Comparative Analysis and EST Mining Reveals High Degree of Conservation among Five Brassicaceae Species

Brassicaceae is an important family of the plant kingdom which includes several plants of major economic importance. The Brassica spp. and Arabidopsis share much-conserved colinearity between their genomes which can be exploited for the genomic research in Brassicaceae crops. In this study, 131,286 ESTs of five Brassicaceae species were assembled into unigene contigs and compared with Arabidopsis gene indices. Almost all the unigenes of Brassicaceae species showed high similarities with Arabidopsis genes except those of B. napus, where 90% of unigenes were found similar. A total of 9,699 SSRs were identified in the unigenes. PCR primers were designed based on this information and amplified across species for validation. Functional annotation of unigenes showed that the majority of the genes are present in metabolism and energy functional classes. It is expected that comparative genome analysis between Arabidopsis and related crop species will expedite research in the more complex Brassica genomes. This would be helpful for genomics as well as evolutionary studies, and DNA markers developed can be used for mapping, tagging, and cloning of important genes in Brassicaceae

Understanding Aquaporin Transport System in Eelgrass (Zostera marina L.), an Aquatic Plant Species

Aquaporins (AQPs) are a class of integral membrane proteins involved in the transport of water and many other small solutes. The AQPs have been extensively studied in many land species obtaining water and nutrients from the soil, but their distribution and evolution have never been investigated in aquatic plant species, where solute assimilation is mostly through the leaves. In this regard, identification of AQPs in the genome of Zostera marina L. (eelgrass), an aquatic ecological model species could reveal important differences underlying solute uptake between land and aquatic species. In the present study, genome-wide analysis led to the identification of 25 AQPs belonging to four subfamilies, plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic proteins (NIPs), small basic intrinsic proteins (SIPs) in eelgrass. As in other monocots, the XIP subfamily was found to be absent from the eelgrass genome. Further classification of subfamilies revealed a unique distribution pattern, namely the loss of the NIP2 (NIP-III) subgroup, which is known for silicon (Si) transport activity and ubiquitously present in monocot species. This finding has great importance, since the eelgrass population stability in natural niche is reported to be associated with Si concentrations in water. In addition, analysis of available RNA-seq data showed evidence of expression in 24 out of the 25 AQPs across four different tissues such as root, vegetative tissue, male flower and female flower. In contrast to land plants, higher expression of PIPs was observed in shoot compared to root tissues. This is likely explained by the unique plant architecture of eelgrass where most of the nutrients and water are absorbed by shoot rather than root tissues. Similarly, higher expression of the TIP1 and TIP5 families was observed specifically in male flowers suggesting a role in pollen maturation. This genome-wide analysis of AQP distribution, evolution and expression dynamics can find relevance in understanding the adaptation of aquatic and land species to their respective environments

Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.)

Rice pericarp colour is one of the nutritional traits that is now gaining attention worldwide. In the present investigation, genome-wide association GWAS) was performed to identify loci governing pericarp colour in rice. A set of 1,349,269 SNPs and precise phenotyping across 325 diverse accessions of rice were used for the GWAS. The accessions belong to five rice isozyme classification groups viz., indica, japonica, aromatic, aus, and admix. The GWAS identified two significant loci gPC5-1and gPC7-1 on chromosomes, 5 and 7, respectively, associated with the pericarp colour in rice. The SNPs on chromosome 7 co-localized with the functionally characterized Os07g0211500 (Rc gene) known to control pericarp colour and Os07g0214900 which is similar to the Chalcone synthase 2(OsCHS2) gene involved in flavonoid synthesis pathway. Linkage disequilibrium analysis across 0.25 Mbp upstream and downstream of these markers suggested three strong linkage blocks on chromosome 7. More interestingly, the novel locus identified on chromosome 5 gPC5-1 does not harbor any homolog of previously reported genes. Therefore, the locus can serve as a basis for identifying a new gene for rice pericarp colour. The results presented here will be helpful to understand the genetic regulation of pericarp colour and for genomic-assisted breeding in rice

Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium

Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database ‘BraMi’ (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot–dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s)

Plant Aquaporins: genome-wide identification, transcriptomics, proteomics, and advanced analytical tools

Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is offered as a resource for AQP research.

Identification and characterization of aquaporin genes in Arachis duranensis and Arachis ipaensis genomes, the diploid progenitors of peanut

Abstract Background Aquaporins (AQPs) facilitate transport of water and small solutes across cell membranes and play an important role in different physiological processes in plants. Despite their importance, limited data is available about AQP distribution and function in the economically important oilseed crop peanut, Arachis hypogea (AABB). The present study reports the identification and structural and expression analysis of the AQPs found in the diploid progenitor genomes of A. hypogea i.e. Arachis duranensis (AA) and Arachis ipaensis (BB). Results Genome-wide analysis revealed the presence of 32 and 36 AQPs in A. duranensis and A. ipaensis, respectively. Phylogenetic analysis showed similar numbers of AQPs clustered in five distinct subfamilies including the plasma membrane intrinsic proteins (PIPs), the tonoplast intrinsic proteins (TIPs), the nodulin 26-like intrinsic proteins (NIPs), the small basic intrinsic proteins (SIPs), and the uncharacterized intrinsic proteins (XIPs). A notable exception was the XIP subfamily where XIP1 group was observed only in A. ipaensis genome. Protein structure evaluation showed a hydrophilic aromatic/arginine (ar/R) selectivity filter (SF) in PIPs whereas other subfamilies mostly contained a hydrophobic ar/R SF. Both genomes contained one NIP2 with a GSGR SF indicating a conserved ability within the genus to uptake silicon. Analysis of RNA-seq data from A. hypogea revealed a similar expression pattern for the different AQP paralogs of AA and BB genomes. The TIP3s showed seed-specific expression while the NIP1s’ expression was confined to roots and root nodules. Conclusions The identification and the phylogenetic analysis of AQPs in both Arachis species revealed the presence of all five sub-families of AQPs. Within the NIP subfamily, the presence of a NIP2 in both genomes supports a conserved ability to absorb Si within plants of the genus. The global expression profile of AQPs in A. hypogea revealed a similar pattern of AQP expression regardless of the subfamilies or the genomes. The tissue-specific expression of AQPs suggests an important role in the development and function of the respective organs. The AQPs identified in the present study will serve as a resource for further characterization and possible exploitation of AQPs to understand their physiological role in A. hypogea