SynMap2 and SynMap3D: web-based whole-genome synteny browsers

Haug-Baltzell, Asher; Stephens, Sean A.; Davey, Sean; Scheidegger, Carlos; Lyons, Eric

doi:10.1093/bioinformatics/btx144

Cited by 146 publications

(158 citation statements)

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“…To identify genes unique to species with spinnable fiber (i.e., G. arboreum and the polyploid species), we extracted any G. arboreum gene contained within orthogroups composed solely of G. arboreum or polyploid A-genome gene annotations, and subjected these to blast2go (as above). Syntenic conservation of genes contained within the Ren Lon region, as compared to G. arboreum , was evaluated using GEvo as implemented in SynMap via COGE (Lyons and Freeling 2008; Haug-Baltzell et al 2017).…”

Section: Methodsmentioning

confidence: 99%

TheGossypium longicalyxgenome 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%

TheGossypium longicalyxgenome as a resource for cotton breeding and evolution

Grover

Pan

Yuan

et al. 2020

Preprint

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“…Locations of repetitive elements in the respective regions were retrieved from the NCBI Genome Viewer (Sayers et al ., ). Chromosome‐wide synteny analyses were performed using SynMap at CoGe (Haug‐Baltzell et al ., ) using masked genomes. Syntenic dotplots of chromosomes containing CYP98 genes were used to manually generate chromosome‐wide graphics.…”

Section: Methodsmentioning

confidence: 99%

Evolution of coumaroyl conjugate 3‐hydroxylases in land plants: lignin biosynthesis and defense

et al. 2019

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Summary Multiple adaptations were necessary when plants conquered the land. Among them were soluble phenylpropanoids related to plant protection and lignin necessary for upright growth and long‐distance water transport. Cytochrome P450 monooxygenase 98 (CYP98) catalyzes a rate‐limiting step in phenylpropanoid biosynthesis. Phylogenetic reconstructions suggest that a single copy of CYP98 founded each major land plant lineage (bryophytes, lycophytes, monilophytes, gymnosperms and angiosperms), and was maintained as a single copy in all lineages but the angiosperms. In angiosperms, a series of independent gene duplications and losses occurred. Biochemical assays in four angiosperm species tested showed that 4‐coumaroyl‐shikimate, a known intermediate in lignin biosynthesis, was the preferred substrate of one member in each species, while independent duplicates in Populus trichocarpa and Amborella trichopoda each showed broad substrate ranges, accepting numerous 4‐coumaroyl‐esters and ‐amines, and were thus capable of producing a wide range of hydroxycinnamoyl conjugates. The gymnosperm CYP98 from Pinus taeda showed a broad substrate range, but preferred 4‐coumaroyl‐shikimate as its best substrate. In contrast, CYP98s from the lycophyte Selaginella moellendorffii and the fern Pteris vittata converted 4‐coumaroyl‐shikimate poorly in vitro, but were able to use alternative substrates, in particular 4‐coumaroyl‐anthranilate. Thus, caffeoyl‐shikimate appears unlikely to be an intermediate in monolignol biosynthesis in non‐seed vascular plants, including ferns. The best substrate for CYP98A34 from the moss Physcomitrella patens was also 4‐coumaroyl‐anthranilate, while 4‐coumaroyl‐shikimate was converted to lower extents. Despite having in vitro activity with 4‐coumaroyl‐shikimate, CYP98A34 was unable to complement the Arabidopsis thaliana cyp98a3 loss‐of‐function phenotype, suggesting distinct properties also in vivo.

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“…We scaffolded the genome using OPERA‐LG with default settings (Gao, Bertrand, Chia, & Nagarajan, ). To achieve chromosome‐level assembly, we created a whole‐genome alignment with the Arabis alpina reference genome (Jiao et al, ; Willing et al, ) and performed synthetic path assembly using the tool Synmap2 (Haug‐Baltzell, Stephens, Davey, Scheidegger, & Lyons, ) available at the CoGe website (Lyons & Freeling, ). The pseudo‐chromosomes had a total size of 192 Mbp and were used for all following analyses.…”

Section: Methodsmentioning

confidence: 99%

Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD‐seq analysis in floodplain Arabis species

et al. 2019

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Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long‐term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay transfer between 1997 and 2014. RAD‐seq genotyping revealed that the stenoecious floodplain species Arabis nemorensis is co‐occurring with individuals that, based on ploidy, ITS‐sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay transfer on genetic diversity also depend on the genetic make‐up of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay transfer for habitat restoration and emphasize the importance of prerestoration characterization of microgeographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, that is maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo‐ and reference‐based RAD‐seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.

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SynMap2 and SynMap3D: web-based whole-genome synteny browsers

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 146 publications

References 4 publications

TheGossypium longicalyxgenome as a resource for cotton breeding and evolution

TheGossypium longicalyxgenome as a resource for cotton breeding and evolution

Evolution of coumaroyl conjugate 3‐hydroxylases in land plants: lignin biosynthesis and defense

Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD‐seq analysis in floodplain Arabis species

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