Biology subjects

GUPTA, S. K.

Publications and source records attributed to GUPTA, S. K..

7 recordsLinked to original sources

bioRxiv2022

Development of an Agrobacterium-delivered codon-optimized CRISPR/Cas9 system for chickpea genome editing

Chickpea is considered recalcitrant to in vitro tissue culture. The Clustered, Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) based genome editing in chickpea can remove the bottleneck of limited genetic variation in this cash crop rich in nutrients and protein. However, the generation of stable mutant lines using CRISPR/Cas9 requires efficient and highly reproducible transformation approaches. We modified a binary vector pPZP200 by introducing a codon-optimized Cas9 gene for chickpea and the promoters of Medicago truncatula U6 snRNA for expressing guide RNA targeted to the Phytoene Desaturase (PDS) gene. The dissected single cotyledons with half embryo of chickpea were used as explants for genetic transformation. A single gRNA was found sufficient to achieve high efficiency (42%) editing with the generation of PDS mutants with albino phenotypes. A simple, rapid, highly reproducible, stable transformation and CRISPR/Cas9-based genome editing system for chickpea was established. For the first time, this study aimed to demonstrate this systems applicability by performing a gene knockout of the chickpea phytoene desaturase gene (CaPDS) in stable shoots using an improved chickpea transformation protocol.

plant biology↗

bioRxiv2021

Avian haemosporidians (Plasmodium and Haemoproteus) in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India and their phylogenetic relationships with other lineages of the world

The avian haemosporidians (Plasmodium and Haemoproteus) are widely distributed and may affect the host populations from body damage at individual level to the extinction of a population. The knowledge about their status may help in future avifauna conservation plans. Hence, we examined the avian haemosporidians status, in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India, and their phylogenetic relationships with other known lineages of the world. We used the common genetic marker (Cytochrome b gene fragment of 479 bp) with information on the geographic distribution of parasite and host species available at MalAvi database. The prevalence of avian haemosporidians, from northern, eastern, and southern parts of India and phylogenetic genetic analysis of lineages was carried out to know the genetic relatedness among them at local and world level. The MCC tree revealed six Haemosporidian lineages in which one was common (H_MSP01) and five were unique (H_CYOPOL01, H_CHD01, H_CYORUB01, H_EUMTHA01, and P_GEOCIT01). The avian host richness Index was 2.0852. 9.9%, prevalence of Haemosporidian infection was found in 111 DNA samples belonging to 6 host species. The Haemoproteus prevalence was found to be 9.0 % across five host species (Phylloscopus trochiloides, Cyornis poliogenys, C. hainanus dialilaemus, C. rubeculoides, Eumiyas thalassinus) and Plasmodium prevalence was 0.9% in Geokichla citrina. Spatial phylogeny at global level showed H_MSP01 lineage, found in different host species in India, was genetically related to H. pallidus lineages (COLL2 and PFC1) in parts of Africa, Europe, North America, Malaysia, and Philippines. The Plasmodium lineage (P_GEOCIT01) was related to PADOM16 in Egypt with poor sequence similarity (93.89%). The statistical analysis suggested that the haemosporidians host species distribution range was directly and significantly associated with the altitude, minimum temperature, and relative humidity. H_MSP01 distribution was in accordance with H. pallidus having a wide geographic and host range.

genetics↗

bioRxiv2021

MITOCHONDRIAL GENOME REVEALS CONTRASTING PATTERN OF ADAPTIVE SELECTION IN TURTLES AND TORTOISES

Testudinoidea represents an evolutionarily unique taxon comprising both turtles and tortoises. The contrasting habitats that turtles and tortoises inhabit are associated with unique physio-ecological challenges hence enable distinct adaptive evolutionary strategies. To comparatively understand the pattern and strength of Darwinian selection and physicochemical evolution in turtle and tortoise mitogenomes, we employed adaptive divergence and selection analyses. We evaluated changes in structural and biochemical properties, and codon models on the mitochondrial protein-coding genes (PCGs) among three turtles and a tortoise lineage. We used mitochondrial PCGs that constitute the crucial oxidative phosphorylation (OXPHOS) respiratory system, a critical metabolic regulator which assumes key significance in energy regulation of ectotherms. We detected strong evidence of positive selection along the turtle lineages: Geoemydidae, Emydidae, and Platysternidae, but relatively weak signals in tortoises. The Platysternidae turtles revealed the highest gene and site-wise positive selection. In turtles, positively selected sites were prevalent in NAD2 and NAD4 genes in OXPHOS Complex I, and COB gene of Complex III, indicating convergent adaptive evolution. Besides, NAD3 was the only subunit that showed adaptive selection in both turtles and tortoises, expressing its relevance for all Testudinoidea. Structural and functional analysis revealed many sites and physiochemical changes in important conserved as well as biomedically significant regions, suggesting the influence of adaptive pressure on mitogenome functions. Hence, our study furnished novel evidence of contrasting evolutionary selective pressure acting on closely related groups such as turtles and tortoises with unique habitat preferences and associated eco-physiological challenges.

evolutionary biology↗

bioRxiv2020

Molecular evidence indicates the existence of multiple lineages of Sperata species in Indian Rivers

Sperata seenghala (Giant river-catfish) and Sperata aor (Long-whiskered catfish) are commercially important freshwater catfishes of India, belongs to family Bagridae. Due to high nutritional significance and the low number of intramuscular bones, both fishes have considerable demand in South Asian countries. Both of the Sperata species are morphologically close and well adapted to the same habitat. In this study, we have assessed the level of genetic diversity and differentiation of S. seenghala and S. aor in the Ganga River based on the mitochondrial DNA (mtDNA) control region and compared with the other major Indian rivers. We found high haplotypes diversity for both the species in the Ganga. However, it was comparatively low for S. seenghala in Mahanadi and Brahmaputra populations. The phylogenetic and median-joining network strongly indicated the presence of two distinct maternal lineages of S. seenghala from the Ganga river. Interestingly, the genetic differentiation between S. seenghala of Ganga-Brahmaputra was much higher (~25.3%) than the S. seenghala and S. aor (~17%), whereas it was comparatively low between Ganges-Mahanadi (~8.0%). Our finding provided evidence that all the three rivers: Ganga, Mahanadi, and the Brahmaputra sustain a highly diverse and genetically distinct stock of giant river catfish; therefore, all populations should be considered as a different management unit for the protection of stocks. Our findings indicated that Brahmaputra lineages qualify the species level variations. This study can be further used as a reference database for proper lineage identification of S. seenghala and S. aor that could formulate the appropriate conservation and management plans.

genetics↗

bioRxiv2020

Complete mitogenome of Kashmir musk deer (Moschus cupreus) and its comparative phylogenetic relationships

The endangered Kashmir musk deer (Moschus cupreus) is native to the high altitudinal region of the Himalayas. In this study, we sequenced, annotated and characterized the complete mitogenome of M. cupreus to gain insight into the molecular phylogeny and evolution of musk deer. The mitogenome of M. cupreus, which is 16,354 bp long comprised 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and non-coding control region. The M. cupreus mitogenome composition was highly A+T biased 68.42%, and exhibited a positive AT skew (0.082) and negative GC skew (0.307). The phylogenetic analysis suggested that KMD is the most primitive extant species in the genus Moschus whereas Alpine musk deer (M. chrysogaster) and Himalayan musk deer (M. leucogaster) are closely related. This result confirmed the placement of M. cupreus within the monotypic family Moschidae of musk deer. This study provides a better understanding of lineage identification and musk deer evolution for further research.

genetics↗

bioRxiv2020

Genetic evidence indicates new distribution record of endangered Kashmir musk deer (Moschus cupreus) with range expansion in Uttarakhand, India

Kashmir musk deer, KMD (Moschus cupreus) is one the most threatened species reported from the Himalayan region of Kashmir, Pakistan and Afghanistan. A comprehensive and reliable distribution range of musk deer is still lacking. Recently, a molecular study confirmed the presence of KMD in Mustang in Nepal, west of Annapurna Himalayas. Here, we investigated the phylogenetic relationship of musk deer from Jammu and Kashmir (J&K), Kedarnath Wildlife Sanctuary (KWLS), and Nanda Devi Biosphere Reserve (NDBR), Uttarakhand region, India based on mitochondrial control region. The Bayesian phylogenetic analysis indicated a close genetic relationship between samples from J&K, KWLS and NDBR with identified lineages of KMD from Nepal with high posterior probabilities (PP[~]100). It confirmed that the musk deer lineage from the Uttarakhand region of KWLS (1025-3662 m) and NDBR (1800-7817 m) to be of KMD (M. cupreus) and hence a distinct Evolutionary Significant Unit (ESU). Besides, as per the IUCN database, the Western Himalayan region also holds the population of M. leucogaster and M. chrysogaster. Hence, we suggest extensive sampling for proper identification and validation of the geographic limits of musk deer species. We report for the first time the existence of KMD from the Uttarakhand region that we recommend to be updated in the IUCN database. It will assist in the effective conservation and management of this enigmatic endangered species.

genetics↗

bioRxiv2020

Phylogeography and population genetic structure of red muntjacs: Evidence of enigmatic Himalayan red muntjac from India

We investigated the phylogeographic pattern of red muntjac across its distribution range, intending to address the presence of distinct lineages from Northwest India. The Complete mitogenome analysis revealed that India holds three mitochondrial lineages of red muntjac, whereas four were identified from its entire distribution range: Himalayan red muntjac (M. (m.) aureus), Northern red muntjac (M. vaginalis), Srilankan and Western Ghat India (M. malabaricus) and Southern red muntjac (M. muntjak) from Sundaland. The newly identified Himalayan red muntjac found in the Northwestern part of India, which was previously described based on their morphological differences. Estimates of the divergence dating indicate that the Northwest and Northern lineage split during the late Pleistocene approximately 0.83 Myr (CI95%:0.53 to 1.26), which is the younger lineages, whereas M. malabaricus is the most primitive lineage among all the red muntjac. Microsatellite results also supported the mitochondrial data and evident the presence of three distinct genetic clusters within India. The pronounced climate fluctuation during the Quaternary period was considered as a critical factor influencing the current spatial distribution of forest-dwelling species that restricted themselves in northwest areas. Based on molecular data, this study provided evidence of a new lineage within the red muntjac group from India that required to be managed as an evolutionary significant unit (ESUs). It highlighted a need for the taxonomic revision of Himalayan red muntjac (M. (m.) aureus) and also suggested its conservation status under IUCN Red List.

evolutionary biology↗