Sunil Kumar Sahu

Sunil Kumar Sahu
Beijing Genomics Institute · BGI-Research

PhD., Biotechnology
Exploring the fascinating world of plant genomics and evolution

About

136
Publications
253,169
Reads
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1,240
Citations
Introduction
I am currently working as a Research Scientist at BGI-Shenzhen. My research is primarily focused on Plant Molecular Biology, Evolution and Bioinformatics. My current project is regarding 'Decoding the genomes of commercially, evolutionarily and agriculturally important plants'. Note: Open for collaborations
Additional affiliations
September 2019 - February 2022
South China Agricultural University
Position
  • Visiting Professor
January 2018 - February 2022
China National Genebank-Shenzhen
Position
  • Research Scientist
January 2018 - February 2022
Beijing Genomics Institute
Position
  • Research Scientist
Education
November 2010 - February 2015
Annamalai University
Field of study
  • Marine Biotechnology
August 2008 - June 2010
Annamalai University
Field of study
  • Marine Biotechnology
August 2005 - May 2008
Pt. Ravishankar Shukla University
Field of study
  • Biotechnology

Publications

Publications (136)
Cover Page
Full-text available
Plant being sessile are more vulnerable to variable environmental constrains particularly salinity and drought stress, thereby causes decline in crop development and yield in arid and semi‐arid regions. In the current scenario of global warming, drought, and salinity – either alone, combined co-occurring or in sequence – are predicted to become mor...
Article
The South China tiger (Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tigers due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first...
Preprint
The gut microbiota is essential for host health and survival. Here, using samples from animals living in the Qinghai-Tibetan Plateau, we recovered 119,568 metagenome-assembled genomes (MAGs) that were clustered into 19,251 species-level genome bins (SGBs) of which most represent novel species. We present a novel mechanism shaping mammalian gut micr...
Article
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A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development,...
Article
The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the “core chlorophytes”. We present a chromosome‐level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and H...
Article
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MADS-box is an important transcription factor family that is involved in the regulation of various stages of plant growth and development, especially flowering regulation and flower development. Being a holoparasitic plant, the body structure of Balanophoraceae has changed dramatically over time, and its vegetative and reproductive organs have been...
Article
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The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of...
Article
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Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas p...
Article
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Herbivores can drastically alter the morphology of macroalgae by directly consuming tissue and by inflicting structural wounds. Macroalgae host abundant and diverse epibiont communities , the dynamics of which tend to be mostly unknown in space and time. As the cultivation of macroalgae gains momentum worldwide, it is key to measure how epibionts c...
Article
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The green peafowl (Pavo muticus) is facing a high risk of extinction due to the long-term and widespread threats of poaching and habitat conversion. Here, we present a high-quality chromosome-level genome assembly of the green peafowl with high contiguity and accuracy assembled by PacBio sequencing, DNBSEQ short-read sequencing, and Hi-C sequencing...
Article
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Sea buckthorn (Hippophae rhamnoides), a horticulturally multipurpose species in the family Elaeagnaceae, can build associations with Frankia actinomycetes to enable symbiotic nitrogen‐fixing. Currently, no high‐quality reference genome is available for an actinorhizal plant, which greatly hinders the study of actinorhizal symbiotic nodulation. Here...
Article
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific commun...
Article
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The masked palm civet ( Paguma larvata ) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory syndrome (SARS) epidemic in 2003, the public has...
Article
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Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with ~2,000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides...
Article
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Seaweeds are macroscopic forms of phylogenetically diverse assemblage of marine algae that grow in oceans, thriving among profoundly harsh environmental conditions. They are cultivated in many maritime nations primarily for edible applications; besides hydrocolloid extraction is the second largest domain of utility for this renewable biomass. The f...
Article
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The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here,...
Preprint
Background The evolution of parasites is often directly affected by the host's environment. Studies on the evolution of the same parasites in different hosts are extremely attractive and highly relevant to our understanding of divergence and speciation. Methods Here we performed whole genome sequencing of Parascaris univalens from different Equus h...
Preprint
Vertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period of time. A major challenge in understanding this process is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of...
Article
Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Therefore, we assembled the first genome of Clausena genus with a total length...
Preprint
Full-text available
The evolution of parasites is often directly affected by the host's environment or behavior. Studies on the evolution of the same parasites in different hosts are extremely attractive and highly relevant to our understanding of divergence and speciation. Here we presented the first molecular evidence of divergence of Equus roundworms in different h...
Poster
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Soummam river sediments were used to isolate a biosurfactant-producing and petroleum-degrading bacterium. The strain was identified as Alcaligenes aquatilis YGD 2906 using phenotypic characterization and 16S ribosomal RNA sequencing. The culture supernatant of the isolated strain showed no haemolytic activity had an oiled displacement of 23.66 ± 0....
Article
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Small RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small...
Article
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Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies...
Article
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Despite being the world’s third largest ocean, the Indian Ocean is one of the least studied and understood with respect to microbial diversity as well as biogeochemical and ecological functions. In this study, we investigated the microbial community and its metabolic potential for nitrogen (N) acquisition in the oligotrophic surface waters of the I...
Article
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Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next‐generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degrada...
Article
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This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diver...
Article
Soummam river sediments were used to isolate a biosurfactant-producing and petroleum-degrading bacterium. The strain was identified as Alcaligenes aquatilis YGD 2906 using phenotypic characterization and 16S ribosomal RNA sequencing. The culture supernatant of the isolated strain showed no haemolytic activity had an oiled displacement of 23.66 ± 0....
Article
Full-text available
Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Marine macroalgae, commonly known as seaweeds have gained considerable biotechnological interest due their versatile applications, and their ability to produce a great diversity of compounds exhibiting a broad spectrum of biological activities. The intellectual property propelling seaweed biotechnology is mainly represented by Asian countries, prim...
Article
Coelastrum proboscideum Bohlin, 1896 (Sphaeropleales, Scenedesmaceae, Chlorophyta) is a coenobial species with cosmopolitan distribution in diverse freshwater habitats. Coelastrum spp. are widely tested for biotechnological applications such as carotenoid and lipid production, and in bioremediation of wastewater. Here, we report the draft genome of...
Preprint
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A few animals have been suspected to be intermediate hosts of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, a large-scale single-cell screening of SARS-CoV-2 target cells on a wide variety of animals is missing. Here, we constructed the single-cell atlas for 11 representative species in pets, livestock, poultry, and wildlif...
Article
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Averrhoa carambola is commonly known as star fruit because of its peculiar shape, and its fruit is a rich source of minerals and vitamins. It is also used in traditional medicines in countries such as India, China, the Philippines, and Brazil for treating various ailments, including fever, diarrhea, vomiting, and skin disease. Here, we present the...
Chapter
An epiphyte is a nonparasitic plant that dwells on another plant and has been well studied in terrestrial plants. However, in the marine ecosystem, these epiphytes thrive on algal thallus for their support and growth, and their infestation has a prime economic impediment in commercial cultivation. They usually belong to various groups, namely, bact...
Article
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The Flos Lonicerae Japonicae (FLJ), Lonicera japonica Thunb, belonging to the Caprifoliaceae family, is an economically important plant that is highly utilized in traditional Chinese medicine as well as in Japanese medicine. The flowers of these plants are rich in chlorogenic acid (CGA) and luteoloside. Our previous study revealed that tetraploid L...
Article
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Mandrill (Mandrillus sphinx) is a primate species, which belongs to the Old World monkey (Cercopithecidae) family. It is closely related to human, serving as a model for human health related research. However, the genetic studies on and genomic resources of mandrill are limited, especially in comparison to other primate species. Here we produced 28...
Article
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Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in fre...
Article
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In plants, parasitism triggers the reductive evolution of plastid genomes (plastomes). To disentangle the molecular evolutionary associations between feeding on other plants below-or aboveground and general transitions from facultative to obligate parasitism, we analyzed 34 complete plastomes of autotrophic, root-and stem-feeding hemiparasitic, and...
Article
Full-text available
In plants, parasitism triggers the reductive evolution of plastid genomes (plastomes). To disentangle the molecular evolutionary associations between feeding on other plants below- or aboveground and general transitions from facultative to obligate parasitism, we analyzed 34 complete plastomes of autotrophic, root- and stem-feeding hemiparasitic, a...
Preprint
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Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source...
Article
The gut microbiome shows individual specificity and is affected by sex, environment, and diet; gut microbiome imbalance is related to cancer, cardiovascular diseases, and autoimmune diseases. Astronauts are faced with a challenging environment and limited diet in outer space. Recent studies indicate that the gut microbiome is altered in space simul...
Preprint
The Averrhoa carambola is commonly known as star fruit because of its peculiar shape and its fruit is a rich source of minerals and vitamins. It is also used in traditional medicines in countries like India, China, the Philippines, and Brazil for treating various ailments such as fever, diarrhea, vomiting, and skin disease. Here we present the firs...
Chapter
Full-text available
The highly conserved catabolic process of autophagy delivers unwanted proteins or damaged organelles to vacuoles for degradation and recycling. This is essential for the regulation of cellular homeostasis, stress adaptation, and programmed cell death in eukaryotes. In particular, emerging evidence indicates that autophagy plays a multifunctional re...
Article
Taxonomic and phylogenetic diversity within forest communities are influenced by many factors, but our understanding concerning diversity patterns along elevational gradients is still unclear. Though there are many studies on diversity patterns such as phylogenetic diversity (PD), there are only handful describing how altitude affects these diversi...
Article
Desmodesmus costato-granulatus (Skuja) Hegewald 2000 (Sphaeropleales, Chlorophyta) is a small, spineless green alga that is abundant in the freshwater phytoplankton of oligo- to eutrophic waters worldwide. It has a high lipid content and is considered for sustainable production of diverse compounds, including biofuels. Here, we report the draft who...
Article
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Main conclusion The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is on...
Article
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Plant subtilases (SBTs) are a widely distributed family of serine proteases which participates in plant developmental processes and immune responses. Although SBTs are divided into seven subgroups in plants, their origin and evolution, particularly in green algae remain elusive. Here, we present a comprehensive large-scale evolutionary analysis of...
Article
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The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including anci...
Article
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Moutai is a world-famous traditional Chinese liquor with complex taste and aroma, which are considered to be strongly influenced by the quality of fermentation starters (Daqu). However, the role of microbial communities in the starters has not been fully understood. In this study, we revealed the microbial composition of 185 Moutai starter samples,...
Article
Although mangroves inhabit only 0.7% of global coastal zone, but they have a significant contribution to the global carbon. Primary production by mangroves provides a substantial source of energy for aquatic food webs. Net primary productivity and carbon sequestration potential play a pivotal role in understanding the characteristics of the forest...
Article
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Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the ev...
Preprint
Full-text available
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the ev...
Preprint
Full-text available
The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a severely destructive pest native to the Americas, but has now become an alien invasive pest in China, and causes significant economic loss. Therefore, in order to make effective management strategies, it is highly essential to understand genomic architecture and its genetic background...
Article
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Trans-splicing mechanisms have been documented in many lineages that are widely distributed phylogenetically, including dinoflagellates. The spliced leader (SL) sequence itself is conserved in dinoflagellates, although its gene sequences and arrangements have diversified within or across different species. In this study, we present 18 Fugacium kawa...
Preprint
Background Chloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. I...