Genomic Organization Research Articles

InvertiaDB: A Database of Inverted Repeats Across Organismal Genomes.

Inverted repeats are repetitive elements that can form hairpin and cruciform structures. They are linked to genomic instability, however they also have various biological functions. Their distribution differs markedly across taxonomic groups in the tree of life, and they exhibit high polymorphism due to their inherent genomic instability. Advances in sequencing technologies and declined costs have enabled the generation of an ever-growing number of complete genomes for organisms across taxonomic groups in the tree of life. However, a comprehensive database encompassing inverted repeats across diverse organismal genomes has been lacking. We present InvertiaDB, the first comprehensive database of inverted repeats spanning multiple taxa, featuring repeats identified in the genomes of 118,070 organisms across all major taxonomic groups. The database currently hosts 30,067,666 inverted repeat sequences, serving as a centralized, user-friendly repository to perform searches, interactive visualization, and download existing inverted repeat data for independent analysis. invertiaDB is implemented as a web portal for browsing, analyzing and downloading inverted repeat data. invertiaDB is publicly available at https://invertiadb.netlify.app/homepage.html.

Evolution of 3D Chromatin Folding.

Studies examining the evolution of genomes have focused mainly on sequence conservation. However, the inner working of a cell implies tightly regulated crosstalk between complex gene networks controlled by small dispersed regulatory elements of physically contacting DNA regions. How these different levels of chromatin organization crosstalk in different species underpins the potential for genome evolutionary plasticity. We review the evolution of chromatin organization across the Animal Tree of Life. We introduce general aspects of the mode and tempo of genome evolution to later explore the multiple layers of genome organization. We argue that both genome and chromosome size modulate patterns of chromatin folding and that chromatin interactions facilitate the formation of lineage-specific chromosomal reorganizations, especially in germ cells. Overall, analyzing the mechanistic forces involved in the maintenance of chromatin structure and function of the germ line is critical for understanding genome evolution, maintenance, and inheritance.

NCBI RefSeq: reference sequence standards through 25years of curation and annotation.

Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life. RefSeq continues to refine its annotation and quality control processes and utilize better quality genomes resulting from advances in sequencing technologies as well as RNA-Seq data to produce high-quality annotated genomes, ortholog predictions across more organisms and other products that are easily accessible through multiple NCBI resources. This report summarizes the current status of the eukaryotic, prokaryotic and viral RefSeq resources, with a focus on eukaryotic annotation, the increase in taxonomic representation and the effect it will have on comparative genomics. The RefSeq resource is publicly accessible at https://www.ncbi.nlm.nih.gov/refseq.

Genetic characteristics of the diploid offsprings in potato Cooperation 88 induced by diploid donor IVP101.

Diploid lines (2n = 2x = 24) derived from tetraploid potato cultivars have been utilized to hybridize with wild diploid potato species, yielding fertile offsprings. Utilizing the pollen of Solanum tuberosum Group Phureja, such as IVP101, IVP35 and IVP48, as an inducer for wide hybridization with tetraploid cultivars represents a common method for producing diploids. In this study, we created a distant hybridization induced population of tetraploid potato cultivar Cooperation 88 (C88) and IVP101, and screened all diploids using flow cytometry and ploidyNGS. We investigated the genetic composition of chloroplast and nuclear genomes in 43 diploid offsprings. We found that all diploid offsprings share the same chloroplast genomic sequence as C88 and no evidence of paternal chloroplast inheritance was found. Used SNP data to calculate the theoretical introgression index of IVP101 with diploid offsprings. The results showed that the inducer's nuclear genome was involved in the nuclear genome of the diploid offsprings with purple stem trait, indicating that the inducer nuclear genome was not completely eliminated in the nuclear genome during distant hybridization. Furthermore, we conducted a comparative analysis of the chloroplast genomes of the Solanum genus. The results indicated that (1) the chloroplast genome sizes of the 14 Solanum species ranged from 154,289 bp to 155,614 bp, with a total number of genes ranging 128-141, and with ycf1 and rps19 pseudogenes appearing at the IRB/SSC and IRA/LSC boundaries, respectively; (2) eight divergent hotspots distributed in the LSC and SSC regions of the Solanum chloroplast genomes were identified; (3) positive selection was detected in the clpP, rbcL, rps15, and rps4 genes, likely contributing to the adaptation of Solanum species to different habitats. These results reveal the variation and evolutionary characteristics of chloroplast genomes in Solanum plants.

Unraveling the impact of genome assembly on bacterial typing: a one health perspective

BackgroundIn the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool).MethodsSimulations of short-read sequencing were conducted for 5 genomes of 27 pathogens of interest in animal, plant, and human health to evaluate the repeatability and reproducibility of cgMLST. Various quality parameters, such as read quality and depth of sequencing were applied, and several read simulations and genome assemblies were repeated using three tools: SPAdes, Unicycler and Shovill. In vitro sequencing were also used to evaluate assembly impact on cgMLST results, for six bacterial species: Bacillus thuringiensis, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, Vibrio parahaemolyticus and Xylella fastidiosa.ResultsThe results highlighted variability in cgMLST, which not only related to the assembly tools, but also induced by the intrinsic composition of the genomes themselves. This variability observed in simulated sequencing was further validated with real data for six of the bacterial pathogens studied.ConclusionThis highlights that the intrinsic genome composition affects assembly and resulting cgMLST profiles, and that variability in bioinformatics tools can induce a bias in cgMLST profiles. In conclusion, we propose that the completeness of cgMLST schemes should be considered when clustering strains.

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.

Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We developed a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implemented it in the SuPreMo-Akita software (Gjoni and Pollard 2024). With this tool, we ranked hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This revealed that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritized candidate variants that disrupt ASD CREints and validated our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study establishes disrupted genome folding as a potential genetic mechanism in ASD and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.

A mini-review of single-cell Hi-C embedding methods

Single-cell Hi-C (scHi-C) techniques have significantly advanced our understanding of the 3D genome organization, providing crucial insights into the spatial genome architecture within individual nuclei. Numerous computational and statistical methods have been developed to analyze scHi-C data, with embedding methods playing a key role. Embedding reduces the dimensionality of complex scHi-C contact maps, making it easier to extract biologically meaningful patterns. These methods not only enhance cell clustering based on chromatin structures but also facilitate visualization and other downstream analyses. Most scHi-C embedding methods incorporate strategies such as normalization and imputation to address the inherent sparsity of scHi-C data, thereby further improving data quality and interpretability. In this review, we systematically examine the existing methods designed for scHi-C embedding, outlining their methodologies and discussing their capabilities in handling normalization and imputation. Additionally, we present a comprehensive benchmarking analysis to compare both embedding techniques and their clustering performances. This review serves as a practical guide for researchers seeking to select suitable scHi-C embedding tools, ultimately contributing to the understanding of the 3D organization of the genome.

Hybrid Origin of ×Leymotrigia bergrothii (Poaceae) as Revealed by Analysis of the Internal Transcribed Spacer ITS1 and trnL Sequences.

×Leymotrigia bergrothii is a presumed hybrid of Leymus arenarius and Elytrigia repens. This article investigates the hybrid origin and genome composition of this species. These plants are sterile, do not undergo pollination, and do not produce seeds; occasionally, underdeveloped stamens containing abortive pollen grains form in individual spikelets. The karyotype analysis of root meristem cells revealed a diploid chromosome number of 49 in ×L. bergrothii, reported here for the first time. Subsequently, we examined the intragenomic polymorphism of the transcribed spacer ITS1 in several species of Elytrigia, Elymus, Leymus, Hordeum, and Psathyrostachys, and compared the ribotype patterns of these species with those of ×L. bergrothii. It is shown that the St-ribotype variants found in Elytrigia repens and Elytrigia pseudocaesia, as well as the ribotypes of the La family, which dominate in the genome of Leymus arenarius, correspond to major ribotypes in ×L. bergrothii. The ribotypes of the St and La families are present in the nuclear genome of ×L. bergrothii in almost equal proportions. A comparison of intron and exon sequences of the trnL gene in the chloroplast DNA of Leymus arenarius, Elytrigia repens, and ×L. bergrothii showed that this region in ×L. bergrothii is identical or very close to that of Elytrigia repens, suggesting that Elytrigia repens was the cytoplasmic donor to ×L. bergrothii. Thus, our study confirms the hypothesis that this species represents a sterile first-generation hybrid of Leymus arenarius and Elytrigia repens, reproducing vegetatively.

Characterization, phylogeny and recombination of Rhynchosia yellow mosaic virus infecting Rhynchosia minima, a wild relative of pigeonpea (Cajanus cajan) from India.

Rhynchosia minima grown at Indian Institute of Pulses Research, Kanpur, India, showed yellow mosaic symptoms on leaves and were suspected to be caused by begomovirus(es). Leaves from five different plants (Rhm1-Rhm5) were tested for the presence of four viruses in PCR. PCR assays revealed the presence of mungbean yellow mosaic India virus in four samples, whereas one sample (Rhm2) was negative. Processing of Rhm2 sample using rolling circle amplification and restriction digestion indicated the presence of DNA molecules of ~ 2.6-2.7kb. These molecules were sequenced after cloning and found to be of 2741 and 2658 nucleotides in size. BLAST analysis revealed that DNA-A (OQ269467) and DNA-B (OQ269468) molecules of rhynchosia yellow mosaic virus (RhYMV) with 99.09% and 93.74% nucleotide similarity with DNA-A (KP752090) and DNA-B (KP752091) of the RhYMV isolate, respectively. These sequences had a genome organization typical of legume-infecting Old World bipartite begomoviruses. Full genome sequences obtained from Rhm2 are, therefore, considered to be an isolate of RhYMV, designated as RhYMV-IN-Knp. The phylogenetic analysis revealed that RhYMV-IN-Knp was grouped with other isolates of RhYMV followed by Cajanus scarabaeoides yellow mosaic virus. DNA-A of RhYMV-IN-Knp showed two recombination events. The Old World bipartite begomovirus squash leaf curl China virus (AM260205) was identified as the major parent, whereas New World bipartite begomovirus rhynchosia golden yellow mosaic Yucatan virus (EU021216) was identified as the minor parent. RhYMV holds the potential of infecting cultivated legume crops, therefore regular monitoring is crucial especially for pigeonpea breeding programs.

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization.

Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR)within the U and V chromosomes are insulated and span the centromeres andwe link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome's 3D chromosomal folding.

Characterisation of LGP2 complex multitranscript system in humans: role in the innate immune response and evolution from non-human primates.

Retinoic acid inducible gene I (RIG-I)-like receptors (RLRs), including RIG-I, MDA5 and LGP2, recognize viral RNA to mount an antiviral interferon (IFN) response RLRs share three different protein domains: C-terminal domain, DExD/H box RNA helicase domain, and an N-terminal domain with two tandem repeats (CARDs). LGP2 lacks tandem CARD and is not able to induce an IFN response. However, LGP2 positively enhances MDA5 and negatively regulates RIG-I signaling. In this study, we determined the LGP2 alternative transcripts in humans to further comprehend the mechanism of its regulation, their evolutionary origin, and the isoforms functionallity. The results showed new eight alternative transcripts in the samples tested. The presence of these transcripts demonstrated that the main mechanisms for the regulation of LGP2 expression are both by insertion of introns and by the loss of exons. The phylogenetic analysis of the comparison between sequences from exon 1 to exon 3 of humans and those previously described in non-human primates showed three well-differentiated groups (lineages) originating from gorillas, suggesting that the transspecies evolution has been maintained for 10 million years. The corresponding protein models (isoforms) were also established, obtaining four isoforms: one complete and three others lacking the C-terminal domain or this domain and the partial or total He2 Helicase domain, which would compromise the functionality of LGP2. In conclusion, this is the first study that elucidate the large genomic organization and complex transcriptional regulation of human LGP2, its pattern of sequence generation, and a mode of evolutionary inheritance across species.

Evolutionary history written in tandem arrays – satellite repeats in the Lagoseris lineage of Crepis sensu lato (Asteraceae)

Abstract Satellite DNA families are excellent markers in evolutionary studies of plant karyotypes. Together with phylogenetic background, they can provide additonal information on different scenarios accompanying the speciation and diversification of related species. The Lagoseris lineage of Crepis sensu lato constitutes an interesting model in such studies, mainly due to: (i) the presence of large chromosomes; (ii) several base chromosome numbers; and (iii) variation in genome sizes. We aimed to characterize the satellite families and compare their genomic and chromosomal organization to better understand the evolutionary pathways that shaped the genomes of the Lagoseris lineage. Eight different families of satellite repeats were identified in Crepis palaestina based on RepeatExplorer raw Illumina read analyses. Most of these satellites were present in five species studied from the Lagoseris lineage and organized in tandem arrays. If the particular repeat was present in the genome of the related species, its genomic organization showed similarity to the one observed in C. palaestina. This similar genomic organization was not often reflected at the chromosomal level, where many distinct distribution patterns were shown, from several major loci to numerous minor ones spread throughout the chromosomal arms. The evolution of satellite repeats is discussed in phylogenetic context.

Evolution of Plant Genome Size and Composition.

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we focus on changes in plant genome size and composition, examining the effects of polyploidy, whole-genome duplication, and alternations in transposable elements on plant genome architecture and evolution, respectively. In addition, to address gaps in the available information, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a comprehensive, up-to-date summary of information on plant genome architecture and evolution in this review.

EXPRESSO: a multi-omics database to explore multi-layered 3D genomic organization.

The three-dimensional (3D) organization of the human genome plays a crucial role in gene regulation. EXPloration of Regulatory Epigenome with Spatial and Sequence Observations (EXPRESSO) is a novel multi-omics database for exploration and visualization of multi-layered 3D genomic features across 46 different human tissues. Integrating 1360 3D genomic datasets (Hi-C, HiChIP, ChIA-PET) and 842 1D genomic and transcriptomic datasets (ChIP-seq, ATAC-seq, RNA-seq) from the same biosample, EXPRESSO provides a comprehensive resource for studying the interplay between 3D genome architecture and transcription regulation. This database offers diverse 3D genomic feature types (compartments, contact matrix, contact domains, stripes as diagonal lines extending from a genomic locus in contact matrix, chromatin loops, etc.) and user-friendly interface for both data exploration and download. Other key features include REpresentational State Transfer application programming interfaces for programmatic access, advanced visualization tools for 3D genomic features and web-based applications that correlate 3D genomic features with gene expression and epigenomic modifications. By providing extensive datasets and tools, EXPRESSO aims to deepen our understanding of 3D genomic architecture and its implications for human health and disease, serving as a vital resource for the research community. EXPRESSO is freely available at https://expresso.sustech.edu.cn.

Development and evolution of Drosophila chromatin landscape in a 3D genome context

Little is known about how the epigenomic states change during development and evolution in a 3D genome context. Here we use Drosophila pseudoobscura with complex turnover of sex chromosomes as a model to address this, by collecting massive epigenomic and Hi-C data from five developmental stages and three adult tissues. We reveal that over 60% of the genes and transposable elements (TE) exhibit at least one developmental transition of chromatin state. Transitions on specific but not housekeeping enhancers are associated with specific chromatin loops and topologically associated domain borders (TABs). While evolutionarily young TEs are generally silenced, old TEs more often have been domesticated as interacting TABs or specific enhancers. But on the recently evolved X chromosome, young TEs are instead often active and recruited as TABs, due to acquisition of dosage compensation. Overall we characterize how Drosophila epigenomic landscapes change during development and in response to chromosome evolution, and highlight the important roles of TEs in genome organization and regulation.

Kosakonia calanthes sp. nov., a plant growth-promoting bacterium, isolated from Calanthe triplicata leaves in China.

A Gram-stain-negative, facultatively aerobic, rod-shaped and motile bacterium, designated as CCTCC AB 2023082T, was isolated from leaves of Calanthe triplicata in China. Optimal growth occurred at 4-45 ℃ and pH 4.0-10.0 and in the presence of 0-7% (w/v) NaCl. The major fatty acids of the strain CCTCC AB 2023082T were C16 : 0, sum of C16 : 1 ω7c/C16 : 1 ω6c, C17 : 0 cyclo and C18 : 1 ω7c. The polar lipids included unidentified lipids, phospholipids, phosphatidylethanolamine, phosphatidylglycerol and amino phospholipid. The DNA G+C content of strain CCTCC AB 2023082T was 54.2 mol%. 16S rRNA gene sequence analysis indicated that strain CCTCC AB 2023082T formed a distinct lineage within the genus Kosakonia and exhibited the highest similarity to Kosakonia quasisacchari, with a 97.9% 16S rRNA gene sequence similarity. Moreover, the preliminary analysis of the organism's genome suggested its potential as a biostimulant for augmenting plant growth. According to its genotypic, phenotypic, phylogenetic and chemotaxonomic characteristics, strain CCTCC AB 2023082T should be categorized as a novel species in the genus Kosakonia. The novel species was named Kosakonia calanthes sp. nov., and its type strain is CCTCC AB 2023082T (=JCM 36393T).

Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.

We investigated the efficiency of target-enriched long-read sequencing (TELSeq) for detecting antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection methods, including short-read shotgun metagenomics, which can lack sensitivity, specificity, and the ability to provide detailed genomic context. By combining biotinylated probe-based enrichment with long-read sequencing, we facilitated the amplification and sequencing of ARGs, eliminating the need for bioinformatic reconstruction. Our experimental design included replicates of human fecal microbiota transplant material, bovine feces, pristine prairie soil, and a mock human gut microbial community, allowing us to examine variables including genomic DNA input and probe set composition. Our findings demonstrated that TELSeq markedly improves the detection rates of ARGs and MGEs compared to traditional sequencing methods, underlining its potential for accurate AMR monitoring. A key insight from our research is the importance of incorporating mobilome profiles to better predict the transferability of ARGs within microbial communities, prompting a recommendation for the use of combined ARG-MGE probe sets for future studies. We also reveal limitations for ARG detection from low-input workflows, and describe the next steps for ongoing protocol refinement to minimize technical variability and expand utility in clinical and public health settings. This effort is part of our broader commitment to advancing methodologies that address the global challenge of AMR.

Non-canonical spatial organization of heterochromatin in mouse preimplantation embryos.

Spatial genome organization refers to the conformation of the chromosomes and their relative positioning within the nucleus. In mammals, fertilization entails intense chromatin remodeling of parental genomes, as well as large-scale structural changes in nuclear organization of the newly formed zygote over the first two cell cleavages. The molecular characteristics, mechanisms and functionality of spatial genome organization during the early steps of development in mouse have been extensively studied and will be presented in this review, with a specific focus on heterochromatin. Concomitantly to maturation of genomic architecture, the embryonic genome activation occurs in transient waves of transcription. Here, we will also discuss the putative link between heterochromatin organization and the regulation of genome expression.

Accurate Detection of scutellata-Hybrids (Africanized Bees) Using a SNP-Based Diagnostic Assay.

Hybrid populations of Africanized honey bees (scutellata-hybrids), notable for their defensive behaviour, have spread rapidly throughout South and North America since their unintentional introduction. Although their migration has slowed, the large-scale trade and movement of honey bee queens and colonies raise concern over the accidental importation of scutellata-hybrids to previously unoccupied areas. Therefore, developing an accurate and robust assay to detect scutellata-hybrids is an important first step toward mitigating risk. Here, we used an extensive population genomic dataset to assess the genomic composition of Apis mellifera native populations and patterns of genetic admixture in North and South American commercial honey bees. We used this dataset to develop a SNP assay, where 80 markers, combined with machine learning classification, can accurately differentiate between scutellata-hybrids and non-scutellata-hybrid commercial colonies. The assay was validated on 1263 individuals from colonies located in Canada, the United States, Australia and Brazil. Notably, we demonstrate that using a reduced SNP set of as few as 10 loci can still provide accurate results.

In silico analysis of R2R3-MYB transcription factors in the basal eudicot model, Aquilegia coerulea

R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, Aquilegia coerulea is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized Arabidopsis thaliana R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon–intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as A. thaliana R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus Aquilegia. AqcoeR2R3-MYB genes are present in all seven chromosomes of A. coerulea, most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in A. coerulea. It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology.