Spatiotemporal variability identification and analysis for non-stationary climatic trends for a tropical river basin of India.

The non-stationary behavior of climatic variables has been increasingly recognized as a challenge that disrupts the equilibrium of human-defined climate-based stationary processes, including hydrological and agricultural practices, and irrigation systems. This study aims to investigate long-term trends and non-stationarity in climatic variables across 23 stations of the Krishna River basin, India. Prominent trends in rainfall, temperature, and their extreme indices were identified using the Modified Mann-Kendall (MMK), Bootstrapped Mann-Kendall (BMK), and Sen's Slope Estimator tests, while the Innovative Trend Analysis (ITA) test uncovered hidden trends and potential shifts in climatic patterns. This study addresses a critical research gap by exploring both significant and hidden trends in climatic variables, providing a better understanding of future dynamics. Traditional methods like MMK and Sen's Slope were insufficient to reveal these hidden trends, but ITA offered a more comprehensive analysis. The findings revealed an increase in total annual rainfall for almost 50% of the basin, which aligns with rising maximum temperatures, suggesting enhanced evaporation rates and subsequent fluctuations in rainfall patterns. Seasonal analysis indicated a shift towards decreased rainfall during winter and pre-monsoon seasons, contrasted by increased precipitation during the monsoon and post-monsoon periods, highlighting a clear alteration in rainfall distribution. The Simple Daily Intensity Index (SDII) and other indices suggest intensified rainfall events despite a decrease in the number of rainy days, indicating fewer but more intense events. Temperature analysis showed an overall increase in maximum temperatures, with the Diurnal Temperature Range (DTR) significantly increasing across all stations, implying greater daily temperature variations and potential for intensified water cycles and extreme climatic events. Furthermore, the study simplifies these trends by classifying them into two attributes: intensity and frequency, aiding policymakers in site-specific management of water resources and planning for future climatic scenarios. The presence of non-stationarity in extreme rainfall was confirmed by the Augmented Dickey-Fuller (ADF), Phillips-Perron (PP), and Kwiatkowski-Phillips-Schmidt-Shin (KPSS) tests. These findings are significant as they conclude how climate change is altering hydrological patterns at each station. The study emphasizes the necessity for adaptive management strategies to mitigate the adverse impacts on agriculture, infrastructure, and human safety.

Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus.

In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Toward this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman (A.hyp.V.2.1). The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly Amaranthus cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus.

Genome duplication event in edible dicots under the orders Rosid and Asterid, common during the oligocene period, is missing for species under the order Caryophyllales. Despite this, grain amaranths not only survived this period but display many desirable traits missing in species under rosids and asterids. For example, grain amaranths display traits like C4 photosynthesis, high-lysine seeds, high-yield, drought resistance, tolerance to infection and resilience to stress. It is, therefore, of interest to look for minor genome rearrangements with potential functional implications that are unique to grain amaranths. Here, by deep sequencing and assembly of 16 transcriptomes (86.8 billion bases) we have interrogated differential genome rearrangement unique to Amaranthus hypochondriacus with potential links to these phenotypes. We have predicted 125,581 non-redundant transcripts including 44,529 protein coding transcripts identified based on homology to known proteins and 13,529 predicted as novel/amaranth specific coding transcripts. Of the protein coding de novo assembled transcripts, we have identified 1810 chimeric transcripts. More than 30% and 19% of the gene pairs within the chimeric transcripts are found within the same loci in the genomes of A. hypochondriacus and Beta vulgaris respectively and are considered real positives. Interestingly, one of the chimeric transcripts comprises two important genes, namely DHDPS1, a key enzyme implicated in the biosynthesis of lysine, and alpha-glucosidase, an enzyme involved in sucrose catabolism, in close proximity to each other separated by a distance of 612 bases in the genome of A. hypochondriacus in a convergent configuration. We have experimentally validated that transcripts of these two genes are also overlapping in the 3' UTR with their expression negatively correlated from bud to mature seed, suggesting a potential link between the high seed lysine trait and unique genome organization.

In vitro evaluation of mitochondrial-chloroplast subcellular localization of heme oxygenase1 (HO1) in Glycine max.

Heme oxygenase1 (HO1) catalyzes the degradation of heme in to biliverdin, carbon monoxide, and ferrous ions. Its role in higher plants has been found as an antioxidant and precursor of phytochrome synthesis. The present study focuses on subcellular localization of HO1 in leaves of soybean has been investigated. Most activity appeared to be located within chloroplast due to its role in phytochrome synthesis but mitochondria also share its localization. Mitochondrial location of HO1 might be on its inner membranous space due to its role in the synthesis of electron donor species which facilitates HO1 catalyzed reaction. Study reports the co-localization of HO1 in both chloroplast and mitochondria.