Finally, these data provide deeper insight into the functional transfers of rpl2 within the PACMAD clade. This allowed us to include genes with sparse coverage that would not have assembled using a short read assembler. A modified version of (, accessed July 20, 2017) was used to produce input for The resulting heat map shows diverse patterns of lineage-specific loss over time in grasses. T. S. CHUAH. BY JAMES R. FULWIDER AND RALPH E. ENGEL Former Research Assistant and Research Specialist in Turf Management, respective!. Our results concur with those previously reported and broaden the perspective of rps19 loss and retention within PACMAD clade. The uptake of foreign DNA by mt is facilitated by the permeability transition pore complex, which shows little, if any, discrimination in the DNA fragments it will import (Koulintchenko et al. babraham. 1992; Zeng and Baird 1997; Buker et al. D K Ved, Suma Tagadur Sureshchandra, Vijay Barve, Vijay Srinivas, Sathya Sangeetha, K. Ravikumar, Kartikeyan R., Vaibhav Kulkarni, Ajith S. Kumar, S.N. 2011. 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. 2015). Caryopsis length ranges from 1.0-1.5 mm. Methods. 2004), rps14 (Sandoval et al. 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. Contig assemblies were validated by support of mate-pair reads mapping across the length of the entire assembly. FRLHT's ENVIS Centre on Medicinal Plants, Bengaluru. Lemmas 2-3 x 1.5-2 mm, ovate-oblong, chartaceous, 3-nerved, sub acute. Stecher G 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. (Accessed: 2011). 2015). The root structure of Eleusine indica was not significantly affected by crude oil. Pres. 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). 2013) using GATK v3.6 (McKenna et al. 5, Supplementary Material online). The rpl10 pseudogene is present in Aristida yet absent throughout the rest of the PACMAD clade samples, suggesting that it was lost subsequent to the divergence of Aristida from all other PACMAD taxa. Brennicke A Pretoria Available at: Thomason B Science Press and Missouri Botanical Garden Press, Beijing and St. Louis. Local Common Names. 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. The AA genome donor was most likely T.uratu (Petersen et al. 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). Yde M —Natural log of mt normalized read depth plus 1e−10. Weed Biol Manag 4:114–121 Google Scholar 2 and 3; supplementary fig. 1996; Sasidh., Fl. Eleusine indica (2n = 2x = 18), commonly known as goosegrass, is an annual, diploid, self-pollinating grass. Systems: Terrestrial; Freshwater David J 2012). Coverage depth plots of rps19 across the PACMAD clade suggest only Andropogoneae, Arundinelleae, and Paspaleae have experienced widespread loss of this gene. | 2016, 2019), we have undertaken the sequencing of the goosegrass mt genome. 4). 28 Several other species have developed resistance to at least three classes. 2005; Atluri et al. 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. Grohmann L 2015), rpl2 (Subramanian and Bonen 2006), and rpl5 (Sandoval et al. Read mapping allows the highly sensitive detection of gene presence but is an unreliable indicator of gene absence in organisms with low mt genomic coverage—often key species most needed to fill in gaps in our understanding. Habitat and Ecology: It grows in moist as well as marshy areas, puddles, shallow ponds, fields, river and stream edges, ditches, canals etc. Goosegrass is normally found in compacted areas or areas of heavy wear; it inhabits agricultural land … Seed Characteristics and Control of Goosegrass, Eleusine indica. In the first experiment, 39 biotypes were tested, mainly Eleusine indica , collected with suspected resistance to glyphosate. Flore de l'Afrique du nord. Mitochondrial translation in green plants uses the universal genetic code, allowing for the ongoing transfer and viability of mt genes in the nucleus. 2011)], confirming the presence of highly conserved genes within our assembly against Zea mays (GenBank accession NC_007982). Okada M Ayliffe MA. Palmer JD. There is considerable variability in the content and conformation of mitochondrial (mt) genomes across Eukaryotes; within plants, mt genome evolution is particularly striking in light of ongoing gene transfer (Palmer and Herbon 1988; Adams et al. Alappuzha Dist. Primary root cells from five dinitroaniline- resistant (R) and three susceptible (S) goosegrass biotypes from North Carolina and South Carolina were observed Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 4). (Poaceae - Chloridoideae)] genome project (Zhang et al. 513. Qiu YL List of Habitats: 4, 4.6, 4.7, 5, 5.2, 5.4, 5.5, 5.6, 5.7, 5.8, 15, 15.6, 15.7, 15.8, 15.9, Open plain areas, roadsides and wastelands. Our analysis also points to an older age for the rpl2 transfer associated with the PACMAD clade. Recombination among subgenomic segments paired with stabilizing selection results in extremely low rates of substitution along with the continual rearrangement observed within plant mt (Palmer and Herbon 1988; Christensen 2014; Gualberto et al. Available at:; Conservatoire et Jardin botaniques de la Villle de Genève and South African National Biodiversity Institute. Top soil was polluted with spent lubricating oil (obtained as pooled) at 5% w/w. with a modified a -tubulin subunit [9, 10] rothioamidates were remarkably similar, and this could and specially produced mutants of Nicotiana plum- determine the similarity of their … Enumerates geographic entities where the taxon lives. Boulos, L. 2005. Year Assessed: 2010 Work by Straub et al. (Hint :- add multiple references separated by a line break (hit Enter)), Additional floral elements to the Ranthambhore Tiger Reserve, Rajasthan, India. Although this seems to generally be the case, there are instances such as in cytoplasmic male sterile lines where mt subgenomic stoichiometry is not constant, and could conceivably change the mt normalization value (Janska et al. ; Wu, Z.Y., Raven, P.H. ... We consider this biotype as a holotype because it possesses typical characteristics of goosegrass grown in row-crop agricultural settings. 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). Codeml was run for chloroid sets with free rates, ambiguous sites removed, a starting κ of 2.0 and a starting ω of 0.4 (supplementary material 1, Supplementary Material online). Supplementary data are available at Genome Biology and Evolution online. Oxford University Press is a department of the University of Oxford. 1934; Manilal & Sivar., Fl. 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). Brazil: ca-a pi-i; … Introduction. Available at: pp. Brennicke A. Thompson JD, Higgins DG, Gibson TJ. Exported on 12 January 2012, State - Kerala, District/s: All Districts, India: Assam, Madhya Pradesh, Punjab; Africa, Ayurveda, Siddha, Traditional chinese medicine, | Parambikulam WLS 392. Eleusine indica is a ANNUAL growing to 0.5 m (1ft 8in) at a fast rate. Specific root length (SRL), surface area, volume and average root diameter (ARD) of plants grown in crude oil-contaminated and uncontaminated soil were compared. The transfer of mt genes to the nucleus is ongoing in plants and requires multiple steps including the fixation of any RNA edits and the acquisition of promoter sequence (Wu et al. In a similar vein, there is a lower limit to mapping resolution imposed by length of the reference sequence. Citation: Watve, A. Silent Valley 353. Thiruvanthapuram 538. 538. 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. Known or potential benefits of the species for humans, at a direct economic level, as instruments of education, prospecting, eco-tourism, etc. Goosegrass is an exotic grass of fields, roadsides, yards and disturbed areas throughout New England. It is tolerant of heavy disturbance like trampling, organic pollution and can grow along sewage lines, gutters easily. Known Hazards. 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. Covers ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. A dinitroaniline-resistant (R) biotype of Eleusine indica (L.) Gaertner. Physical Characteristics. All of the above six species are grasses, and it is interesting to speculate that grasses may have an increased ability to adapt to … Chuah TS, Salmijah S, Teng YT, Ismail BS (2004) Changes in seed bank size and dormancy characteristics of the glyphosate-resistant biotype of goosegrass (Eleusine indica [L.] Gaertn.). Thenmala Div. The progressive loss of a mt sequence may vary dramatically for any given gene; for example, rps19 was transferred in the common ancestor of Poaceae, yet its current distribution and function within grass mitochondria is variable. First tier (+) genes possess sufficient depth of coverage to assemble an intact reading frame. 1993; Adams and Palmer 2003; Bonen 2006). ; Clayton, W.D., Harman, K.T. Identify a weed; List of all weeds; Key to weeds in turf; Goosegrass, also called wiregrass, is an annual summer grass and occasionally, a perennial. Sequencing of the three DNA libraries, SRR7085643, SRR7085644, and SRR7085644, yielded 202 million reads, reduced to 178 million after filtering and quality control (supplementary table 1, Supplementary Material online). Seasonal migration and reproduction are usually treated separately. Both laboratory and field trials were of temperature and light on germination conducted during 1957 and 1958 at of seed of goosegrass as follows: parviglumis). 2010). 2019). Gaertn.) 2004), rps14 (Sandoval et al. In contrast, several genes (rps10, sdh3, and sdh4) are absent from all Poaceae species, indicating that they were lost prior to the origin of grasses. To construct the backbone phylogeny, a full codon by gene partition scheme was examined with Partition-Finder v2.0.0 (Lanfear et al. However, benefits to ecosystems not specific to humans are best treated under Risk statement (what happens when the organism is removed). Final assembly was verified by visually confirming a uniform mapping depth of reads mapping across the reference using Bowtie 2 (Langmead and Salzberg 2012). ac. C–U edits were counted for coding regions by tallying all C–T variants within mt CDS sequences, and for noncoding regions, C–U edits were tallied C–T or T–C variants on the mt genome after the exclusion of coding region using vcftools v0.1.14-14 (Danecek et al. The development of herbicide resistant ecotypes has occurred to multiple modes of action. In the case of the chloroidoid grasses examined here, increased rates involve increased neutral substitutions as described and elsewhere and no species exhibited particularly high rates of substitution (Cui et al. 2016. ); 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. Best supported on Google Chrome, Firefox 3.0+, Internet Explorer 8.0+, Safari 4.0+, Opera 10+. 3, Supplementary Material online). 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. Nilambur 824. Assessor/s: Watve, A. 572. Genes marked on the outside of the circle run counterclockwise, genes marked on the inside run clockwise. and Williamson, H. 2006 onwards. 469. 1994. (eds). Although, foreign DNA is typically nonfunctional (Mower et al. It includes published material or suggestions from the author or others. Shenduruny WLS 384. 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. Agris PF. 1988; Antony, Syst. Palmer JD. 2014). 2004) and rps19 from Bromus inermis (Atluri et al. Al Hadara Publishing, Cairo. Palghat Dist. other, a dose-response curve experiment, as well as a study of the botanical characteristics of the species. The multipartite nature and frequent recombination of the mt genome likely promotes its incorporation and preservation (Rice et al. It appears that the rps14 and rpl5 were lost from T. uratu prior to the hybrid formation of T. turgidum because these genes are also missing from T. monococcum (GenBank accession SRR445609), sister to T. uratu (Michikawa et al. We wanted to explore the utility of assembled sequences for informing a reference phylogeny and examining mt genome rate variation within the chloroidoid clade that contains Eleusine. RNA editing has been extensively reviewed (Fey et al. RAxML (Stamatakis 2014) analyses consistently recovered a Chloroid clade, correctly placing Eleusine sister to Oropetium and Sporobolus sister to Eleusine and Oropetium. 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. Brit. 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. This transfer has halted in metazoans owing to a shift in codon usage that occurred 600 Ma, with their mt genome content relatively fixed as a result (Boore 1999; Adams and Palmer 2003; Cantara et al. Characterization of complete mt genomes is, presumably, the best way to assess mt gene loss, but in the absence of fully assembled genomes mt gene content is commonly inferred through Southern blot analyses (Palmer et al. Habitat and Ecology: It grows in moist as well as marshy areas, puddles, shallow ponds, fields, river and stream edges, ditches, canals etc. The apparent pseudogenization of rpl2 in all surveyed PACMAD sequences suggests a common transfer of rpl2 at the base of PACMAD clade. 2000; Palmer et al. Sequences were taken from consensus sequences prepared as before and gene alignments were created with codon aware Mega-cc (Kumar et al. 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. Malappuram Dist. (2012) also demonstrate an inverse relationship between the rate of recombination and the rate of substitution. Manual assembly, detailed mapping analyses or physical sequencing may be required to confirm their presence. Common Name(s): Goosegrass; Wiregrass; Phonetic Spelling el-YOO-sy-nee IN-dih-kuh Description. Alignments are available from 1997; Sivar. 2002). © The Author(s) 2020. Schuster W. Cantara WA It could also cover phenomena such as "plant flowering" or "chewing rates". 2011.1)., Describes the likelihood of the species becoming extinct in the present day or in the near future. Mt genes performed weakly in phylogenetic analyses, not surprising given the long-known degree of sequence conservation (Palmer and Herbon 1988). 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. Scoring ranges from absent (black) to ultrahigh-coverage (light yellow or white), with loci lacking 50% coverage >5 automatically scored as absent. Whitehill NS 2009. The loss of rps14 in the context of its ancestral spatial relationship relative to rpl5 provides further insight into the rate and scale of sequence loss within plant mt genomes. 4, Supplementary Material online). Justification: Eleusine indica is common and widespread species. 1985; Manilal, Fl. Notable exceptions are S.michauxianus (Genbank accession SRR486071) and L.perrieri (Genbank accession SRR1528439) in which rps14 has been lost independently of rpl5. Michikawa A However, a similar effect could be achieved in three stages. Of the seven older transfers, rpl10 occurred at the base of monocots (Adams et al. Considering this, the species is listed as Least Concern. Two other pseudogenized sequences, rps11 and rpl10, are sparsely reported on within Poaceae but also provide insight into the heterogeneous loss of mt sequence. Coverage plots for a subset of genes was constructed with the n-fold + 1e−5 mt depth transformed with the natural log and plotted across the length of the gene. Eleusine indica General Information. 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. Input for conservation action does not include altitudinal distribution, which is covered under Habitat adventitious,... 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