IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae

Plant Direct
Daniel S CarvalhoJames C Schnable

Abstract

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses-Poaceae-have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C4 were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference ge...Continue Reading

Associated Datasets

Aug 18, 2017·Rajeev K. VarshneyLiu Xin

References

Apr 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·C A Glackin, J W Grula
Feb 3, 2005·PLoS Biology·Jun YuHuanming Yang
Jul 7, 2007·Current Biology : CB·Pascal-Antoine ChristinGuillaume Besnard
Feb 14, 2008·The Plant Journal : for Cell and Molecular Biology·Eric Lyons, Michael Freeling
Feb 4, 2009·Nature·Andrew H PatersonDaniel S Rokhsar
Jun 25, 2009·Genome Biology·Xiyin WangAndrew H Paterson
Dec 8, 2009·Science·Patrick S SchnableRichard K Wilson
Feb 12, 2010·Nature·UNKNOWN International Brachypodium Initiative
Aug 10, 2010·The Plant Cell·Thomas P BrutnellJoyce Van Eck
Feb 16, 2011·Journal of Experimental Botany·Sylvain AubryJulian M Hibberd
Apr 20, 2011·BMC Bioinformatics·Haibao TangMichael Freeling
Nov 26, 2011·The New Phytologist·UNKNOWN Grass Phylogeny Working Group II
May 15, 2012·Nature Biotechnology·Jeffrey L BennetzenKatrien M Devos
Jul 28, 2013·Current Biology : CB·Elizabeth A Kellogg
Oct 22, 2013·Trends in Ecology & Evolution·Hans Ellegren
Apr 12, 2014·PLoS Computational Biology·Remco BouckaertAlexei J Drummond
Jan 15, 2015·Molecular Biology and Evolution·Pascal-Antoine ChristinErika J Edwards
Sep 17, 2015·American Journal of Botany·Jacob D WashburnJ Chris Pires
Mar 19, 2016·Genome Biology and Evolution·Michael R McKainJames H Leebens-Mack
Jul 21, 2016·Journal of Experimental Botany·Pu HuangThomas P Brutnell
Oct 30, 2016·Genome Biology·Anthony J StuderThomas P Brutnell
Jun 13, 2017·Nature·Yinping JiaoDoreen Ware
Jul 25, 2017·The Plant Cell·Yang ZhangJames C Schnable
Oct 19, 2017·Molecular Biology and Evolution·Jose J Moreno-VillenaPascal-Antoine Christin
Jul 8, 2018·Nature Communications·Olivier GarsmeurAngélique D'Hont
Oct 6, 2018·The Plant Journal : for Cell and Molecular Biology·Guoqiang ZhangBing Zhang
Dec 13, 2018·Nature Communications·John T LovellThomas E Juenger
Jan 27, 2019·Nature Communications·Changsong ZouHeng Zhang

❮ Previous
Next ❯

Citations

Nov 5, 2020·International Journal of Molecular Sciences·Stephanie SchaarschmidtEllen Zuther

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
electrophoresis
flow

Software Mentioned

BEAST2
BLASTN
IsoSeq
QuotaAlign
Densitree
GBlocks
Kalign
LASTZ
CoGe
Ensembl

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.