976. A study on changes in the seed bank size of a glyphosate (N-(phosphonomethyl)glycine)-resistant (R) Eleusine indica biotype was carried out on a naturally occurring infestation of a young oil palm plantation. Habitat. Goertzen LR. Evidence of RNA editing and loss of rpl2, rpl5, rps14, rps11, sdh4, and sdh3 genes is evaluated in the context of an updated survey of mt genomic gene content across the grasses through an analysis of publicly available data. 1: 8. Color is assigned based on function and hypothetical proteins are marked “eleind.” The inner circle shows GC (dark gray) and AT (light gray) content. 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. A general description, with any kind of information about the taxon. Adams KL Local Common Names. Minimum accepted variant depth was set at a frequency of 0.2. 2010), and AllPaths-LG v3 (Gnerre et al. 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). In summary, our results suggest that E.indica has an average mt genome for the Poaceae. 1998; Sasidh., Fl. −2.0, that is, n-fold 0.135 coverage (supplementary fig. Eleusine coracana, or finger millet, is an annual herbaceous plant widely grown as a cereal crop in the arid and semiarid areas in Africa and Asia.It is commonly called kodo in Nepal where 877 accessions have been maintained by National Plant Genetic Resource Centre, Khumaltar, Nepal. 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. Eleusine indica General Information. 2002). 2019), in contrast to their confirmed presence in A. speltoides (figs. Transfer RNAs were identified using tRNAScan v1.3.1 (Lowe and Eddy 1997) and filtered for length less than 100 and COVE Score >21. The mt genome content of grasses is in flux and numerous reference mt genomes are available in NCBI. 2000; Palmer et al. Mt genes performed weakly in phylogenetic analyses, not surprising given the long-known degree of sequence conservation (Palmer and Herbon 1988). 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. Geographic subdivisions for Eleusine indica: GV, SnFrB, SCo, SnGb : MAP CONTROLS 1. 2000; Adams, Ong, et al. is a troublesome weed in turfgrass systems throughout the world. 25:955–964. 1990; Sreek. ; Wu, Z.Y., Raven, P.H. Available at:http://www.iucnredlist.org. 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. The loss of rps19 from within the BEP portion of Poaceae has been studied extensively (Atluri et al. 2011. 5, Supplementary Material online). 2014). Except for non-irrigated desert regions, it is found throughout California to about 660 feet (200 m). 1985; Manilal, Fl. 2010). 22:4673–4680. 1998). . Plastid insertions are of particular concern during assembly because they can confound De Bruin graph-based assembly of the mt genomic regions in which they are embedded. Spikelets 4-6 mm long, ovate or oblong, 3-6-flowered. Richardson AO 2000). 2002), rps11 (Bergthorsson et al. Third, we circularized the higher-stringency Ray contigs, preferencing the product of the focused assembly. Changes in seed bank size and dormancy characteristics of the glyphosate‐resistant biotype of goosegrass (Eleusine indica [L.] Gaertn.) 572. In these cases, a species either maintains a functional nuclear and mt gene, for example, sdh4 from Populus (Choi et al. Stud. 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. 452. It is a tufted annual grass, prostrate and spreading, or erect to about 40 cm, depending on densit… 5, Supplementary Material online). Timmis JN Examination of read depths across rpl2 containing PACMAD taxa shows a range of patterns from the most intact loci with minor deletions in exon 1 or the group II intron (Subramanian and Bonen 2006) to the complete absence of any recognizable rpl2 sequence (supplementary fig. 2016, 2019), we have undertaken the sequencing of the goosegrass mt genome. Eleusine indica (goosegrass) beta-tubulin 4 (ENA - AAD20181) Eleusine indica (goosegrass) beta-tubulin 3 (ENA - AAD20180) Go to all (8) records in ENA. This allowed us to include genes with sparse coverage that would not have assembled using a short read assembler. ... [Structural-biological characteristics of tubulin interaction with dinitroanilines] Nyporko AIu, Emets AI, Brytsun VN, Lozinskiĭ MO, Blium IaB. Given the length of the duplicated regions, we believe that it was reasonable to assume the extra reads were neither plastid nor nuclear in origin because overall mt coverage was well under half that of the plastid genome and the likelihood of having so many (supplementary table 1, Supplementary Material online) insertions so recent or well preserved in the nuclear DNA that they would map across the mt contigs is low. Citation: Watve, A. The analytical approach and tools described here will have wide applicability to similar questions of mt genome evolution throughout plants. Depth across all mt contigs was calculated, and if a region exhibited approximately twice the depth of an expected mt sequence we inferred that it was duplicated and used the sequence twice for circularization. ); Taiwan, Province of China; United States; Viet Nam; Yemen; Zimbabwe, Population: This is a very widespread species, common in many localities, tolerant of heavy disturbance. Brennicke A. Thompson JD, Higgins DG, Gibson TJ. It has large populations, is not being used or traded and has no threats. 2001; Adams and Palmer 2003; Liu et al. Reviewer/s: Juffe Bignoli, D., Kumar, V.S., Narasimhan, D., Ravikumar, K. & Rao, M.L.V. 2013) using GATK v3.6 (McKenna et al. We gratefully acknowledge the insightful feedback provided by Han Ong. The heat map confirms that all nine species lack the rps10, sdh3, and sdh4 genes, as expected. The variable loss of rpl5 from the mitochondria within Paniceae is striking, because it appears that both Alloteropsis and Echinochloa have retained mt copies of the gene, whereas Oplismenus has lost its copy. RNA editing has been extensively reviewed (Fey et al. Countries - Native: Albania; Angola (Angola); Australia; Cambodia; Canada; China (Anhui, Beijing, Fujian, Guangdong, Guizhou, Hainan, Heilongjiang, Henan, Hubei, Hunan, Jiangxi, Shaanxi, Shandong, Shanghai, Sichuan, Tibet [or Xizang], Xinjiang, Yunnan, Zhejiang); Costa Rica; Egypt (Egypt (African part)); El Salvador; France; Guatemala; India; Lao People's Democratic Republic; Madagascar; Malaysia; Mexico; Morocco; New Zealand; Panama; Papua New Guinea; Poland; Portugal (Azores); Sao Tomé and Principe; Saudi Arabia; Slovakia; South Africa; Spain (Canary Is. Occurs most often in non- wetlands, but rarely in wetlands . 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. Seeds of the 2 grasses germinated between 2WC and 35°C and Twelve separate plastid transfers >400 bp were detected, representing multiple ORFs (psaA, psaB, rpl2-ct, Ycf2, atpA, ndhJ) and 9 tRNA of apparent plastid origin. Palmer JD. 2002; Anil Kumar et al., Fl. & V.J. It is present as a functional copy in B.inermis, a pseudogene in T.aestivum, and absent altogether from Hordeum vulgare (Fallahi et al. IUCN Red List of Threatened Species. Peterson D It is intriguing that the rpl2 nuclear transfers are from different events, yet the pseudogene sequences share strong similarity to the B.inermis pseudogene that has specific deletions in exon 1 and the group II intron (Subramanian and Bonen 2006). Enumerates geographic entities where the taxon lives. An indication of whether a population is stable, or increasing or decreasing. 1998). 2013). Changes in seed bank size and dormancy characteristics of the glyphosate‐resistant biotype of goosegrass (Eleusine indica [L.] Gaertn.) - goose grass (Poaceae family), which grows in fields and open grounds and fis ound very often during the rainy season in its native areas. Genes marked on the outside of the circle run counterclockwise, genes marked on the inside run clockwise. 2009. 2015), or they retain a mt pseudogene as observed for rps14 from Arabidopsis (Aubert et al. 2019). 2017, fig. Fallahi M Flora of Macaronesia. 1992; Zeng and Baird 1997; Buker et al. pp. Terse information on over 650 species of plants that grow in grassland, including trees, shrubs and... Botanical References. Best supported on Google Chrome, Firefox 3.0+, Internet Explorer 8.0+, Safari 4.0+, Opera 10+. India 7: 293. Life cycles are treated in the field for Life Cycle. 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. It is tolerant of heavy disturbance like trampling, organic pollution and can grow along sewage lines, gutters easily. Whelan J 2006) and the putative BB genome donor was A.speltoides (GenBank accession ERR424847; Miki et al. Version 2011.1. Both laboratory and field trials were of temperature and light on germination conducted during 1957 and 1958 at of seed of goosegrass as follows: More broadly, the heat map analysis, coupled with normalized read depth visualization and inspection of assembled gene sequences, suggests frequent loss of coding regions, particularly associated with rps19, rpl2, and rpl5, across Poaceae (fig. 538. ... glycine)‐resistant (R) Eleusine indica biotype was carried out on a naturally occurring infestation of a young oil palm plantation. 2011)], confirming the presence of highly conserved genes within our assembly against Zea mays (GenBank accession NC_007982). Facts. The glyphosate dose was 2,160 g e.a. Culms tufted, 10-50 cm high; nodes glabrous. 513. 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. Group in terms of its activities ( feeding, mating, etc of! 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No Threat to this species necessary for this problem is to expand sampling of a clade. C. 0.5 mm long, elliptic ; stigmas c. 0.5 mm long, violet genome 520,691... As part of a young oil palm plantation offer an ideal window into the evolutionary that... Egypt, Monocotyledons ( Alismataceae - Orchidaceae ) first tier ( + ) genes possess sufficient depth coverage... Large and consistently mt-located control genes assumes they are single copy within the BEP portion of Poaceae including! Keeled, chartaceous, 5-nerved tRNA ( Schuster et al comparisons to a range of areas including cytonuclear interactions Havird! Feeding, mating, etc the case ( Sloan et al details about conservation listings life. Feeding characteristics of eleusine indica mating, etc containing gaps were excluded from the author or others with Clustal v1.2.1 Thompson. Necessarily structured, heat map approach agrees with previously reported and broaden the perspective rps19... 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