VIII. Subfamily Panicoideae Link (1827)

Kellogg, Elizabeth A.

doi:10.1007/978-3-319-15332-2_22

Cited by 5 publications

(3 citation statements)

References 86 publications

(166 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Chasmanthium laxum belongs to the grass tribe Chasmanthieae (7 species). The Chasmanthieae all appear to utilize C 3 photosynthesis (Kellogg, ) and are generally placed as early diverging lineage within the Panicoideae, the grass sub‐family containing maize, sorghum, sugarcane, miscanthus, switchgrass, foxtail millet, and proso millet (GPWG II, ). C. laxum can occur in a variety of environments such as woods, meadows, and swamps (Yates, ).…”

Section: Introductionmentioning

confidence: 99%

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

2020

View full text Add to dashboard Cite

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 genomes and consensus long‐read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses—wild species and species utilizing C3 photosynthesis—will aid in future studies of domestication and C4 evolution by decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.

show abstract

Section: Introductionmentioning

confidence: 99%

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

2020

View full text Add to dashboard Cite

show abstract

“…Chasmanthium laxum belongs to the grass tribe Chasmanthieae (7 species). The Chasmanthieae all appear to utilize C 3 photosynthesis (Kellogg, 2015) and are generally placed as early diverging lineage within the Panicoideae, the grass sub-family containing maize, sorghum, sugar cane, miscanthus, switchgrass, foxtail millet, and proso millet (Edwards et al, 2011). C. laxum can occur in a variety of environments such as: woods, meadows and swamps (Yates, 1966).…”

Section: Introductionmentioning

confidence: 99%

IsoSeq transcriptome assembly of C₃panicoid grasses provides tools to study evolutionary change in the Panicoideae

Carvalho

Schnable

2019

Preprint

View full text Add to dashboard Cite

7The number of plant species with genomic and transcriptomic data has been increasing 8 rapidly. The grasses -Poaceae -have been well represented among species with published 9 reference genomes. However, as a result the genomes of wild grasses are less frequently tar-10 geted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses 11 can aid the study of domestication, gene discovery for breeding and crop improvement, and 12 improve our understanding of the evolution of C4 photosynthesis. Here we used long read 13 sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: 14Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on 15 alignments to the sorghum genome we estimate that assembled consensus transcripts from 16 each species capture between 54.2 and 65.7% of the conserved syntenic gene space in grasses. 17Genes co-opted into C4 were also well represented in this dataset, despite concerns that, be-18 cause these genes might play roles unrelated to photosynthesis in the target species, they 19 would be expressed at low levels and missed by transcript-based sequencing. A combined 20 analysis using syntenic orthologous genes from grasses with published reference genomes and 21 consensus long read sequences from these wild species was consistent with previously pub-22 lished phylogenies. It is hoped that this data, targeting under represented classes of species 23 within the PACMAD grasses -wild species and species utilizing C3 photosynthesis -will aid 24 in futurue studies of domestication and C4 evolution by decreasing the evolutionary distance 25 between C4 and C3 species within this clade, enabling more accurate comparisons associated 26

show abstract

“…Panicoideae is the second largest subfamily of the grass family (Poaceae), which is composed of approximately 3316 species in 12 tribes [19], such as lawn grasses (Eremo chloaophiuroides and Stenotaphrum secundatum) [20], biofuel stocks (Panicum virgatum) [21], and some important crops like maize (Zea mays L.), sugarcane (Saccharum officinarum L.), sorghum (Sorghum bicolor L.), and broomcorn millet (Panicum miliaceum L.) as well as foxtail millet (Setaria_italica L.) [22,23]. In light of its economic and evolutionary significance, extensive studies have been performed to investigate the phylogenetic relationships and genetic divergence in the Panicoideae subfamily [24,25].…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

et al. 2018

View full text Add to dashboard Cite

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

show abstract

VIII. Subfamily Panicoideae Link (1827)

Cited by 5 publications

References 86 publications

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

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

IsoSeq transcriptome assembly of C₃panicoid grasses provides tools to study evolutionary change in the Panicoideae

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Contact Info

Product

Resources

About

VIII. Subfamily Panicoideae Link (1827)

Cited by 5 publications

References 86 publications

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

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

IsoSeq transcriptome assembly of C3panicoid grasses provides tools to study evolutionary change in the Panicoideae

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Contact Info

Product

Resources

About

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

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

IsoSeq transcriptome assembly of C₃panicoid grasses provides tools to study evolutionary change in the Panicoideae