De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

E. M. B. Mollison; S. Barth; D. Milbourne; L. Milne; C. Halpin; M. McCabe; C. Creevey; D. F. Marshall

doi:10.1007/978-3-319-28932-8_19

De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

E. M. B. Mollison, S. Barth, D. Milbourne, L. Milne, C. Halpin, M. McCabe, C. Creevey, D. F. Marshall

Department of Life Sciences

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract

Abstract
A 1.11Gbp de novo assembly of the Lolium perenne genome was generated, containing 424,745 scaffolds and with N50 of 25,193. Gene prediction on genomic, mitochondrial and chloroplast scaffolds was carried out using both ab initio and RNA-Seq based methods. Ab initio gene prediction, carried out using wheat-based gene models, identified a total of 188,822 potential gene models from genomic scaffolds and 109 from mitochondrial. Mapping of reads from a broad-based RNA-Seq study identified 67,706 potential genes from genomic scaffolds, 90 from mitochondrial and 18 from chloroplast. Comparison of ab initio predicted genes with RNA-Seq genes identified 44,252 predicted gene models from genomic scaffolds and three from mitochondrial that overlapped with RNA-Seq derived transcripts by more than 20 % of their length.

Original language	English
Title of host publication	Breeding in a World of Scarcity
Subtitle of host publication	Proceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia
Editors	Isabel Roldán-Ruiz , Joost Baert, Dirk Reheul
Publisher	Springer Nature
Pages	127-131
ISBN (Electronic)	978-3-319-28932-8
ISBN (Print)	978-3-319-28930-4, 3319289306
DOIs	https://doi.org/10.1007/978-3-319-28932-8_19
Publication status	Published - 14 Jun 2016

Keywords

perennial ryegrass
genome sequencing
RNA-Seq
transcriptome
gene predicition

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10.1007/978-3-319-28932-8_19

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Mollison, E. M. B., Barth, S., Milbourne, D., Milne, L., Halpin, C., McCabe, M., Creevey, C., & Marshall, D. F. (2016). De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass. In I. Roldán-Ruiz , J. Baert, & D. Reheul (Eds.), Breeding in a World of Scarcity: Proceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia (pp. 127-131). Springer Nature. https://doi.org/10.1007/978-3-319-28932-8_19

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abstract = "AbstractA 1.11Gbp de novo assembly of the Lolium perenne genome was generated, containing 424,745 scaffolds and with N50 of 25,193. Gene prediction on genomic, mitochondrial and chloroplast scaffolds was carried out using both ab initio and RNA-Seq based methods. Ab initio gene prediction, carried out using wheat-based gene models, identified a total of 188,822 potential gene models from genomic scaffolds and 109 from mitochondrial. Mapping of reads from a broad-based RNA-Seq study identified 67,706 potential genes from genomic scaffolds, 90 from mitochondrial and 18 from chloroplast. Comparison of ab initio predicted genes with RNA-Seq genes identified 44,252 predicted gene models from genomic scaffolds and three from mitochondrial that overlapped with RNA-Seq derived transcripts by more than 20 % of their length.",

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Mollison, EMB, Barth, S, Milbourne, D, Milne, L, Halpin, C, McCabe, M, Creevey, C & Marshall, DF 2016, De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass. in I Roldán-Ruiz , J Baert & D Reheul (eds), Breeding in a World of Scarcity: Proceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia. Springer Nature, pp. 127-131. https://doi.org/10.1007/978-3-319-28932-8_19

De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass. / Mollison, E. M. B.; Barth, S.; Milbourne, D. et al.
Breeding in a World of Scarcity: Proceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia. ed. / Isabel Roldán-Ruiz ; Joost Baert; Dirk Reheul . Springer Nature, 2016. p. 127-131.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

TY - CHAP

T1 - De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

AU - Mollison, E. M. B.

AU - Barth, S.

AU - Milbourne, D.

AU - Milne, L.

AU - Halpin, C.

AU - McCabe, M.

AU - Creevey, C.

AU - Marshall, D. F.

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N2 - AbstractA 1.11Gbp de novo assembly of the Lolium perenne genome was generated, containing 424,745 scaffolds and with N50 of 25,193. Gene prediction on genomic, mitochondrial and chloroplast scaffolds was carried out using both ab initio and RNA-Seq based methods. Ab initio gene prediction, carried out using wheat-based gene models, identified a total of 188,822 potential gene models from genomic scaffolds and 109 from mitochondrial. Mapping of reads from a broad-based RNA-Seq study identified 67,706 potential genes from genomic scaffolds, 90 from mitochondrial and 18 from chloroplast. Comparison of ab initio predicted genes with RNA-Seq genes identified 44,252 predicted gene models from genomic scaffolds and three from mitochondrial that overlapped with RNA-Seq derived transcripts by more than 20 % of their length.

AB - AbstractA 1.11Gbp de novo assembly of the Lolium perenne genome was generated, containing 424,745 scaffolds and with N50 of 25,193. Gene prediction on genomic, mitochondrial and chloroplast scaffolds was carried out using both ab initio and RNA-Seq based methods. Ab initio gene prediction, carried out using wheat-based gene models, identified a total of 188,822 potential gene models from genomic scaffolds and 109 from mitochondrial. Mapping of reads from a broad-based RNA-Seq study identified 67,706 potential genes from genomic scaffolds, 90 from mitochondrial and 18 from chloroplast. Comparison of ab initio predicted genes with RNA-Seq genes identified 44,252 predicted gene models from genomic scaffolds and three from mitochondrial that overlapped with RNA-Seq derived transcripts by more than 20 % of their length.

KW - perennial ryegrass

KW - genome sequencing

KW - RNA-Seq

KW - transcriptome

KW - gene predicition

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Mollison EMB, Barth S, Milbourne D, Milne L, Halpin C, McCabe M et al. De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass. In Roldán-Ruiz I, Baert J, Reheul D, editors, Breeding in a World of Scarcity: Proceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia. Springer Nature. 2016. p. 127-131 doi: 10.1007/978-3-319-28932-8_19

De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

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