Search

Calmodulin-binding transcription activator (CAMTA) is one of the key transcription factor families possessing calcium receptors (calmodulins, CaM). It modulates the expression levels of genes associated with ontogeny and various biotic and abiotic stress factors. The CAMTA family genes were known to be involved in different abiotic stress in several crop species. However, their functional relevance in sesame remains unexplored. To understand the role of CAMTA in stress tolerance in sesame, we performed a genome-wide analysis to identify the members of the SiCAMTA gene family. We have identified and reported here the five SiCAMTA genes localized on four chromosomes within the sesame genome. In silico analysis of the putative 2-kilobase (kb) promoter regions for these five SiCAMTA genes showed that phytohormone and stress response-related cis-elements were predominated in SiCAMTA2 and SiCAMTA5. Also, we studied its modulated expression levels, with special reference to drought and waterlogging stress. It revealed that the SiCAMTA5 and SiCAMTA2 genes were the most responsive to the studied stress factors. The target prediction and network analysis suggested that SiCAMTAs could bind the CGCG cis element in the target gene promoters and predicted 1202 SiCAMTA target genes in the sesame genome, including abiotic stress-responsive genes viz. LEA, PIP1–2, PPO1, SAP, ARF17, and GA3OX1. These findings were validated using qPCR analysis for five CAMTA and 10 CAMTA target genes and establish a foundation for future functional research of SiCAMTA genes towards sesame stress tolerance.

Abstract Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR‐National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics‐assisted double‐digest restriction‐associated DNA sequencing (ddRAD‐seq) approach. A total of 64,910 filtered single‐nucleotide polymorphisms (SNPs) were utilized to assess the genome‐scale diversity. Applications of this genome‐scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid‐density panel (MDP) comprising 2515 hyper‐variable SNPs, representing almost equally the genic and non‐genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k‐mer (subsequence of length “k” in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India‐originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics‐assisted accelerated sesame improvement program.

The genome size variation is an important attribute in evolutionary and species characterization. Musa L. is regarded as one of the taxonomically complicated genera within the order Zingiberales, with more than 75 species from wild seeded to seedless cultivars that may be diploid, triploid or tetraploid. The knowledge of total nuclear DNA content in terms of genome size and ploidy level in wild species of Musa is absolutely important in evolutionary and genomic studies. Methods: In this paper, chromosome spreading was performed via protoplast isolation and a fast air-dry dropping method and flow cytometry were used with Raphanus sativus L. (Brassicaceae) as a standard for ploidy and genome size estimation. Results: The results showed that genome size (2C) varied amongst Musa species, based on the ratio of G1 peak positions. The lowest genome size (2C) was found in M. balbisiana var. andamanica (1.051 ± 0.060 pg) and the highest genome size (2C) was recorded for Musa ABB.cv. Meitei-hei (1.812 ± 0.108 pg) for the section Eumusa. Among the species belonging to the section Rhodochlamys, M. rosae had the lowest 2C content of 1.194 ± 0.033 pg whereas the highest nuclear DNA content (2C) was observed in M. velutina (1.488 ± 0.203 pg). Cytogenetic analysis revealed that the chromosome number of 14 wild Musa species was 2n = 22, while 1 species—Ensete glaucum—showed a chromosome number of 2n = 18 (diploid), and for 3 species, the chromosome number was 2n = 33 (triploids). An association study based on the Pearson correlation coefficient showed 2C nuclear DNA content was significant and positively correlated with ploidy level (R = 0.9) and chromosome number (R = 0.84). Conclusions: The present study provides reliable information on the genome size and ploidy level of wild Musa species from the Indian region through flow cytometric analysis, which could be further utilized in taxonomic and crop improvement programs. For the first time, the nuclear DNA content of eight wild diploid and three triploid Indian species were estimated and reported. Genome size could be an effective indicator in identification of species and evolutionary studies in Musa with varying ploidy levels and morphological similarities.

To reduce the genome sequence representation, restriction site-associated DNA sequencing (RAD-seq) protocols is being widely used either with single-digest or double-digest methods. In this study, we genotyped the sesame population (48 sample size) in a pilot scale to compare single and double-digest RAD-seq (sd and ddRAD-seq) methods. We analysed the resulting short-read data generated from both protocols and assessed their performance impacting the downstream analysis using various parameters. The distinct k-mer count and gene presence absence variation (PAV) showed a significant difference between the sesame samples studied. Additionally, the variant calling from both datasets (sdRAD-seq and ddRAD-seq) exhibits a significant difference between them. The combined variants from both datasets helped in identifying the most diverse samples and possible sub-groups in the sesame population. The most diverse samples identified from each analysis (k-mer, gene PAV, SNP count, Heterozygosity, NJ and PCA) can possibly be representative samples holding major diversity of the small sesame population used in this study. The best possible strategies with suggested inputs for modifications to utilize the RAD-seq strategy efficiently on a large dataset containing thousands of samples to be subjected to molecular analysis like diversity, population structure and core development studies were discussed.

Sesame, one of the ancient oil crops, is an important oilseed due to its nutritionally rich seeds with high protein content. Genomic scale information for sesame has become available in the public databases in recent years. The genes and their families involved in oil biosynthesis in sesame are less studied than in other oilseed crops. Therefore, we retrieved a total of 69 genes and their translated amino acid sequences, associated with gene families linked to the oil biosynthetic pathway. Genome-wide in silico mining helped identify key regulatory genes for oil biosynthesis, though the findings require functional validation. Comparing sequences of the SiSAD (stearoyl-acyl carrier protein (ACP)-desaturase) coding genes with known SADs helped identify two SiSAD family members that may be palmitoyl-ACP-specific. Based on homology with lysophosphatidic acid acyltransferase (LPAAT) sequences, an uncharacterized gene has been identified as SiLPAAT1. Identified key regulatory genes associated with high oil content were also validated using publicly available transcriptome datasets of genotypes contrasting for oil content at different developmental stages. Our study provides evidence that a longer duration of active oil biosynthesis is crucial for high oil accumulation during seed development. This underscores the importance of early onset of oil biosynthesis in developing seeds. Up-regulating, identified key regulatory genes of oil biosynthesis during early onset of seed development, should help increase oil yields.

A series of cyclohexyl‐fused SPINOL‐derived phosphoric acids (Cy‐SPA) have been developed to catalyze the kinetic resolution of 2‐N‐acylamido tertiary allylic alcohols, providing access to chiral oxazolines bearing C‐2 alkyl substituents with high enantioselectivities (with s‐factors up to 153). Gram‐scale reaction with 1 mol% catalyst loading and transformations of the chiral products demonstrates the value of these methods. [ABSTRACT FROM AUTHOR]

An efficient protocol for kinetic resolution of tertiary alcohols has been developed through an unprecedented asymmetric enamide-imine tautomerism process enabled by chiral phosphoric acid catalysis. A broad range of racemic 2-arylsulfonamido tertiary allyl alcohols could be kinetically resolved with excellent kinetic resolution performances (with s-factor up to >200). This method is particularly effective for a series of 1,1-dialkyl substituted allyl alcohols, which produced chiral tertiary alcohols that would be difficult to access via other asymmetric methods. Facile and versatile transformations of the chiral α-hydroxy imine and enamide products, especially the efficient stereodivergent synthesis of all four stereoisomers of β-amino tertiary alcohols using one enantiomer of the catalyst, demonstrated the value of this kinetic resolution method., (© 2021 Wiley-VCH GmbH.)

Immuno-positron emission tomography (immuno-PET) is a rapidly growing imaging technique in which antibodies are radiolabeled to monitor their in vivo behavior in real time. However, effecting the controlled conjugation of a chelate-bearing radioactive atom to a bulky antibody without affecting its immunoreactivity at a specific site is always challenging. The in vivo stability of the radiolabeled chelate is also a key issue for successful tumor imaging. To address these points, a facile ultra-stable radiolabeling platform is developed by using the propylene cross-bridged chelator (PCB-TE2A-alkyne), which can be instantly functionalized with various groups via the click reaction, thus enabling specific conjugation with antibodies as per choice. The PCB-TE2A-tetrazine derivative is selected to demonstrate the proposed strategy. The antibody trastuzumab is functionalized with the trans -cyclooctene (TCO) moiety in the presence or absence of the PEG linker. The complementary 64 Cu-PCB-TE2A-tetrazine is synthesized via the click reaction and radiolabeled with 64 Cu ions, which then reacts with the aforementioned TCO-modified antibody via a rapid biorthogonal ligation. The 64 Cu-PCB-TE2A-trastuzumab conjugate is shown to exhibit excellent in vivo stability and to maintain a higher binding affinity toward HER2-positive cells. The tumor targeting feasibility of the radiolabeled antibody is evaluated in tumor models. Both 64 Cu-PCB-TE2A-trastuzumab conjugates show high tumor uptakes in biodistribution studies and enable unambiguous tumor visualization with minimum background noise in PET imaging. Interestingly, the 64 Cu-PCB-TE2A-PEG 4 -trastuzumab containing an additional PEG linker displays a much faster body clearance compared to its counterpart with less PEG linker, thus affording vivid tumor imaging with an unprecedentedly high tumor-to-background ratio.

An efficient method for the asymmetric synthesis of 4H-3,1-benzoxazines was developed by kinetic resolution of 2-amido benzyl alcohols using chiral phosphoric acid catalyzed intramolecular cyclizations. A broad range of benzyl alcohols (both secondary and tertiary alcohols) were kinetically resolved with high selectivities, with an s factor of up to 94. Mechanistic studies were performed to elucidate the mechanism of these reactions, wherein the amide moieties reacted as the electrophiles. Gram-scale reaction and facile transformations of the chiral products demonstrate the potential of this method in asymmetric synthesis of biologically active chiral heterocycles., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A highly enantioselective kinetic resolution of tertiary 2-alkoxycarboxamido allylic alcohols has been achieved through a chiral phosphoric acid catalyzed intramolecular transesterification reaction. Both alkyl,aryl- and dialkyl-substituted tertiary allylic alcohols were resolved with excellent efficiencies, affording both the recovered tertiary alcohols and the carbamate products with high enantioselectivities (with s factors up to 164.6). A gram-scale reaction with 1 mol % catalyst loading and the facile conversion of the enantioenriched products into useful chiral building blocks, such as chiral oxazolidinones and β-amino alcohols, demonstrate the value of this reaction., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The regioselective and enantioselective synthesis of β-indolyl cyclopentenamides, a versatile chiral building block, by asymmetric addition of indoles to α,β-unsaturated iminium intermediates has been achieved through chiral anion catalysis. Key to the success of this methodology is the generation of a chiral anion-paired ketone-type α,β-unsaturated iminium intermediate from α-hydroxy enamides. Preliminary mechanistic studies and DFT calculations are consistent with a mechanism involving multiple, concurrent pathways for isomerization of the initially formed azaallylcation into the key α,β-unsaturated iminium intermediate, all mediated by the phosphoric acid catalyst., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Bipolaris sorghicola (Lefebvre and Sherwin) is a well known and economically important seed-borne pathogen with the specific species of sorghum (Sorghum bicolor [L] Moench) as host. Thirty-two strains were obtained from different geographical area of sorghum growing places in India. Molecular characterization using three marker systems i.e., universal rice primers (URP), inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) was carried out. Molecular marker work revealed differences along with geographical origin clustering of various B. sorghicola strains which could not be revealed through conventional method of characterization. Out of 13 URPs, 20 ISSR and 50 RAPD primers screened, 8 primers each from URP and ISSR, and 10 primers from RAPD marker were found to result in reproducible banding pattern. One hundred per cent of polymorphic bands was recorded in all three molecular markers. Total number of bands was recorded 1986 with average of 248.25 in URP marker, and 2026 bands with average of 253.25 in ISSR marker and 2158 bands with average of 215.80 in RAPD markers. Maximum heterozygosity (Hn) was revealed by URP 17R (0.40), ISSR 10 (0.41) and RAPD marker OPC-5 (0.34). The polymorphism information content (PIC) values ranged between 5.89 to 8.28 in URP, 4.57 to 8.79 in ISSR and 4.44 to 9.64 in RAPD marker profiles. Maximum cophenetic correlation was found in URP (r = 0.910) followed by ISSR (r = 0.904) and RAPD (r = 0.870). The combined analysis of all three marker systems showed high cophenetic correlation (r = 0.911), which indicated a very good fit of the data for genetic diversity analysis. To best of our knowledge, this is a first report of genetic characterization of B. sorghicola. Hence, combined use of three marker systems would be more sensitive and reliable in characterizing genetic variability in B. sorghicola strains.