A segmental duplication in the common ancestor of Brassicaceae is responsible for the origin of the paralogs KCS6-KCS5, which are not shared with other angiosperms

Comparative genomics, microsynteny, ancestral state reconstruction and selection pressure analysis across distinctive genomes and sub-genomes of Brassicaceae for analysis of evolutionary history of VQ gene family

Any unfavorable condition that affects the metabolism, growth, or development of plants is considered plant stress. The molecular response of plants towards abiotic stresses involves signaling to cellular components, repressing transcription factors, and subsequently induced metabolic changes. Most valine-glutamine (VQ) motif-containing genes in plants encode regulatory proteins that interact with transcription factors and modulate their activity as transcription regulators. Several VQ proteins regulate plant development and stress responses. In spite of the functional importance of VQs, there is relatively little information about their evolutionary history in Brassicaceae or beyond. Brassicaceae is characterized by paleoploidy, mesopolyploidy, and neopolyploidy, offering a resource for studying evolution and diversification. In current study we performed phylogeny of the VQ gene family along with comparative genomics, microsynteny and evolutionary rates analysis across seven species of Brassicaceae. Our findings revealed the following; (1) a large segmental duplication in the shared common ancestor of the family Brassicaceae, resulted in paralogies of VQ1-VQ10, VQ15-VQ24, VQ16-VQ23, VQ17-VQ25, VQ18-VQ26, VQ22-VQ27; (2) chromosomal mapping revealed diverse distributions of the gene family; (3) duplicated segments undergo varying degrees of retention and loss; and (4) Out of the 12 paralogous members, most of the genes are under purifying selection. However, VQ23 in Brassicaceae stands out as it is under positive selection, indicating the need for further investigation. Overall, our results clearly establish that the ancestral VQ1/VQ10, VQ15/VQ24, VQ16/VQ23, VQ17/VQ25, VQ18/VQ26, VQ22/VQ27 genes duplicated in shared common ancestor of Brassicaceae.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01347-z.

A prescient evolutionary model for genesis, duplication and differentiation of MIR160 homologs in Brassicaceae

MicroRNA160 is a class of nitrogen-starvation responsive genes which governs establishment of root system architecture by down-regulating AUXIN RESPONSE FACTOR genes (ARF10, ARF16 and ARF17) in plants. The high copy number of MIR160 variants discovered by us from land plants, especially polyploid crop Brassicas, posed questions regarding genesis, duplication, evolution and function. Absence of studies on impact of whole genome and segmental duplication on retention and evolution of MIR160 homologs in descendent plant lineages prompted us to undertake the current study. Herein, we describe ancestry and fate of MIR160 homologs in Brassicaceae in context of polyploidy driven genome re-organization, copy number and differentiation. Paralogy amongst Brassicaceae MIR160a, MIR160b and MIR160c was inferred using phylogenetic analysis of 468 MIR160 homologs from land plants. The evolutionarily distinct MIR160a was found to represent ancestral form and progenitor of MIR160b and MIR160c. Chronology of evolutionary events resulting in origin and diversification of genomic loci containing MIR160 homologs was delineated using derivatives of comparative synteny. A prescient model for causality of segmental duplications in establishment of paralogy in Brassicaceae MIR160, with whole genome duplication accentuating the copy number increase, is being posited in which post-segmental duplication events viz. differential gene fractionation, gene duplications and inversions are shown to drive divergence of chromosome segments. While mutations caused the diversification of MIR160a, MIR160b and MIR160c, duplicated segments containing these diversified genes suffered gene rearrangements via gene loss, duplications and inversions. Yet the topology of phylogenetic and phenetic trees were found congruent suggesting similar evolutionary trajectory. Over 80% of Brassicaceae genomes and subgenomes showed a preferential retention of single copy each of MIR160a, MIR160b and MIR160c suggesting functional relevance. Thus, our study provides a blue-print for reconstructing ancestry and phylogeny of MIRNA gene families at genomics level and analyzing the impact of polyploidy on organismal complexity. Such studies are critical for understanding the molecular basis of agronomic traits and deploying appropriate candidates for crop improvement.

Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator

Intra- and epicuticular-waxes primarily comprising of very long chain aliphatic lipid (VLCFA), terpenoids and secondary metabolites such as sterol and flavonoids played a major role in successful colonization of terrestrial ecosystem by aquatic plants and are thus considered as a key evolutionary innovation. The key rate limiting step of Fatty Acid (FA) biosynthesis of condensation/elongation are catalyzed by the enzyme, β-ketoacyl coenzyme A synthase (KCS), part of FAE (Fatty Acid Elongase) complex. KCS6 has been shown to be responsible for elongation using C22 fatty acid as substrate and is considered essential for synthesis of VLCFA for cuticular waxes. Earlier studies have established KCS5 as a close paralog of KCS6 in Arabidopsis thaliana, albeit with non-redundant function. We subsequently established segmental duplication responsible for origin of KCS6-KCS5 paralogy which is exclusive to Brassicaceae. In the present study, we aim to understand impact of duplication on regulatory diversification and evolution, through sequence and functional analysis of cis-regulatory element of KCS5 and KCS6. High level of sequence variation leading to conservation of only the proximal end of the promoter corresponding to the core promoter was observed among Brassicaceae members; such high diversity was also revealed when sliding window analysis revealed only two to three phylogenetic footprints. Profiling of transcription factor binding sites (TFBS) across Brassicaceae shows presence of light, hormone and stress responsive motifs; a few motifs involved in tissue specific expression (Skn-1; endosperm) were also detected. Functional characterization using transcriptional fusion constructs revealed regulatory diversification when promoter activity of homologs from A. thaliana and Brassica juncea were compared. When subjected to 5-Azacytidine, altered promoter activity was observed, implying role of DNA methylation in transcriptional regulation. Finally, investigation of the role of an 87 bp fragment from first intron that is retained in a splice variant, revealed it to be a transcriptional repressor. This is a first report on comparative sequence and functional analysis of transcriptional regulation of KCS5 and KCS6; further studies are required before manipulation of cuticular waxes as a strategy for mitigating stress.

Stress induced dynamic adjustment of conserved miR164:NAC module

Aims including the rationale

Salinity and drought are the two major stresses limiting the productivity of economically important crops such as Glycine max (soybean). The incidence of these stresses during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NAC module has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NAC module in salt stress in soybean is not fully understood.

Methods

In this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets.

Key results

It was found that four salt stress deregulated miRNAs targeted the NAC transcription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (-2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co-expression assay validated that gma-miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC-TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions.

Main conclusion

Collectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC-TF module may play an important role in determining the adaptive response of plants to stress.

Ancestral segmental duplication in Solanaceae is responsible for the origin of CRCa-CRCb paralogues in the family

CRABS CLAW (CRC), a member of YABBY transcription factor family, has been previously reported to be principally involved in carpel development across angiosperms, and nectary development in core eudicots. Most of the studies suggest that CRC exists as a single copy gene, except in the Solanaceae where CRC occurs as paralogous pairs-CRCa-CRCb in Solanum lycopersicum, and CRC1-CRC2 in Petunia hybrida. In spite of their crucial role in carpel and nectary development, there is no information about the evolutionary history of the CRC paralogy in Solanaceae and whether the paralogy extends beyond Solanaceae. We analyzed homologues of CRC across angiosperms including genome sequence of fourteen species of Solanaceae available at Sol Genomics Network database, Phytozome and NCBI, to address the questions. Our phylogenetic reconstruction across angiosperms combined with comparative genomic, microsynteny and genome-fractionation analyses across the Solanaceae genomes revealed that (1) the CRCa-CRCb lineage is represented by a single copy in other flowering plants; (2) putative homologues of CRCa and CRCb are present in all the Solanaceae genomes studied; (3) the CRCa-CRCb paralogy in Solanaceae is associated with a large segmental duplication within Solanaceae (perhaps in its common ancestor), and (4) the duplicated segments have undergone different degrees of retention and loss of genes. Also, the CRC gene lineage expanded in Solanaceae following Solanaceae-α hexaploidy event and that two CRC duplicate copies were subsequently retained during the course of evolution. Besides the first detailed description of CRC evolution in Solanaceae, the study identifies potential candidate genes for future functional investigations.

Genome sequences of horticultural plants: past, present, and future

Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials for beverages, and herbal medicines and by acting as ornamentals. They have also shaped human art, culture, and environments and thereby have influenced the lifestyles of humans. With the advent of sequencing technologies, there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication. Here we summarize the advances in the genome sequencing of horticultural plants, the reconstruction of pan-genomes, and the development of horticultural genome databases. We also discuss past, present, and future studies related to genome sequencing, data storage, data quality, data sharing, and data visualization to provide practical guidance for genomic studies of horticultural plants. Finally, we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.

Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae

The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landscape and in expansion of gene families is crucial toward developing insights into evolutionary trends and consequences such as sequence and functional diversification. Members of Brassicaceae are known to have experienced several rounds of whole-genome duplication (WGD) that have been termed as paleopolyploidy, mesopolyploidy, and neopolyploidy. Such repeated events led to the creation and expansion of a large number of gene families. MIR319 is reported to be one of the most ancient and conserved plant MIRNA families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of miR319 in Brassica oleracea affecting leaf architecture; however, the evolutionary history of the MIR319 gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without MIR319, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of MIR319a, MIR319b, and MIR319c were compared either between themselves or against Arabidopsis thaliana genome which was taken as the base genome. The highest levels of shared genes were found between A. thaliana and Capsella rubella in both MIR319b- and MIR319c-containing genomic segments, and with the closest species of A. thaliana, A. lyrata, only in MIR319a-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed MIR319c to be the most conserved MIRNA loci (present in 27 genomes/sub-genomes) followed by MIR319a (present in 23 genomes/sub-genomes); MIR319b was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of MIRNA homeologous loci and flanking genes from various sub-genomes of Brassica species that is in accordance with their older history of polyploidy when compared to Camelina sativa, a recent neopolyploid, where the effect of genome fractionation was least. Finally, estimation of phylogenetic relationship using precursor sequences of MIR319 reveals MIR319a and MIR319b form sister clades, with MIR319c forming a separate clade. An intra-species synteny analysis between MIR319a-, MIR319b-, and MIR319c-containing genomic segments suggests segmental duplications at the base of Brassicaceae to be responsible for the origin of MIR319a and MIR319b.

Identification and Analysis of OVATE Family Members from Genome of the Early Land Plants Provide Insights into Evolutionary History of OFP Family and Function

Mosses, liverworts, hornworts and lycophytes represent transition stages between the aquatic to terrestrial/land plants. Several morphological and adaptive novelties driven by genomic components including emergence and expansion of new or existing gene families have played a critical role during and after the transition, and contributed towards successful colonization of terrestrial ecosystems. It is crucial to decipher the evolutionary transitions and natural selection on the gene structure and function to understand the emergence of phenotypic and adaptive diversity. Plants at the "transition zone", between aquatic and terrestrial ecosystem, are also the most vulnerable because of climate change and may contain clues for successful mitigation of the challenges of climate change. Identification and comparative analyses of such genetic elements and gene families are few in mosses, liverworts, hornworts and lycophytes. Ovate family proteins (OFPs) are plant-specific transcriptional repressors and are acknowledged for their roles in important growth and developmental processes in land plants, and information about the functional aspects of OFPs in early land plants is fragmentary. As a first step towards addressing this gap, a comprehensive in silico analysis was carried out utilizing publicly available genome sequences of Marchantia polymorpha (Mp), Physcomitrella patens (Pp), Selaginella moellendorffii (Sm) and Sphagnum fallax (Sf). Our analysis led to the identification of 4 MpOFPs, 19 PpOFPs, 6 SmOFPs and 3 SfOFPs. Cross-genera analysis revealed a drastic change in the structure and physiochemical properties in OFPs suggesting functional diversification and genomic plasticity during the evolutionary course. Knowledge gained from this comparative analysis will form the framework towards deciphering and dissection of their developmental and adaptive role/s in early land plants and could provide insights into evolutionary strategies adapted by land plants.