Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

Mapleson, Daniel; Venturini, Luca; Kaithakottil, Gemy; Swarbreck, David

doi:10.1093/gigascience/giy131

Cited by 109 publications

(65 citation statements)

References 29 publications

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“…BRAKER2 [v2.1.2] (Hoff et al 2019) was used in conjunction with GeneMark [v4.36] (Borodovsky and Lomsadze 2011) generated annotations to train Augustus [v3.3.2] (Stanke et al 2006). Mikado [v1.2.4] (Venturini et al 2018) was used to produce high quality RNA-seq based gene predictions by combining the RNA-seq assemblies produced by StringTie [v1.3.6] (Pertea et al 2015) and Cufflinks [v2.2.1] (Ghosh and Chan 2016) with a reference-guided assembly from Trinity [v2.8.5] (Grabherr et al 2011) and a splice junction analysis from Portcullis [v1.2.2] (Mapleson et al 2018). The Trinity assembly was formatted using GMAP [v2019-05-12] (Wu and Watanabe 2005).…”

Section: Methodsmentioning

confidence: 99%

The Gossypium longicalyx genome as a resource for cotton breeding and evolution

Grover

Pan

Yuan

et al. 2020

Preprint

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40Cotton is an important crop that has made significant gains in production over the last century. 41 Emerging pests such as the reniform nematode have threatened cotton production. The rare 42 African diploid species Gossypium longicalyx is a wild species that has been used as an 43 important source of reniform nematode immunity. While mapping and breeding efforts have 44 made some strides in transferring this immunity to the cultivated polyploid species, the 45 complexities of interploidal transfer combined with substantial linkage drag have inhibited 46 progress in this area. Moreover, this species shares its most recent common ancestor with the 47 cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, 48 spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx. 49This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C 50 chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level 51 assembly. The utility of the G. longicalyx genome for understanding reniform immunity and 52 fiber evolution is discussed. 53 54 55 73 species exhibit degrees of resistance, only G. longicalyx exhibits immunity to infection (Yik and 74 Birchfield 1984). This is significant as reniform nematode has emerged as a major source of 75 cotton crop damage, reducing cotton production by over 205 million bales per year (Lawrence et 76 al. 2015) and accounting for ~11% of the loss attributable to pests (Khanal et al. 2018). Current 77 reniform resistant lines are derived from complex breeding schemes which are required to 78 introgress reniform immunity from the diploid G. longicalyx into polyploid G. hirsutum (Bell 79 and Robinson 2004; Dighe et al. 2009; Khanal et al. 2018); however, undesirable traits have 80 3 accompanied this introgression (Nichols et al. 2010) extreme stunting of seedlings and plants 81 exposed to dense nematode populations, prohibiting commercial deployment (Zheng et al. 2016). 83The genome of G. longicalyx is also valuable because it is phylogenetically sister to the only 84 diploid clade with spinnable fiber (Wendel and Albert, 1992; Wendel and Grover, 2015; Chen et 85 al., 2016), the A-genome species, which contributed the maternal ancestor to polyploid cotton. 86 Consequently, there has been interest in this species as the ancestor to spinnable fiber (Hovav et 87 al. 2008; Paterson et al. 2012), although progress has been limited due to lack of genomic 88 resources in G. longicalyx. Comparisons between the G. longicalyx genome and other cotton 89 genomes, including the domesticated diploids (Du et al. 2018), may provide clues into the 90 evolutionary origin of "long" fiber. 92Here we describe a high-quality, de novo genome sequence for G. longicalyx, a valuable 93 resource for understanding nematode immunity in cotton and possibly other species. This 94 genome also provides a foundation to understand the evolutionary origin of spinnable fiber in 95 Gossypium. 96 97 98

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Section: Methodsmentioning

confidence: 99%

The Gossypium longicalyx genome as a resource for cotton breeding and evolution

Grover

Pan

Yuan

et al. 2020

Preprint

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“…All assemblers generated a GFF3 as the final output except for Trinity, for which assembled transcripts in fasta format were mapped back to the gmap (v2019-05-12) indexed genome to generate a GFF3 file (by setting the output format option -f to gff3_match_cdna). Portcullis (v1.1.2) [49] was used to generate a high confidence set of splice junctions for the B73-Ab10 genome from the merged mapped reads. Mikado was configured to use all transcript assemblies (with strandedness marked as True for all except for Trinity, and with equal weights), portcullis-generated splice sites, and a plants.yaml scoring matrix.…”

Section: Gene Annotationmentioning

confidence: 99%

Gapless assembly of maize chromosomes using long-read technologies

et al. 2020

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Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.

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“…Mapleson et al 2018). The Trinity assembly was formatted using GMAP [v2019-05-12](Wu and Watanabe 2005).MAKER2 [v2.31.10] …”

mentioning

confidence: 99%

The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

Grover

Pan

Yuan

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Cotton is an important crop that has made significant gains in production over the last century.Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx.This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed.

show abstract

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

Cited by 109 publications

References 29 publications

The Gossypium longicalyx genome as a resource for cotton breeding and evolution

The Gossypium longicalyx genome as a resource for cotton breeding and evolution

Gapless assembly of maize chromosomes using long-read technologies

The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

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