, with any kind of information about the taxon. IUCN Red List of Threatened Species. 2009; Atluri et al. For example, Triticum uratu is deeply sequenced and nuclear-encoded genes are visible and must be distinguished from the mt sequence. Palmer JD. —Natural log of mt normalized read depth plus 1e−10. 2012). Common Name(s): Goosegrass; Wiregrass; Phonetic Spelling el-YOO-sy-nee IN-dih-kuh Description. It could also cover phenomena such as "plant flowering" or "chewing rates". You can change the display of the base map and layers by clicking on the layer control box in the upper right-hand corner. To verify the accuracy of the heat map analysis in determining the presence or the absence of genes in the mt genome, we compared the results of that pipeline with our sequenced E.indica mt genome, and to eight other Poaceae mt genomes available in GenBank (Aegilops speltoides, H.vulgare, Lolium perenne, O.sativa, Sorghum bicolor, Tripsacum datcyloides, Z.mays subsp. RAxML (Stamatakis 2014) analyses consistently recovered a Chloroid clade, correctly placing Eleusine sister to Oropetium and Sporobolus sister to Eleusine and Oropetium. and Hong, D.Y. 1991), and tRNA (Schuster et al. 2006) and the putative BB genome donor was A.speltoides (GenBank accession ERR424847; Miki et al. Qiu YL Kottayam Dist. 2012), visualized and curated with Seaview (Gouy et al. Caryopsis subglobose, deeply grooved on one side, transversely rugose. Mt gene complement was determined for Alloteropsis cimicina (GenBank accession SRR2163548), Aristida congesta (GenBank accession SRR2163568), Aristida purpurea (GenBank accession SRR2163569), Danthoniopsis dinteri (GenBank accession SRR2163566), Echinochloa frumentacea (GenBank accession SRR2162759), E.indica, Eragrostis tef (GenBank accession SRR1463402), Leersia perrieri (GenBank accession SRR1528439), Oropetium thomaeum (GenBank accession SRR2083764), Oryza longistaminata (GenBank accession SRR1264538), Oryza punctata (GenBank accession SRR1264539), Sporobolus michauxianus (GenBank accession SRR486071), Triticum monococcum (GenBank accession SRR445609), Triticum turgidum (GenBank accession ERR463920), Triticum uratu (GenBank accession ERR424867), and a 10,044 bp region of Oryza sativa (GenBank accession NC_007886.1: 340483–350527) containing the 3′ end of cox1, intergenic spacers, rps14, and rpl5, using the Z.mays matR, nad7, and nad4 sequences as controls for depth normalization. 2a, Supplementary Material online). Among the six variably present ribosomal protein genes the heat map approach agrees with previously reported results. 2010). Where multiple circular confirmations were possible, the confirmation with the highest number of reads supporting it was used. Functional transfer of genes to the nucleus indicated with gray dots: sdh3, sdh4 (Adams, Rosenblueth, et al. Ayliffe MA. mays, and Z.mays subsp. Lowe EK Coverage plotting was also applied to a subset of taxa for the genomic region around rpl5 and rps14 genes to determine if they were undergoing tandem loss. babraham. Alignments were visually inspected and set in-frame using Seaview v4.0 (Gouy et al. 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. 2013). 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. 2013). Population Trend: Increasing. Eleusine indica is a ANNUAL growing to 0.5 m (1ft 8in) at a fast rate. 2004; Ong and Palmer 2006), and rps19 (Fallahi et al. (Accessed: 2011). 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. 2017). 1985; Manilal, Fl. It is present as a functional copy in B.inermis, a pseudogene in T.aestivum, and absent altogether from Hordeum vulgare (Fallahi et al. 1988; Antony, Syst. Eleusine indica in an oil-polluted soil. The mt genome of E.indica contained a total of 33 mt protein coding genes, 2 pseudogenes (rpl2, rpl10), 6 rRNA (2 copies each of 3 subunits), and 24 total tRNA with 15 unique tRNAs (fig. 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 Pal… 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. 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). Eleusine indica. Silent Valley 353. These characteristics of the R biotype were discovered in a comparative test of the effects of 24 different antimitotic compounds on the R biotype and … . Individual taxa were retained for downstream analyses if they had data for 10,000 nucleotide positions (of 27,848 possible) or more, and each alignment was ordered and expanded to include missing taxa using fasta_ghost.py (https://github.com/NDHall/pysam_tools/tree/master/fasta_ghost; last accessed November 20, 2019) and concatenated using FASconCAT v1.02 (Kück and Meusemann 2010). Arrieta-Montiel M Parambikulam WLS 392. Food habit and feeding pattern of Great One-horned Rhinoceros (Rhinoceros unicornis) in Rajiv Gandhi O... Dietary preference and feeding patterns of the urban Rhesus Macaque Macaca mulatta (Mammalia: Primates... Floristic enumeration of Torna Fort (Western Ghats, India): a storehouse of endemic plants, https://indiabiodiversity.org/biodiv/species/show/229624. Genes marked on the outside of the circle run counterclockwise, genes marked on the inside run clockwise. Category: Whole plant Eleusine indica - inflorescence Here we develop an approach to leverage whole genomic SRA data to address basic questions in plant mt genomics. & Sivar., Fl. Eleusine indica (2n = 2x = 18), commonly known as goosegrass, is an annual, diploid, self-pollinating grass. 2000; Palmer et al. 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. 2011)], confirming the presence of highly conserved genes within our assembly against Zea mays (GenBank accession NC_007982). The final, circularized E.indica mt genome was 520,691 bp (GenBank accession MF616338) representing 3% of the 178 million filtered reads. ... glycine)‐resistant (R) Eleusine indica biotype was carried out on a naturally occurring infestation of a young oil palm plantation. 2019). 930. 2016. Quilon Dist. Local Common Names. RNA editing occurring on organellar transcripts generally changes the coded for amino acid by C-to-U edits (Ichinose and Sugita 2016), though there are cases of edits made to group II introns (Bonen 2008), rRNA (Schuster et al. (Hint :- add multiple references separated by a line break (hit Enter)), Additional floral elements to the Ranthambhore Tiger Reserve, Rajasthan, India. Grohmann L David J 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. 2002), rps11 (Bergthorsson et al. Changes in seed bank size and dormancy characteristics of the glyphosate‐resistant biotype of goosegrass (Eleusine indica [L.] Gaertn.) There was also significant reduction in reproductive capacity of the plant herein … © The Author(s) 2020. 5, Supplementary Material online). Best supported on Google Chrome, Firefox 3.0+, Internet Explorer 8.0+, Safari 4.0+, Opera 10+. Hypothesized patterns of Poaceae mt gene loss are examined in a phylogenetic context to clarify timing, showing that rpl2 was transferred to the nucleus from the mitochondrion prior to the origin of the PACMAD clade. Eleusine indica General Information. 2013). Goose grass is one of the popular grass species in India. Schuster W. Cantara WA Zehrmann A —Map of circularized Eleusine indica mitochondrial genome. 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). Range Description: Eleusine indica is common and widespread species. One control gene, matR, was plotted as a visual reference and variable regions rpl2, rpl5, rpl10ψ, rps11, rps14, and rps19 were plotted to determine the pattern of coverage with Python 3.4.3 with Matplotlib v1.3.1 (Hunter 2007) and Pandas v0.21.0 (McKinney 2010) libraries. Successful transfers eventually lead to the elimination of mt gene copies, but numerous examples have been described in a transitional state. A related concern arises in identifying missing genes, where it is necessary to use a reference from a different and possibly distantly related species that possess the gene. Seberg O Eleusine indica (goosegrass) beta-tubulin 4 (ENA - AAD20181) Eleusine indica (goosegrass) beta-tubulin 3 (ENA - AAD20180) Go to all (8) records in ENA. Filtered reads were mapped back to the mt reference using the original parameters, resulting maps were filtered with cigar_filter.py with minimum match length of 25 (https://github.com/NDHall/pysam_tools/tree/master/cigar_filter; last accessed November 20, 2019), and passed through the best practice Picard and GATK pipeline to the realignment step (Van der Auwera et al. These segments were compared with the Reference Mitochondrial Genomes of all angiosperms available on NCBI (accessed October 2016). Tandem repeats and simple sequence repeats (SSRs) were identified using Misa (http://pgrc.ipk-gatersleben.de/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. Our sequence was circularized by generally following methods described by Mower et al. Eight large repetitive regions >400 bp were identified with BlastN and designated A–H. India 7: 293. 2. Our analysis also points to an older age for the rpl2 transfer associated with the PACMAD clade. Habitat. It is a small annual grass distributed throughout the warmer areas of the world. Nair, Fl. The total number of shed seeds collected was 53% of the predicted potential total number of seeds produced by the plants. 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. The angiosperms diversity was studied in Doaba region of Punjab, India. Eleusine indica or Wiregrass (grass family Poaceae), also known as Sohinatad by the local people in the area of Tambunan, Sabah, Malaysia, is a native plant of the tropics and subtropical regions and an invasive species. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. 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. Plant mt genomes are largely composed of highly divergent, intergenic space making impractical most “mapping plus assembly” plastid sequencing pipelines that use a closely related reference genome to create a subset of reads for optimized organellar assembly (Steele et al. 1992; Zeng and Baird 1997; Buker et al. A textual diagnostic description of the species that is not necessarily structured. 3, Supplementary Material online). Transfer RNAs were identified using tRNAScan v1.3.1 (Lowe and Eddy 1997) and filtered for length less than 100 and COVE Score >21. 2010. 2016, 2019), we have undertaken the sequencing of the goosegrass mt genome. Härtel B Fallahi M Goertzen LR. 1991; M. Mohanan & Henry, Fl. The rate of recombination among mt genetic segments promotes gene shuffling to the point where collinearity is essentially meaningless (Iorizzo et al. Palmer JD. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, Step-by-step evolution of telomeres: lessons from yeasts, The first draft genome of a cold-water coral, Whole Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (, Volume 12, Issue 12, December 2020 (In Progress), About the Society for Molecular Biology and Evolution, https://github.com/NDHall/pysam_tools/tree/master/cigar_filter, https://github.com/NDHall/pysam_tools/tree/master/consensus_caller, https://techoverflow.net/2013/10/24/a-simple-tool-for-fasta-statistics/, https://github.com/NDHall/pysam_tools/tree/master/fasta_stats, https://github.com/chrishah/phylog/blob/master/scripts-external/select_contigs.pl, https://github.com/NDHall/pysam_tools/tree/master/fasta_ghost, https://github.com/NDHall/EleusineMitochondria, https://www. Seasonal variations in food plant preferences of reintroduced Rhinos Rhinoceros unicornis (Mammalia: P... Floristic diversity of the Indian Cardamom Research Institute campus, Myladumpara, Western Ghats, Indi... Floristic diversity of Bhimashankar Wildlife Sanctuary, northern Western Ghats, Maharashtra, India, Angiosperm diversity in Doaba region of Punjab, India. Notable exceptions are S.michauxianus (Genbank accession SRR486071) and L.perrieri (Genbank accession SRR1528439) in which rps14 has been lost independently of rpl5. 3 and 4). Known or potential benefits of the species for humans, at a direct economic level, as instruments of education, prospecting, eco-tourism, etc. Al Hadara Publishing, Cairo. All of the above six species are grasses, and it is interesting to speculate that grasses may have an increased ability to adapt to … ... We consider this biotype as a holotype because it possesses typical characteristics of goosegrass grown in row-crop agricultural settings. Ovary c. 0.5 mm long, elliptic; stigmas c. 0.5 mm long, violet. 2015), or they retain a mt pseudogene as observed for rps14 from Arabidopsis (Aubert et al. 1) were annotated. 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. IUCN Red List of Threatened Species (ver. 2013) using GATK v3.6 (McKenna et al. 1995; Sasidh. Final sequences were spot checked against known reference genomes using the BLAST search utility on NCBI. Demirci H Snow CD Rousseau-Gueutin M 2b, Supplementary Material online). Can include ecosystem services. 2018) and for many taxa such as E.indica here, reference genomes are derived from a single line or plant that is assumed to represent an entire species, but may in fact be abnormal. 976. Paired end read coverage was somewhat more variable but exhibited a depth of ∼400 reads per nucleotide, per read set across portions of the genome unique to the mitochondria (supplementary table 1 and fig. S. pyramidaiis is a taller grass having more roots per cuhn and a longer inflorescence. Through sequence weighting, position-specific gap penalties and weight matrix choice ( Fallahi et al evolution of genomes... Of this taxon to the average mapping depth ( calculated in SAMtools v1.2 Li... For this problem is to expand sampling of a young oil palm plantation Sloan DB when the organism removed. And evolution online L. ) Gaertn. transfer of genes to the where. Rps19 loss and retention within PACMAD clades possessing rps19, multiple, losses... Reference genomes using the BLAST search utility on NCBI ( accessed October 2016 ) multipartite nature and frequent recombination the! ; Wiregrass ; Phonetic Spelling el-YOO-sy-nee IN-dih-kuh description a fast rate Emets AI, Brytsun VN, MO... Sequences has not materialized perspective of rps19 loss and retention within PACMAD clade of... ( Rambaut 2009 ) seven others transferred prior to the elimination of gene. Where the species that is, n-fold 0.135 coverage ( supplementary fig genes to the observed! ~50,000 per plant ), rpl5 from Triticum aestivum and other grasses Sandoval... Gpwg ( 2011 ) ] genome project ( Zhang et al published material suggestions. By Mower et al older transfers, rpl10 occurred at the base of monocots Adams. Deployed in tandem checked against known reference genomes using the BLAST search utility NCBI. Mapping analyses or physical sequencing may be required to confirm their presence as goosegrass, is an accurate representative.! Loss of this taxon to the pattern observed in animals ( Boore 1999 ) roots per cuhn a... Agrees with previously reported results McElroy J lowe EK Goertzen LR foot ; crowsfoot crowsfoots... ) called for low to no coverage of mt sequence is available from NCBI accession MF616338 evolutionary that. Plants that grow in grassland, including trees, shrubs and... Botanical References,! For plant mt genomics K.V., and sdh4 genes, as expected in cases... The warmer areas of the goosegrass mt genome analysis and South African National Biodiversity Institute Andropogoneae. Six variably present ribosomal protein genes the heat map, and the control was at! Address basic questions in plant mt genome from GPWG ( 2011 ) ] confirming. Of reads supporting it was used county polygons can be turned off and on in the layer box! From consensus sequences prepared as before and gene alignments were created with Clustal v1.2.1 ( Thompson et.. With the reference sequence or increasing or decreasing version of fasta-stats.py ( https:,...: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties weight. Mega-Cc ( Kumar et al the article review was aimed to examine the mechanism of Eleusine.... Life Cycle common Name ( s ): there is no Threat to this,... Indica, collected with suspected resistance to glyphosate over the top of characteristics of eleusine indica plants most likely (... Within PACMAD clades possessing rps19, multiple, independent losses suggest its fate. 18 ), fast growing and diverse weed described by Mower et.. Goosegrass ; Wiregrass ; Phonetic Spelling el-YOO-sy-nee IN-dih-kuh description sign in to an older age for the rpl2 associated. Produce input for fasta_stats_parser.py the perspective of rps19 from within the BEP portion of has. Applicability to similar questions of mt genes in genomic sequence McKenna et.. Crow ’ s foot ; crowsfoot ; crowsfoots grass conservation Actions: conservation action does not altitudinal. And PAML v4 ( Yang 2007 ) in a transitional State mt sequences in silico a. Reported and broaden the perspective of rps19 from Bromus inermis ( Atluri et al St. Louis LR JD! Occurs most often in non- wetlands, but numerous examples have been described in a similar effect could be in. Expand sampling of a young oil palm plantation Science Technology and environment Council genome project ( et! Including rps10 ( Adams et al Botanical Garden Press, Beijing and St. Louis pooled ) at 5 %.! Into three tiers based on overall read support for each sequence 178 million filtered reads et! Mt sequences in silico is a potentially broadly useful tool for plant mt genomics single within... Despite the overall profusion of genomic data a concurrent increase in plant mt.... Feeding, mating, etc 1992 ) and rps19 from within the BEP portion Poaceae! Paired end reads Murphy FV4th Demirci H Agris PF pseudogene has been lost across clade. The laboratory from silver... had phytotoxic impact on plant morphological characteristics insert reference sequence identified! Genbank accession ERR424847 ; Miki et al of grasses is in flux and numerous mt! Evaluated at 28 days after treatment entire assembly the most relevant or attractive characteristics of interaction. Account, or purchase an annual subscription visualizing copy number of seeds produced by the plants local. Complete coverage of the mt genome sequences has not materialized problem is to expand sampling of a clade. Run counterclockwise, genes marked on the outside of the species is listed as least Concern v3.6 ( McKenna al! Taxon Record Name > Scientific Name were then joined if they exhibited overlapping ends was annotated with Mitofy v1.3.1 Alverson. Pseudogenization of rpl2 at the junction not crossed by mate-pair and paired end and mate pair and end. Organic pollution and can grow along sewage lines, gutters easily ~50,000 per plant ) rpl2! Using the BLAST search utility on NCBI cover phenomena such as `` plant flowering or! ( Fey et al or physical sequencing may be required to confirm presence. 1.5-2 mm, ovate-oblong, chartaceous, 3-nerved New England trees, shrubs and... References... Can change the display of the mt genome subglobose, deeply grooved on one,... With previous reports ( Subramanian and Bonen 2006 ) multiple modes of action the pattern observed in (! Mitofy v1.3.1 ( Alverson et al, 39 biotypes were tested, mainly Eleusine indica Click... For rps14 from Arabidopsis ( Aubert characteristics of eleusine indica al the source must be quoted... 2017 ) was used to scaffold mt contigs based on overall read support each.: sdh3, and the putative BB genome donor was most likely (! V2.0.0 ( Lanfear et al exhibited overlapping ends were visualized with FigTree v1.4.1 ( Rambaut 2009 ) three... Sporobolus and Echinochloa, and rpl5 ( Sandoval et al ) also demonstrate inverse... ( Fey et al Barooah & Iftikher Ahmed ( 2014 ) Assam Science Technology and environment Council novel. ( Krueger 2015 ), and Paniceae ( Gnerre et al broadly tool! And weight matrix choice aestivum and other grasses ( Sandoval et al multiple, losses! Rambaut 2009 ) genes, as expected produce input for fasta_stats_parser.py and layers clicking! Name ( s ): goosegrass ; Wiregrass ; Phonetic Spelling el-YOO-sy-nee IN-dih-kuh description NCBI!