The Evolution of Haploid Chromosome Numbers in the Sunflower Family

A chromosome-level genome of Lobelia seguinii provides insights into the evolution of Campanulaceae and the lobeline biosynthesis

Lobelia seguinii is a plant with great ecological and medicinal value and belongs to Campanulaceae. Lobelia contains lobeline, a well-known compound used to treat respiratory diseases. Nevertheless, lobeline biosynthesis needs further exploration. Moreover, whole-genome duplication (WGD) and karyotype evolution within Campanulaceae still need to be better understood. In this study, we obtained a chromosome-level genome of L. seguinii with a size of 1.4 Gb and 38253 protein-coding genes. Analyses revealed two WGDs within Campanulaceae, one at the most recent common ancestor (MRCA) of Campanula and Adenophora, and another at the MRCA of Lobelioideae. Analyses further revealed that the karyotype of Platycodon grandiflorus represents the ancient type within Asterales. We proposed eight enzymes involved in the lobeline biosynthesis pathway of L. seguinii. Molecular cloning and heterologous expression of phenylalanine ammonia-lyase (PAL), a candidate enzyme involved in the first step of lobeline biosynthesis, verified its function to catalyze the deamination of phenylalanine to cinnamic acid. This study sheds light on the evolution of Campanulaceae and lobeline biosynthesis.

Chromosome-scale Reference Genome and RAD-based Genetic Map of Yellow Starthistle (Centaurea solstitialis) Reveal Putative Structural Variation and QTL Associated With Invader Traits

Invasive species offer outstanding opportunities to identify the genomic sources of variation that contribute to rapid adaptation, as well as the genetic mechanisms facilitating invasions. The Eurasian plant yellow starthistle (Centaurea solstitialis) is highly invasive in North and South American grasslands and known to have evolved increased growth and reproduction during invasion. Here, we develop new genomic resources for C. solstitialis and map the genetic basis of invasiveness traits. We present a chromosome-scale (1N = 8) reference genome using PacBio CLR and Dovetail Omni-C technologies, and functional gene annotation using RNAseq. We find repeat structure typical of the family Asteraceae, with over 25% of gene content derived from ancestral whole-genome duplications (paleologs). Using an F2 mapping population derived from a cross between native and invading parents, with a restriction site-associated DNA (RAD)-based genetic map, we validate the assembly and identify 13 quantitative trait loci underpinning size traits that have evolved during invasion. We find evidence that large effects of quantitative trait loci may be associated with structural variants between native and invading genotypes, including a variant with an overdominant and pleiotropic effect on key invader traits. We also find evidence of significant paleolog enrichment under two quantitative trait loci. Our results add to growing evidence of the importance of structural variants in evolution, and to understanding of the rapid evolution of invaders.

ND-FISH with New Oligo Probes for Chromosome Identification of Cichorium intybus Revealing Karyotypic Variation and Divergence of Asteraceae Species

Chicory (Cichorium intybus L., 2n = 18), belonging to the Asteraceae family, exhibits significant edible, medicinal, and pasture values. Moderate research has been performed on identifying Chicory species' chromosomes using fluorescence in situ hybridization (FISH) and C-banding. Detailed karyotype comparisons with chromosome nomenclature have not yet been performed for Chicory and similar species. In this study, the tandem repeats (TRs) were predicted and mapped to chromosomal regions based on released C. intybus L. ASM2352571 genome assembly v1, and then compared to the genome of Lettuce (Lactuca sativa L.). Nine new oligo probes were then developed and employed for karyotypic investigation of endive, Lettuce, and Chicory mitotic metaphase using non-denaturing FISH (ND-FISH). By combining the conserved oligo probes for 5S rDNA and 18S rDNA with the unique ND-FISH signals of new TR-oligo probes, we can develop a high-resolution standard karyotype for the cultivars of Lettuce and Chicory. The occurrence of chromosome structure variations from the natural population of Chicory and Lettuce was also revealed by ND-FISH with multiple oligo probes. The current observation of the karyotype differences and divergences of Lactuca and Cichorium and the genomic research offers crucial information about the Asteraceae family's genetic diversity, chromosomal dynamics, and evolutionary routes.

PloiDB: the plant ploidy database

See also the Commentary on this article by Spoelhof et al., 240: 909–911.

Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.

An Overview to the Index to Chromosome Numbers in Asteraceae Database: Revisiting Base Chromosome Numbers, Polyploidy, Descending Dysploidy, and Hybridization

A brief overview to the Index to Chromosome Numbers in Asteraceae database is provided. The database contains karyological information on Asteraceae and has been repeatedly improved and updated and is now hosted at the National Bioscience Database center. Also, we take the opportunity to revisit the evolution of base chromosome numbers in Asteraceae, emphasizing the phenomena of polyploidy, descending dysploidy, and hybridization, common in the family. Chromosome numbers for species included in one of the most recent phylogenetic treatments of the Asteraceae were obtained from the Index to Chromosome Numbers in Asteraceae database were mapped on to the modified phylogeny diagram, and base chromosome numbers were determined for each branch of the phylogeny. Results for tribal base numbers were the same as those hypothesized in our previous work with additional base numbers added for tribes not previously recognized but supported by newer phylogenetic methods. The Asteraceae show an ancestral base chromosome number of x = 9 and originated in the Antarctica (Gondowanaland) in Cretaceous (80 Mys ago). The x = 9 number has been retained through successive South American lineages of the Barnadesieeae, Gochnatieae, Stiffieae, Wunderlichieae, Astereae, and Senecioneae following northward migration. Northward migration to Africa was accompanied with x = 10 becoming the dominant base chromosome number as the family evolved multiple additional tribes. Northward migration to Australasia with x = 9 was in Astereae and the families Goodeneaseae, Menyanthaceae, and Stylydiaceae. The evolution of the North American Heliantheae alliance began with the appearance of x2 = 19 which persisted in multiple additional new tribes. Frequent dysploidy decreases, polyploidy and hybridization occurred throughout the history of the family.

The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae)

The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.

A critical review on cytogenetics of Cucurbitaceae with updates on Indian taxa

The cytogenetic relationships in the species of Cucurbitaceae are becoming immensely important to answer questions pertaining to genome evolution. Here, a simplified and updated data resource on cytogenetics of Cucurbitaceae is presented on the basis of foundational parameters (basic, zygotic and gametic chromosome numbers, ploidy, genome size, karyotype) and molecular cytogenetics. We have revised and collated our own findings on seven agriculturally important Indian cucurbit species in a comparative account with the globally published reports. Chromosome count (of around 19% species) shows nearly three-fold differences while genome size (of nearly 5% species) shows 5.84-fold differences across the species. There is no significant correlation between chromosome numbers and nuclear genome sizes. The possible trend of evolution is discussed here based on molecular cytogenetics data, especially the types and distribution of nucleolus organizer regions (NORs). The review supersedes the scopes of general chromosome databases and invites scopes for continuous updates. The offline resource serves as an exclusive toolkit for research and breeding communities across the globe and also opens scope for future establishment of web-database on Cucurbitaceae cytogenetics.

Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato

Although Crepis was the first model plant group in which chromosomal changes were considered to play an important role in speciation, their chromosome structure and evolution have been barely investigated using molecular cytogenetic methods. The aim of the study was to provide a better understanding of the patterns and directions of Crepis chromosome evolution, using comparative analyses of rDNA loci number and localisation. The chromosome base number and chromosomal organisation of 5S and 35S rDNA loci were analysed in the phylogenetic background for 39 species of Crepis, which represent the evolutionary lineages of Crepis sensu stricto and Lagoseris, including Lapsana communis. The phylogenetic relationships among all the species were inferred from nrITS and newly obtained 5S rDNA NTS sequences. Despite high variations in rDNA loci chromosomal organisation, most species had a chromosome with both rDNA loci within the same (usually short) chromosomal arm. The comparative analyses revealed several independent rDNA loci number gains and loci repositioning that accompanied diversification and speciation in Crepis. Some of the changes in rDNA loci patterns were reconstructed for the same evolutionary lineages as descending dysploidy.

Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View

Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.

Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae

Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae.

Pre- and postzygotic mechanisms preventing hybridization in co-occurring species of the Impatiens purpureoviolacea complex

In the species-rich genus Impatiens, few natural hybrids are known, even though closely related species often occur sympatrically. In this study, we aim to bridge the gap between micro- and macro-evolution to disentangle pre- and postzygotic mechanisms that may prevent hybridization in the Impatiens purpureoviolacea complex from Central Africa. We analyzed habitat types, species distribution, pollination syndromes, pollinator dependency, genome sizes, and chromosome numbers of seven out of the ten species of the complex as well as of one natural hybrid and reconstructed the ancestral chromosome numbers of the complex. Several species of the complex occur in sympatry or geographically very close to each other. All of them are characterized by pre- and/or postzygotic mechanisms potentially preventing hybridization. We found four independent polyploidization events within the complex. The only known natural hybrid always appears as single individual and is self-fertile. But the plants resulting from self-pollinated seeds often die shortly after first flowering. These results indicate that the investigated mechanisms in combination may effectively but not absolutely prevent hybridization in Impatiens and probably occur in other genera with sympatric species as well.

Conservation of floral, fruit and chromosomal diversity: a review on diploid and polyploid Capsicum annuum complex in India

Capsicum as a spice crop, has wild and cultivated forms admired globally, including Indian subcontinent with vast climatic ranges. Systematic representation of the Indian Capsicum is required to address species relationships and sustainable agriculture, in face of unpredictable climatic conditions. We have updated the catalogue of Indian 'C. annuum complex' with 28 landraces and populations from different agro-climatic regions. The agro-climatic influence on the origin of stable chili landraces in India is remarkable, especially in the North East. The floral and fruit morphotype standards and chromosomal attributes have been considered for four distinct 'C. annuum complex' members under three species. The highlights of study are: (1) comparative profiling of Indian Capsicum species revealing less infraspecific variation within C. frutescens and C. chinense than C. annuum, at par with cultivation status, (2) karyotype analysis of some unique diploid landraces of C. annuum, (3) karyotypic confirmation of the polyploid Dalle Khursani landraces exclusive to India. To obtain more information, we attempted to correlate diversity of fruit and floral morphotype with chromosomal diversity. Existence of elite and rare germplasm found in the regional pockets offer great scope for enriching the agricultural tradition. The present dataset may serve as a template to be continuously upgraded by taxonomists, genomicists and breeders.

A phylogenetic analysis of Momordica (Cucurbitaceae) in India based on karyo-morphology, nuclear DNA content and rDNA ITS1-5.8S-ITS2 sequences

The infrageneric delimitation of Momordica, a medicinally important genus of Cucurbitaceae, is ill-defined until date. Momordica chromosomes are extremely small and are difficult to stain and visualize because of the dense cytoplasmic background. We have conducted karyomorphometric analysis by EMA method in five Indian Momordica species, and the nuclear genome sizes were estimated by flow cytometry for the first time. The somatic chromosome numbers ranged from 2n = 18 to 56 in the species. We have resolved previously disputed chromosome numbers in M. cymbalaria and M. dioica as 2n = 18 (lowest) and 2n = 56, respectively. Chromosome counts in the other species were re-confirmed as 2n = 22 in M. charantia, 2n = 28 in M. cochinchinensis and 2n = 56 in M. subangulata. The largest genome size was recorded in M. cymbalaria (3.74 pg 2C^-1), while the smallest size (0.72 pg 2C^-1) was detected in M. charantia var. charantia. The nuclear genome sizes were analysed in comparison to chromosome numbers and total chromosome lengths of the species. Karyomorphometric indices showed comparable symmetric karyotypes in the species except in M. cymbalaria having tendency towards asymmetry. The UPGMA phenogram and principle component analysis based on nuclear DNA contents and karyomorphometric parameters demonstrated interspecies differences, intraspecific distinction within M. charantia varieties and highlighted distinction of M. cymbalaria. This study was further supported by the rDNA ITS sequence-based phylogenetic analysis which revealed the monophyletic origin of the Indian members of Momordica and clarified the intraspecies relationship among the studied members. As a whole, the study brought out new insights on species diversification within the genus Momordica in India and would benefit further studies on biosystematics and plant breeding programmes.

How much do we know about the frequency of hybridisation and polyploidy in the Mediterranean region?

Natural hybridisation and polyploidy are currently recognised as drivers of biodiversity, despite early scepticism about their importance. The Mediterranean region is a biodiversity hotspot where geological and climatic events have created numerous opportunities for speciation through hybridisation and polyploidy. Still, our knowledge on the frequency of these mechanisms in the region is largely limited, despite both phenomena are frequently cited in studies of Mediterranean plants. We reviewed information available from biodiversity and cytogenetic databases to provide the first estimates of hybridisation and polyploidy frequency in the Mediterranean region. We also inspected the most comprehensive modern Mediterranean Flora (Flora iberica) to survey the frequency and taxonomic distribution of hybrids and polyploids in Iberian Peninsula. We found that <6% of Mediterranean plants were hybrids, although a higher frequency was estimated for the Iberian Peninsula (13%). Hybrids were concentrated in few families and in even fewer genera. The overall frequency of polyploidy (36.5%) was comparable with previous estimates in other regions; however our estimates increased when analysing the Iberian Peninsula (48.8%). A surprisingly high incidence of species harbouring two or more ploidy levels was also observed (21.7%). A review of the available literature also showed that the ecological factors driving emergence and establishment of new entities are still poorly studied in the Mediterranean flora, although geographic barriers seem to play a major role in polyploid complexes. Finally, this study reveals several gaps and limitations in our current knowledge about the frequency of hybridisation and polyploidy in the Mediterranean region. The obtained estimates might change in the future with the increasing number of studies; still, rather than setting the complete reality, we hope that this work triggers future studies on hybridisation and polyploidy in the Mediterranean region.