Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.

Genome Biology
Kankshita SwaminathanMatthew E Hudson

Abstract

Miscanthus x giganteus (Mxg) is a perennial grass that produces superior biomass yields in temperate environments. The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively propagated interspecific hybrid. A survey of the complex Mxg genome was conducted using 454 pyrosequencing of genomic DNA and Illumina sequencing-by-synthesis of small RNA. We found that the coding fraction of the Mxg genome has a high level of sequence identity to that of other grasses. Highly repetitive sequences representing the great majority of the Mxg genome were predicted using non-cognate assembly for de novo repeat detection. Twelve abundant families of repeat were observed, with those related to either transposons or centromeric repeats likely to comprise over 95% of the genome. Comparisons of abundant repeat sequences to a small RNA survey of three Mxg organs (leaf, rhizome, inflorescence) revealed that the majority of observed 24-nucleotide small RNAs are derived from these repetitive sequences. We show that high-copy-number repeats match more of the small RNA, even when the amount of the repeat sequence in the genome is accounted for. We show that major repeats are prese...Continue Reading

References

Jul 1, 1995·Current Biology : CB·G MooreM D Gale
Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Apr 5, 2002·Genome Research·W James Kent
May 4, 2002·Nature Reviews. Genetics·Cédric FeschotteSusan R Wessler
Jan 17, 2003·Genome Research·Scott SchwartzWebb Miller
Feb 13, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·G. AtienzaA. Martín
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Nov 15, 2003·Molecular Phylogenetics and Evolution·I Alvarez, J F Wendel
Oct 19, 2004·Genetics·Jeong-Soon KimDavid M Stelly
Dec 15, 2004·Annals of Botany·H James PriceJ Spencer Johnston
Jan 22, 2005·PLoS Biology·Joseph A BedellRobert A Martienssen
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Aug 16, 2005·Nature·UNKNOWN International Rice Genome Sequencing Project
Aug 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Yan FuPatrick S Schnable
Sep 6, 2005·Science·Cheng LuPamela J Green
Dec 13, 2005·Genome Research·Andrew H PatersonTakuji Sasaki
Dec 13, 2005·Plant Physiology·Georg HabererJoachim Messing
Oct 28, 2006·BMC Genomics·Thomas WickerNils Stein
Feb 13, 2007·Current Opinion in Plant Biology·Jeffrey L Bennetzen
Nov 9, 2007·Genome Research·Deborah E Stage, Thomas H Eickbush
Nov 24, 2007·BMC Bioinformatics·Daniel H HusonRegula Rupp
Dec 14, 2007·Annual Review of Genetics·Cédric Feschotte, Ellen J Pritham
Sep 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Kan NobutaBlake C Meyers
Feb 4, 2009·Nature·Andrew H PatersonDaniel S Rokhsar
Dec 8, 2009·Science·Patrick S SchnableRichard K Wilson
Jan 1, 2008·Molecular Ecology Resources·Matthew E Hudson

❮ Previous
Next ❯

Citations

Oct 12, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Laura J Kelly, Ilia J Leitch
Aug 21, 2010·Briefings in Bioinformatics·Konrad Paszkiewicz, David J Studholme
Jun 29, 2013·Genome Biology·Savio de Siqueira FerreiraGlaucia Mendes Souza
Jan 19, 2012·PloS One·Philippe ChouvarineDaniel G Peterson
Mar 12, 2013·Annual Review of Plant Biology·Stephen P Long, Ashley K Spence
Feb 14, 2016·Current Opinion in Biotechnology·Raissa Estrela, Jamie Harrison Doudna Cate
Jan 6, 2011·Journal of Integrative Plant Biology·Martin A J Parry, Hai-Chun Jing
Dec 30, 2011·Current Opinion in Biotechnology·Martín Calviño, Joachim Messing
Oct 8, 2013·Plant Science : an International Journal of Experimental Plant Biology·Yanchong YuGongke Zhou
May 31, 2017·Plant Biotechnology Journal·Rakesh BhatiaMaurice Bosch
Oct 8, 2016·Cell·Caren ChangElliot M Meyerowitz
Aug 26, 2014·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gang NieHai-Dong Yan
Jul 6, 2014·BMC Genomics·Nathalia de SettaMarie-Anne Van Sluys
Mar 8, 2021·Biotechnology for Biofuels·Jose J De VegaSusanne Barth

❮ Previous
Next ❯

Datasets Mentioned

BETA
AC169373
AC169376
AC169372
AJ426562
AJ426563
SRA010791.2
GSE20056

Methods Mentioned

BETA
whole-genome shotgun sequencing
genotyping
whole-genome
flow cytometry
454 sequencing
454 survey
454
methylation filtration
Illumina sequencing

Software Mentioned

GMAP ( Genomic Mapping and Alignment Program )
Sequencher
phrap
Modeltest3
blastz
BLAST
BLAT
MrBayes
Trace
BLASTN

Related Concepts

Related Feeds

Artificial Chromosomes

Artificial chromosomes are genetically engineered chromosomes derived from the DNA of a species. Discover the latest research on artificial chromosomes here.