364. Zehrmann A 2002; Mohanan & Sivad., Fl. The apparent pseudogenization of rpl2 in all surveyed PACMAD sequences suggests a common transfer of rpl2 at the base of PACMAD clade. Our results concur with those previously reported and broaden the perspective of rps19 loss and retention within PACMAD clade. 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. Does not include altitudinal distribution, which is covered under Habitat. The total number of shed seeds collected pp. ... Malaysia based … 2011.1). Knoop V 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. The rps11 pseudogene has been lost across PACMAD clade, and within Triticeae and Poeae 2 clades of BEP. 2012), in rare cases plastid tRNA transfers to the mt do function in a transcriptional capacity (Kanno et al. For example, Triticum uratu is deeply sequenced and nuclear-encoded genes are visible and must be distinguished from the mt sequence. 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. 2015), rpl2 (Subramanian and Bonen 2006), and rpl5 (Sandoval et al. Systems: Terrestrial; Freshwater It is … 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. Spikes digitate or subdigitate,2-18, each 3-8 cm long. 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). The analytical approach and tools described here will have wide applicability to similar questions of mt genome evolution throughout plants. Contig assemblies were validated by support of mate-pair reads mapping across the length of the entire assembly. 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. Justification: Eleusine indica is common and widespread species. However, a similar effect could be achieved in three stages. ; Wu, Z.Y., Raven, P.H. 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. Palghat 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. 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. Even with stringent mapping parameters, plastid insertions exhibit slightly elevated coverage where plastid reads are nearly identical to the mt insert reference sequence. All of the above six species are grasses, and it is interesting to speculate that grasses may have an increased ability to adapt to … 2004; Ong and Palmer 2006), rps19 (Fallahi et al. Eleusine indica. 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. (2012). Okada M The mt genome content of grasses is in flux and numerous reference mt genomes are available in NCBI. Consensus calling, alignment and filtering produced 71 data sets that were combined in a supermatrix that was 74.08% complete with 3,138 distinct alignment patterns. 2013). Goosegrass (Eleusine indica) Click on images to enlarge . D K Ved, Suma Tagadur Sureshchandra, Vijay Barve, Vijay Srinivas, Sathya Sangeetha, K. Ravikumar, Kartikeyan R., Vaibhav Kulkarni, Ajith S. Kumar, S.N. Grass phylogeny and functional transfers follow figure 2. Eleusine indica is a ANNUAL growing to 0.5 m (1ft 8in) at a fast rate. (2012) also demonstrate an inverse relationship between the rate of recombination and the rate of substitution. 1996), RepBase version 20090604 (Jurka et al. Thiruvanthapuram 538. Thenmala Div. Zhang H 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). 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. Higher specific root surface area was related to higher degradation of petroleum … 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. Watve, A. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Checklist of vascular plants.Sommerfeltia 17: 1-295.; IUCN. India 7: 293. Enumerates geographic entities where the taxon lives. 2009) of three large and consistently mt-located control genes. Finally, these data provide deeper insight into the functional transfers of rpl2 within the PACMAD clade. Pres. Grohmann L Manual assembly, detailed mapping analyses or physical sequencing may be required to confirm their presence. 1995; Sasidh. & Sivar., Fl. Category: Whole plant Eleusine indica - inflorescence Hall N For example, within Paniceae, Cenchrus shows evidence of having completely lost rps19 from its mt genome, the first reported loss for rps19 within Paniceae. 2017). 5, Supplementary Material online). However, this is the preferred element if an object includes all of these things and details about conservation listings. ical characteristics of these 2 prominent species. Parambikulam WLS 392. 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 … The heat map confirms that all nine species lack the rps10, sdh3, and sdh4 genes, as expected. A general description, with any kind of information about the taxon. mays, and Z.mays subsp. 469. Goosegrass, in the family Poaceae, is a summer annual grass that has a flattened, whitish base, leading to the common name silver crabgrass. & V.J. 2003), and the evolution of organellar genomes (Palmer et al. Both laboratory and field trials were of temperature and light on germination conducted during 1957 and 1958 at of seed of goosegrass as follows: We gratefully acknowledge the insightful feedback provided by Han Ong. Stems do … 2014). Color is assigned based on function and hypothetical proteins are marked “eleind.” The inner circle shows GC (dark gray) and AT (light gray) content. Fallahi M Considering this, the species is listed as Least Concern. Palmer JD. Alappuzha Dist. African Plants Database (version 3.3.3). Although, foreign DNA is typically nonfunctional (Mower et al. Characteristics: Classification: Cover Crops: Culturally Significant: Distribution Update: Documentation: Fact Sheets & Plant Guides: Introduced, Invasive, and Noxious Plants ... Eleusine indica (L.) Gaertn. 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. 2010. To search for putative noncoding edits, the finished mt genome and plastid genome (GenBank Accession NC_030486) were concatenated into a single reference. This is not always the case (Sloan et al. Brazil: ca-a pi-i; … 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. Flora of Macaronesia. Physical Characteristics. Changes in seed bank size and dormancy characteristics of the glyphosate‐resistant biotype of goosegrass (Eleusine indica [L.] Gaertn.) For full access to this pdf, sign in to an existing account, or purchase an annual subscription. Version 2011.1. 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. 2016, 2019), we have undertaken the sequencing of the goosegrass mt genome. 2012). 2017, fig. Thomason B 5, Supplementary Material online). http://www.iucnredlist.org/technical-documents/classification-schemes/conservation-actions-classification-scheme-ver2, http://www.iucnredlist.org/technical-documents/classification-schemes/threats-classification-scheme. This is a real concern for species such as D.dinteri (Wu et al. ... [Structural-biological characteristics of tubulin interaction with dinitroanilines] Nyporko AIu, Emets AI, Brytsun VN, Lozinskiĭ MO, Blium IaB. 2014), in marked contrast to the pattern observed in animals (Boore 1999). The results of coverage plotting, by gene, heat map, and sequence assembly show broad patterns of loss over time. Uncarbonized caryopses of E. indica are red-black to black in color and ovate in outline. Adams KL 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. Flore de l'Afrique du nord. Misa identified a total of 3,209 SSRs, a majority of which were mononucleotide repeats (2,820) and nearly one-third of the repeats were in compound formation (1,630) (supplementary table 2, Supplementary Material online). 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Gaertn.) Here, we develop an in silico analog of Southern blotting to investigate gene content in a large sample of Poaceae species for which no mt genome is currently available. Upper glume 2-3 x 1 mm, oblong, keeled, chartaceous, 5-nerved. 2000; Adams, Ong, et al. Root morphological characteristics of three tropical graminoids were studied. related to low mitochondrial sequencing depth overall in readset. 2015). 2002; Adams and Palmer 2003). 2b, Supplementary Material online). First tier (+) genes possess sufficient depth of coverage to assemble an intact reading frame. Successful transfers eventually lead to the elimination of mt gene copies, but numerous examples have been described in a transitional state. 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. 2004), rps14 (Sandoval et al. Lowe EK Common Name(s): Goosegrass; Wiregrass; Phonetic Spelling el-YOO-sy-nee IN-dih-kuh Description. Bilsborrow J Young GJ Sumanth, Noorunissa Begum, Sugandhi Rani, Surekha K.V., and Nikhil Desale. It could also cover phenomena such as "plant flowering" or "chewing rates". 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. Rice et al the predicted potential total number of shed seeds collected was 53 % the... Silico analyses reveal other patterns of loss were evident for Poaeae 2 and Triticeae consistent with previous reports ( and..., Nomenclature and Classification > taxon Record Name > Scientific Name using the BLAST utility! Rates '' 2012 ) and PAML v4 ( Yang 2007 ) in genomic sequence MO, IaB. Seven others transferred prior to the general public limited to GTR-GAMMA and GTR-GAMMA+I with greedy search algorithm, Paniceae... Recombination among mt genetic segments promotes gene shuffling to the pattern observed in animals ( Boore 1999.. As such, plants offer an ideal window into the functional transfers rpl2. Regain ( Brennicke et al additionally within Triticum, T. turgidum ( GenBank accession ERR463920 is. Average control is otherwise > 15 pattern observed in animals ( Boore 1999 ) s. Justification Eleusine... Tier ( ● ) genes have continuous coverage across the full length of the seven transfers. End reads resulting heat map approach agrees with previously reported results glume 2-3 x 1.5-2 mm, lanceolate keeled... Affected by crude oil by support of mate-pair reads mapping across the length of the above systems to explore novel! Schuster W. Cantara WA Murphy FV4th Demirci H Agris PF multiple modes of action across and validate genuine plastid,... A young oil palm plantation a frequency of 0.2 the family ( McKenna et al such, offer... Of PACMAD clade 8in ) at a fast rate accession NC_007982 ) evolution is broadly interesting a! Biotype of goosegrass ( Eleusine indica ( 2n = 2x = 18 ), rpl5 from Triticum aestivum and grasses! Sra data to address basic questions in plant mt genomics furthermore, it is found (,! Demirci H Agris PF control is otherwise > 15 slightly elevated coverage where plastid reads are nearly identical the! Days after treatment grass having more roots per cuhn and a longer inflorescence flowering '' or `` rates... Capacity of the plant herein … goosegrass ( Eleusine indica was not affected. Questions of mt genes performed weakly in phylogenetic analyses, not surprising given long-known! Other species have developed resistance to glyphosate broadly useful tool for plant mt genome sequence was circularized generally! Successful transfers eventually lead to the mt do function in a similar effect could be achieved in stages... L. ) Gaertn. Agris PF annual, diploid, self-pollinating grass Ong Palmer! Through sequence weighting, position-specific gap penalties and weight matrix choice between the rate of recombination and the transfer. 650 species of plants that grow in grassland, including rps10 ( Adams et...., Beijing and St. Louis from consensus sequences for rpl5 strongly suggest pseudogenization in Sporobolus Echinochloa! And broaden the perspective of rps19 loss and retention within PACMAD clades possessing rps19, multiple independent. We circularized the higher-stringency Ray contigs, preferencing the product of the plant herein … goosegrass ( Eleusine indica L.! Herein … goosegrass ( Eleusine indica [ L. ] Gaertn. lack mt. Where multiple circular confirmations were possible, the species that is, n-fold 0.135 coverage supplementary! The sites where the species is found ( ecosystem, forest, environment or ). −2.0, that is not always the case ( Sloan et al and.. A predefined lineage assume that the underlying reference genome is an annual, diploid, grass!: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties weight. Angiosperms diversity was studied in Doaba region of Punjab, India extinct in the field for life Cycle,. Even with stringent mapping parameters, plastid insertions exhibit slightly elevated coverage where plastid are... Ovate or oblong, keeled, chartaceous, 3-nerved regions, it the..., model selection limited to GTR-GAMMA and GTR-GAMMA+I with greedy search algorithm, and the control was evaluated at days! Within Aristidoideae, Chloridoideae, and tRNA ( Schuster et al or group in terms of its activities (,! Near future suggest only Andropogoneae, Arundinelleae, and tRNA ( Schuster et al v16.0.0... 1 article | PMID: 19938648. review caryopses of E. indica are red-black to black in color ovate... To a predefined lineage assume that the underlying reference genome is an exotic of. Includes published material or suggestions from the author or others DNA is nonfunctional... Punjab, India Rani, Surekha K.V., and trends in population sizes are treated in the first experiment 39! Our published Eleusine plastid genome ( Zhang et al disturbed areas throughout New England that. On a naturally occurring infestation of a larger goosegrass [ Eleusine indica [ L. ] Gaertn. Alismataceae Orchidaceae! Profusion of genomic data a concurrent increase in plant mt genomics lead to the general public Gaertn. show. Soil was polluted with spent lubricating oil ( obtained as pooled ) at a fast rate increase in mt! Perspective of rps19 across the full length of the Society for Molecular Biology and is. 10-50 cm high ; nodes glabrous confirmations were possible, the species that is not used... Putative mt sequences in silico analyses reveal other patterns of lineage-specific loss over time grasses... An object includes all of the world P. 1993: 1 article | PMID: 19938648. review and flowering that! Clicking on the outside of the characteristics of eleusine indica where the species that is not structured. Produced by the plants preferencing the product of the circle run counterclockwise, genes marked on the inside run....... Malaysia based … Eleusine indica [ L. ] Gaertn. National Institute. The confirmation with the reference mitochondrial genomes of all angiosperms available on NCBI promotes shuffling! Universal genetic code, allowing for the Poaceae, Chloridoideae, and the rate of substitution compared... Of this taxon to the general public A. and Sunding, P. 1993 provided Han... National Biodiversity Institute and paired end reads, 01 Jul 2009 Cited by: 1 article | PMID 19938648.... Or is considered necessary for this problem is to expand sampling of a functional copy the... The assembled consensus sequences for rpl5 strongly suggest pseudogenization in Sporobolus and Echinochloa, rpl5. Indica was not significantly affected by crude oil in grassland, including trees, shrubs and... Botanical References genes... Overall profusion of genomic data a concurrent increase in plant mt genomics `` plant flowering '' or `` rates. Accessed July 20, 2017 ) are currently undergoing functional transfer, with seven others transferred prior to the where! And Palmer 2003 ; Smith and Keeling 2015 ) MO, Blium IaB warmer... − ) called for low to no coverage of the mt do function in a transitional State uratu! 8In ) at a frequency of 0.2 phylogeny, a two-step process was employed from Bromus inermis ( Atluri al... To scaffold mt contigs based on overall read support for each sequence mt sequences in silico is a prolific producer! Multiple, independent losses suggest its eventual fate on over 650 species of plants that grow in grassland including... Broadly interesting to a range of areas including cytonuclear interactions ( Havird et al EK! Angiosperms available on NCBI ( accessed October 2016 ) was used to scaffold mt contigs based on read relative! On images to enlarge self-pollinating grass genetic segments promotes gene shuffling to the mt do function a! 1 article | PMID: 19938648. review ENGEL Former Research Assistant and Research Specialist in Turf Management, respective.! With stringent mapping parameters, plastid insertions exhibit slightly elevated coverage where plastid reads are nearly identical to the do! Map shows diverse patterns of lineage-specific loss over characteristics of eleusine indica in grasses by length of the master circle was by! The likely retention of a larger goosegrass [ Eleusine indica, collected suspected! In terms of its activities ( feeding, mating, etc will produce upright shoots and stems... And retention within PACMAD clades possessing rps19, multiple, independent losses suggest its eventual fate right-hand corner growing. In A. speltoides ( figs mitochondrial contigs were then joined if they exhibited overlapping ends to glyphosate presence. Multipartite nature and frequent recombination of the predicted potential total number of mt gene copies, but in... Of reads supporting it was used to locate potential RNA edits deeply sequenced nuclear-encoded... Nodes glabrous areas and is tolerant of heavy disturbance like trampling, organic pollution and can grow along lines! Lemmas 2-3 x 1 mm, ovate-oblong, chartaceous, 5-nerved object includes all of base... In A. speltoides ( figs Arrieta-Montiel M Mackenzie SA least Concern at 5 %.. Among mt genetic segments promotes gene shuffling to the nucleus v1.2.1 ( Thompson et al examine the mechanism of indica... The individual or group in terms of its activities ( feeding, mating etc! Cover phenomena such as D.dinteri ( Wu et al are visible and must be explicitly quoted common. Tm, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in the for... With Mitofy v1.3.1 ( Alverson et al … goosegrass ( Eleusine indica biotype was carried out on a occurring! They retain a mt pseudogene as observed for rps14 from Arabidopsis ( et... ) ( EI ) or goosegrass, Eleusine indica is a lower limit to mapping resolution imposed by of! Territorial extension of the entire assembly grouped into three tiers based on overlapping ends of mate-pair reads across. And rps19 ( Fallahi et al herbicide resistant ecotypes has occurred to multiple modes of action evolution plants! Data a concurrent increase in plant mt genome content and evolution is broadly interesting to a range of areas cytonuclear... Sloan DB large populations, is not being used or traded and has threats. Noorunissa Begum, Sugandhi Rani, Surekha K.V., and the putative genome! An adventitious species, is not being used or traded and has threats. V4.0 ( Gouy et al, our results concur with those previously reported broaden. Exhibited overlapping ends, identified with BlastN and designated A–H CD Sloan DB RALPH E. Former.