Chapter 9. Core Eudicots

Developmental stochasticity and variation in floral phyllotaxis

Journal of Plant Research ◽

10.1007/s10265-021-01283-7 ◽

2021 ◽

Author(s):

Miho Stephanie Kitazawa

Keyword(s):

Pattern Formation ◽

Gene Networks ◽

Recent Progress ◽

Phyllotactic Pattern ◽

Floral Diversity ◽

Core Eudicots ◽

Common Process ◽

The Mean ◽

Floral Phyllotaxis ◽

Regular Patterns

AbstractFloral phyllotaxis is a relatively robust phenotype; trimerous and pentamerous arrangements are widely observed in monocots and core eudicots. Conversely, it also shows variability in some angiosperm clades such as ‘ANA’ grade (Amborellales, Nymphaeales, and Austrobaileyales), magnoliids, and Ranunculales. Regardless of the phylogenetic relationship, however, phyllotactic pattern formation appears to be a common process. What are the causes of the variability in floral phyllotaxis and how has the variation of floral phyllotaxis contributed to floral diversity? In this review, I summarize recent progress in studies on two related fields to develop answers to these questions. First, it is known that molecular and cellular stochasticity are inevitably found in biological systems, including plant development. Organisms deal with molecular stochasticity in several ways, such as dampening noise through gene networks or maintaining function through cellular redundancy. Recent studies on molecular and cellular stochasticity suggest that stochasticity is not always detrimental to plants and that it is also essential in development. Second, studies on vegetative and inflorescence phyllotaxis have shown that plants often exhibit variability and flexibility in phenotypes. Three types of phyllotaxis variations are observed, namely, fluctuation around the mean, transition between regular patterns, and a transient irregular organ arrangement called permutation. Computer models have demonstrated that stochasticity in the phyllotactic pattern formation plays a role in pattern transitions and irregularities. Variations are also found in the number and positioning of floral organs, although it is not known whether such variations provide any functional advantages. Two ways of diversification may be involved in angiosperm floral evolution: precise regulation of organ position and identity that leads to further specialization of organs and organ redundancy that leads to flexibility in floral phyllotaxis.

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Dating the Monocot?Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes

Journal of Molecular Evolution ◽

10.1007/s00239-003-2564-9 ◽

2004 ◽

Vol 58 (4) ◽

pp. 424-441 ◽

Cited By ~ 242

Author(s):

Chien-Chang Chang ◽

Hsin-Liang Chen ◽

Wen-Hsiung Li ◽

Shu-Miaw Chaw

Keyword(s):

Chloroplast Genomes ◽

Core Eudicots

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A genome triplication associated with early diversification of the core eudicots

Genome Biology ◽

10.1186/gb-2012-13-1-r3 ◽

2012 ◽

Vol 13 (1) ◽

pp. R3 ◽

Cited By ~ 220

Author(s):

Yuannian Jiao ◽

Jim Leebens-Mack ◽

Saravanaraj Ayyampalayam ◽

John E Bowers ◽

Michael R McKain ◽

...

Keyword(s):

The Core ◽

Early Diversification ◽

Core Eudicots ◽

A Genome ◽

Genome Triplication

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Nonself-recognition-based self-incompatibility can alternatively promote or prevent introgression

10.1101/2020.09.29.318790 ◽

2020 ◽

Author(s):

Alexander Harkness ◽

Yaniv Brandvain

Keyword(s):

Pollen Limitation ◽

List Type ◽

Self Incompatibility ◽

Core Eudicots ◽

S Alleles ◽

Self Fertilization ◽

Nonself Recognition ◽

Negative Frequency Dependent Selection ◽

Incompatibility Alleles ◽

S Allele

1SummaryTraditionally, we expect that self-incompatibility alleles (S-alleles), which prevent self-fertilization, should benefit from negative-frequency dependent selection and rise to high frequency when introduced to a new population through gene flow. However, the most taxonomically widespread form of self-incompatibility, the ribonuclease-based system ancestral to the core eudicots, functions through nonself-recognition, which drastically alters the process of S-allele diversification.We analyze a model of S-allele evolution in two populations connected by migration, focusing on comparisons among the fates of S-alleles originally unique to each population and those shared among populations.We find that both shared and unique S-alleles originating from the population with more unique S-alleles were usually fitter than S-alleles from the population with fewer. Resident S-alleles were often driven extinct and replaced by migrant S-alleles, though this outcome could be averted by pollen limitation or biased migration.Nonself-recognition-based self-incompatibility will usually either disfavor introgression of S-alleles or result in the whole-sale replacement of S-alleles from one population with those from another.

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The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding

10.1101/2021.09.08.459545 ◽

2021 ◽

Cited By ~ 1

Author(s):

Priyanka Sharma ◽

Valentine Murigneux ◽

Jasmine Haimovitz ◽

Catherine J. Nock ◽

Wei Tian ◽

...

Keyword(s):

Genome Assembly ◽

Morphological Characteristics ◽

Single Copy ◽

Protein Coding ◽

Core Eudicots ◽

Wide Range ◽

Genes Encoding ◽

Long Read ◽

In The Wild

SummaryMacadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.

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Isolation and Characterization of APETALA3 Orthologs and Promoters from the Distylous Fagopyrum esculentum

Plants ◽

10.3390/plants10081644 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1644

Author(s):

Lingtian Zeng ◽

Jiao Zhang ◽

Xuan Wang ◽

Zhixiong Liu

Keyword(s):

Transgenic Arabidopsis ◽

Floral Organ ◽

Fagopyrum Esculentum ◽

Small Scale ◽

Common Buckwheat ◽

Model Species ◽

Gus Staining ◽

Stamen Development ◽

Isolation And Characterization ◽

Core Eudicots

Common buckwheat (Fagopyrum esculentum) produces distylous flowers with undifferentiated petaloid tepals, which makes it obviously different from flowers of model species. In model species Arabidopsis, APETALA3 (AP3) is expressed in petal and stamen and specifies petal and stamen identities during flower development. Combining with our previous studies, we found that small-scale gene duplication (GD) event and alternative splicing (AS) of common buckwheat AP3 orthologs resulted in FaesAP3_1, FaesAP3_2 and FaesAP3_2a. FaesAP3_2 and FaesAP3_2a were mainly expressed in the stamen of thrum and pin flower. Promoters functional analysis suggested that intense GUS staining was observed in the whole stamen in pFaesAP3_2::GUS transgenic Arabidopsis, while intense GUS staining was observed only in the filament of stamen in pFaesAP3_1::GUS transgenic Arabidopsis. These suggested that FaesAP3_1 and FaesAP3_2 had overlapping functions in specifying stamen filament identity and work together to determine normal stamen development. Additionally, FaesAP3_2 and FaesAP3_2a owned the similar ability to rescue stamen development of Arabidopsis ap3-3 mutant, although AS resulted in a frameshift mutation and consequent omission of the complete PI-derived motif and euAP3 motif of FaesAP3_2a. These suggested that the MIK region of AP3-like proteins was crucial for determining stamen identity, while the function of AP3-like proteins in specifying petal identity was gradually obtained after AP3 Orthologs acquiring a novel C-terminal euAP3 motif during the evolution of core eudicots. Our results also provide a clue to understanding the early evolution of the functional specificity of euAP3-type proteins involving in floral organ development in core eudicots, and also suggested that FaesAP3_2 holds the potential application for biotechnical engineering to develop a sterile male line of F. esculentum.

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The evolutionary history of plant T2/S-type ribonucleases

10.7287/peerj.preprints.3171 ◽

2017 ◽

Author(s):

Karolis Ramanauskas ◽

Boris Igić

Keyword(s):

Self Incompatibility ◽

Class Iii ◽

Widespread Occurrence ◽

Public Resource ◽

Core Eudicots ◽

Evolutionary Context ◽

Female Component ◽

History Of ◽

Genome Assemblies ◽

Source Of Information

A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution.

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