<i>EyeChrom</i> and <i><scp>CCDB</scp>curator:</i> Visualizing chromosome count data from plants

Rivero, Rodrigo; Sessa, Emily B.; Zenil‐Ferguson, Rosana

doi:10.1002/aps3.1207

Cited by 16 publications

(11 citation statements)

References 29 publications

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“…Chromosome number data were obtained for all Solanaceae taxa in the Chromosome Counts Database (CCDB; Rice et al ., ), and the c . 14,000 records were curated semiautomatically using the CCDBcurator R package (Rivero et al ., ). CCDB contains records from original sources that have multiple complex symbol patterns denoting multivalence, or irregularities of chromosome counts.…”

Section: Methodsmentioning

confidence: 97%

Interaction among ploidy, breeding system and lineage diversification

et al. 2019

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If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs polyploid states) and breeding system (self-incompatible vs self-compatible states) are both thought to be drivers of differential diversification in angiosperms.We fit 29 diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits.We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.Among life history traits, reproductive characters that determine mating patterns are perhaps the most influential in governing macroevolution.

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Section: Methodsmentioning

confidence: 97%

Interaction among ploidy, breeding system and lineage diversification

et al. 2019

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“…CCDB contains records from original sources that have irregularities of chromosome counts, so that the ca. 150,000 records were curated semiautomatically using the CCDBcurator package 36 and custom R scripts. After a first round of automatic cleaning, we examined results by hand and corrected records where needed.…”

Section: Methodsmentioning

confidence: 99%

A deep dive into the ancestral chromosome number and genome size of flowering plants

Carta

Bedini

Peruzzi

2020

Preprint

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7Chromosome rearrangements are a well-known evolutionary feature in eukaryotic organisms 1 , 8 especially plants. The remarkable diversity of flowering plants (angiosperms) has been 9 attributed, in part, to the tremendous variation in their chromosome number 2 . This variation has 10 stimulated a blossoming number of speculations about the ancestral chromosome number of 11 angiosperms 2-7 , but estimates so far remain equivocal and relied on algebraic approaches lacking 12 an explicit phylogenetic framework. Here we used a probabilistic approach to model haploid 13 chromosome number (n) changes 8 along a phylogeny embracing more than 10 thousands taxa, 14 to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms 15 and the most recent common ancestor for single angiosperm families. 16Bayesian inference revealed an ancestral haploid chromosome number for angiosperms n = 7, 17 reinforcing previous hypotheses 2-7 that suggested a low ancestral basic number. Inferred n for 18 single families, more than half of which are provided here for the first time, are mostly 19 congruent with previous evaluations. Chromosome fusion (loss) and duplication (polyploidy) 20 are the predominant transition types inferred along the phylogenetic tree, emphasising the 21 importance of both dysploidy 6,9,10 and genome duplication 2,7,11-13 in chromosome number 22 evolution. Significantly, while dysploidy is equally distributed early and late across the whole 23 phylogeny, polyploidy is detected mainly towards the tips of the tree. Therefore, little evidence 24 exists for a link between ancestral chromosome numbers and putative ancient polyploidization 25 events 14 , suggesting that further insights are needed to elucidate the organization of genome 26 packaging into chromosomes. 27 28 Each eukaryotic organism has a characteristic chromosome complement, its karyotype, which 29 represents the highest level of structural and functional organization of the nuclear genome 15 . 30 Karyotype constancy ensures the transfer of the same genetic material to the next generation, 31 while karyotype variation provides genetic support to ecological differentiation and 32 adaptation 2,15 . Cytogenetic studies have shown that the tremendous inter-and intra-taxonomic 33 variation of chromosome number documented in flowering plants 2,5,16 is mostly driven by two 34 major mechanisms: a) increases through polyploidy (which may entail a Whole Genome 35 Duplication [WGD] or an increase by half of the genome, demi-duplication 8 ); b) decreases or 36 increases through structural chromosomal rearrangements like chromosome fusion, i.e. 37descending dysploidy, and chromosome fission, i.e. ascending dysploidy. 38Polyploidy is a common and ongoing phenomenon, especially in plants 13 , that has played an 39 important role in many lineages, with evidence of several rounds of both ancient and recent 40 polyploidization 11,17,18 , albeit its distribution in time remains contested 14 . Indeed, although the 41 crucial role of polyploidy i...

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“…Solanum species ploidy was assessed from Rivero et al . [ 35 ], where they classified ploidy by curating all the records available from the chromosome count database CCDB [ 36 ] and then manually checking for multiplicities of 12 to decide what was a diploid (2 n = 24 or close to that number in the presence of aneuploidies) or a polyploid (3 x = 36, 4 x = 48, and so forth). In the original database, populations that have mixed ploidies were recorded (e.g.…”

Section: Methodsmentioning

confidence: 99%

Interactions between breeding system and ploidy affect niche breadth in Solanum

et al. 2022

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Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for agricultural sustainability. The geography of crop wild relatives, including wild potatoes ( Solanum section Petota ), have received attention; however, such information has not been analysed in combination with phylogenetic histories, genomic composition and reproductive systems to identify potential species for use in breeding for abiotic stress tolerance. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that make up the climate niche that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate classes within a climate niche inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche breadth through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.

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EyeChrom and CCDBcurator: Visualizing chromosome count data from plants

Cited by 16 publications

References 29 publications

Interaction among ploidy, breeding system and lineage diversification

Interaction among ploidy, breeding system and lineage diversification

A deep dive into the ancestral chromosome number and genome size of flowering plants

Interactions between breeding system and ploidy affect niche breadth in Solanum

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