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Article ; Online: Near-chromosomal-level genome of the red palm weevil (Rhynchophorus ferrugineus), a potential resource for genome-based pest control.

Sudalaimuthuasari, Naganeeswaran / Kundu, Biduth / Hazzouri, Khaled M / Amiri, Khaled M A

2024 Volume 11, Issue 1, Page(s) 45

Abstract: The red palm weevil (RPW) is a highly destructive pest that mainly affects palms, particularly date palms (Phoenix dactylifera), in the Arabian Gulf region. In this study, we present a near-chromosomal-level genome assembly of the RPW using a combination ...

Abstract	The red palm weevil (RPW) is a highly destructive pest that mainly affects palms, particularly date palms (Phoenix dactylifera), in the Arabian Gulf region. In this study, we present a near-chromosomal-level genome assembly of the RPW using a combination of PacBio HiFi and Dovetail Omini-C reads. The final genome assembly is around 779 Mb in size, with an N50 of ~43 Mb, consistent with our previous flow cytometry estimates. The completeness of the genome was confirmed through BUSCO analysis, which indicates the presence of 99.5% of BUSCO single copy orthologous genes. The genome annotation identified a total of 29,666 protein-coding, 1,091 tRNA and 543 rRNA genes. Overall, the proposed genome assembly is significantly superior to existing assemblies in terms of contiguity, integrity, and genome completeness.
MeSH term(s)	Animals ; Flow Cytometry ; Weevils/genetics ; Genome, Insect
Language	English
Publishing date	2024-01-06
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-024-02910-3
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Article ; Online: Contrasting genome patterns of two pseudomonas strains isolated from the date palm rhizosphere to assess survival in a hot arid environment

Malik, Shahana Seher / Sudalaimuthuasari, Naganeeswaran / Kundu, Biduth / AlMaskari, Raja S. / Mundra, Sunil

World J Microbiol Biotechnol. 2022 Nov., v. 38, no. 11, p. 207

2022 , Page(s) 207

Abstract: The plant growth-promoting rhizobacteria (PGPRs) improve plant growth and fitness by multiple direct (nitrogen fixation and phosphate solubilization) and indirect (inducing systematic resistance against phytopathogens, soil nutrient stabilization, and ... ...

Abstract	The plant growth-promoting rhizobacteria (PGPRs) improve plant growth and fitness by multiple direct (nitrogen fixation and phosphate solubilization) and indirect (inducing systematic resistance against phytopathogens, soil nutrient stabilization, and maintenance) mechanisms. Nevertheless, the mechanisms by which PGPRs promote plant growth in hot and arid environments remain poorly recorded. In this study, a comparative genome analysis of two phosphate solubilizing bacteria, Pseudomonas atacamensis SM1 and Pseudomonas toyotomiensis SM2, isolated from the rhizosphere of date palm was performed. The abundance of genes conferring stress tolerance (chaperones, heat shock genes, and chemotaxis) and supporting plant growth (plant growth hormone, root colonization, nitrogen fixation, and phosphate solubilization) were compared among the two isolates. This study further evaluated their functions, metabolic pathways, and evolutionary relationship. Results show that both bacterial strains have gene clusters required for plant growth promotion (phosphate solubilization and root colonization), but it is more abundant in P. atacamensis SM1 than in P. toyotomiensis SM2. Genes involved in stress tolerance (mcp, rbs, wsp, and mot), heat shock, and chaperones (hslJ and hslR) were also more common in P. atacamensis SM1. These findings suggest that P. atacamensis SM1could have better adaptability to the hot and arid environment owing to a higher abundance of chaperone genes and heat shock proteins. It may promote plant growth owing to a higher load of root colonization and phosphate solubilization genes and warrants further in vitro study.
Keywords	Phoenix dactylifera ; Pseudomonas ; chemotaxis ; dry environmental conditions ; genes ; growth promotion ; heat stress ; nitrogen fixation ; phosphates ; plant growth ; plant growth-promoting rhizobacteria ; plant hormones ; plant pathogens ; rhizosphere ; sequence analysis ; soil nutrients ; solubilization ; stress tolerance
Language	English
Dates of publication	2022-11
Size	p. 207
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	1499109-3
ISSN	1573-0972 ; 0959-3993
ISSN (online)	1573-0972
ISSN	0959-3993
DOI	10.1007/s11274-022-03392-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Contrasting genome patterns of two pseudomonas strains isolated from the date palm rhizosphere to assess survival in a hot arid environment.

Malik, Shahana Seher / Sudalaimuthuasari, Naganeeswaran / Kundu, Biduth / AlMaskari, Raja S / Mundra, Sunil

World journal of microbiology & biotechnology

2022 Volume 38, Issue 11, Page(s) 207

Abstract	The plant growth-promoting rhizobacteria (PGPRs) improve plant growth and fitness by multiple direct (nitrogen fixation and phosphate solubilization) and indirect (inducing systematic resistance against phytopathogens, soil nutrient stabilization, and maintenance) mechanisms. Nevertheless, the mechanisms by which PGPRs promote plant growth in hot and arid environments remain poorly recorded. In this study, a comparative genome analysis of two phosphate solubilizing bacteria, Pseudomonas atacamensis SM1 and Pseudomonas toyotomiensis SM2, isolated from the rhizosphere of date palm was performed. The abundance of genes conferring stress tolerance (chaperones, heat shock genes, and chemotaxis) and supporting plant growth (plant growth hormone, root colonization, nitrogen fixation, and phosphate solubilization) were compared among the two isolates. This study further evaluated their functions, metabolic pathways, and evolutionary relationship. Results show that both bacterial strains have gene clusters required for plant growth promotion (phosphate solubilization and root colonization), but it is more abundant in P. atacamensis SM1 than in P. toyotomiensis SM2. Genes involved in stress tolerance (mcp, rbs, wsp, and mot), heat shock, and chaperones (hslJ and hslR) were also more common in P. atacamensis SM1. These findings suggest that P. atacamensis SM1could have better adaptability to the hot and arid environment owing to a higher abundance of chaperone genes and heat shock proteins. It may promote plant growth owing to a higher load of root colonization and phosphate solubilization genes and warrants further in vitro study.
MeSH term(s)	Bacteria/metabolism ; Indoleacetic Acids/metabolism ; Phoeniceae/metabolism ; Phosphates/metabolism ; Phylogeny ; Plant Growth Regulators/metabolism ; Pseudomonas/metabolism ; Rhizosphere ; Soil Microbiology
Chemical Substances	Indoleacetic Acids ; Phosphates ; Plant Growth Regulators
Language	English
Publishing date	2022-08-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1499109-3
ISSN	1573-0972 ; 0959-3993
ISSN (online)	1573-0972
ISSN	0959-3993
DOI	10.1007/s11274-022-03392-4
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Article: Virome diversity of

Perveen, Nighat / Kundu, Biduth / Sudalaimuthuasari, Naganeeswaran / Al-Maskari, Raja Saeed / Muzaffar, Sabir Bin / Al-Deeb, Mohammad Ali

Veterinary world

2023 Volume 16, Issue 3, Page(s) 439–448

Abstract: Background and aim: Viruses are important components of the microbiome of ticks. Ticks are capable of transmitting several serious viral diseases to humans and animals. Hitherto, the composition of viral communities in : Materials and methods: We ... ...

Abstract	Background and aim: Viruses are important components of the microbiome of ticks. Ticks are capable of transmitting several serious viral diseases to humans and animals. Hitherto, the composition of viral communities in Materials and methods: We collected ticks, extracted, and sequenced RNA, using Illumina (NovaSeq 6000) and Oxford Nanopore (MinION). Results: From the total generated sequencing reads, 180,559 (~0.35%) and 197,801 (~0.34%) reads were identified as virus-related reads in male and female tick samples, respectively. Taxonomic assignment of the viral sequencing reads was accomplished based on bioinformatic analyses. Further, viral reads were classified into 39 viral families. Poxiviridae, Phycodnaviridae, Phenuiviridae, Mimiviridae, and Polydnaviridae were the most abundant families in the tick viromes. Notably, we assembled the genomes of three RNA viruses, which were placed by phylogenetic analyses in clades that included the Bole tick virus. Conclusion: Overall, this study attempts to elucidate the RNA virome of ticks associated with camels in the UAE and the results obtained from this study improve the knowledge of the diversity of viruses in
Language	English
Publishing date	2023-03-16
Publishing country	India
Document type	Journal Article
ZDB-ID	2456277-4
ISSN	2231-0916 ; 0972-8988
ISSN (online)	2231-0916
ISSN	0972-8988
DOI	10.14202/vetworld.2023.439-448
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Article: Melatonin increases AKT and SOD gene and protein expressions in diabetic rats.

Lotfy, Mohamed / Khattab, Aalaa / Shata, Mohammed / Alhasbani, Ahmad / Khalaf, Abdallah / Alsaeedi, Saeed / Thaker, Mahdi / Said, Hazza / Tumi, Harun / Alzahmi, Hassan / Alblooshi, Omar / Hamdan, Mohamad / Hussein, Amjad / Kundu, Biduth / Adeghate, Ernest A

Heliyon

2024 Volume 10, Issue 7, Page(s) e28639

Abstract: Diabetes mellitus (DM) is a chronic metabolic disease marked by hyperglycemia due to insulin deficiency or insulin resistance leading to many chronic complications. It is thus important to manage diabetes effectively in order to prevent and or delay ... ...

Abstract	Diabetes mellitus (DM) is a chronic metabolic disease marked by hyperglycemia due to insulin deficiency or insulin resistance leading to many chronic complications. It is thus important to manage diabetes effectively in order to prevent and or delay these complications. Melatonin is produced by the pineal gland and regulates the wake-sleep circadian rhythm. Existing evidence suggests that melatonin may be effective in the management of DM. However, the evidence on the mechanism of the beneficial effect melatonin as a treatment for DM is limited. In this study, we investigated the effect of melatonin treatment on blood glucose, insulin (INS), AKT and superoxide dismutase (SOD) gene levels in diabetic rats. Non-diabetic and diabetic rats were treated orally for 4 weeks with either 25 mg or 50 mg/kg body weight of melatonin. At the end of the study, pancreatic and liver tissues morphology, glucose homeostasis, serum insulin and SOD levels, hepatic gene and protein expression of SOD as protecting antioxidant enzyme and AKT as central element involved in PI3K/AKT insulin signaling pathway were estimated. Melatonin treated diabetic rats showed reduced hyperglycemia, and increased serum insulin and SOD levels. In addition, melatonin induced an increased gene and protein expression of SOD and AKT. In conclusion, melatonin may play a role in treating diabetic rats via stimulation of insulin secretion, insulin signaling and reduction in oxidative stress.
Language	English
Publishing date	2024-03-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e28639
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Article: Microbiome of

Procter, Miranda / Kundu, Biduth / Sudalaimuthuasari, Naganeeswaran / AlMaskari, Raja S / Saeed, Esam E / Hazzouri, Khaled M / Amiri, Khaled M A

Microorganisms

2022 Volume 10, Issue 10

Abstract: Citrullus ... ...

Abstract	Citrullus colocynthis
Language	English
Publishing date	2022-10-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10102083
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Article ; Online: Complete Genome Sequences of Pseudomonas atacamensis Strain SM1 and Pseudomonas toyotomiensis Strain SM2, Isolated from the Date Palm Rhizosphere.

Elmahi, Yassine / Alshamsi, Mohammed Saeed / Sudalaimuthuasari, Naganeeswaran / Kundu, Biduth / AlMaskari, Raja S / Hazzouri, Khaled M / Chandran, Subha / Malik, Shahana Sehar / Mundra, Sunil / Amiri, Khaled M A

Microbiology resource announcements

2021 Volume 10, Issue 18

Abstract: Here, we announce the complete genome sequences of two phosphate-solubilizing rhizobacteria, ...

Abstract	Here, we announce the complete genome sequences of two phosphate-solubilizing rhizobacteria,
Language	English
Publishing date	2021-05-06
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00253-21
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Article ; Online: Salt flat microbial diversity and dynamics across salinity gradient.

Hazzouri, Khaled M / Sudalaimuthuasari, Naganeeswaran / Saeed, Esam Eldin / Kundu, Biduth / Al-Maskari, Raja Saeed / Nelson, David / AlShehhi, Alya Ali / Aldhuhoori, Maryam Abdulla / Almutawa, Dhabiah Saleh / Alshehhi, Fatema Rashed / Balan, Jithin / Mundra, Sunil / Alam, Mohammad / Salehi-Ashtiani, Kourosh / Purugganan, Michael / Amiri, Khaled M A

Scientific reports

2022 Volume 12, Issue 1, Page(s) 11293

Abstract: Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally studied for their community composition, but less is known about their genetic structure ... ...

Abstract	Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally studied for their community composition, but less is known about their genetic structure and heterogeneity. In this study, we analyzed a coastal sabkha for its microbial composition using 16S rDNA and whole metagenome, as well as for its population genetic structure. Our 16S rDNA analysis show high alpha diversity in both inner and edge sabkha than outer sabkha. Beta diversity result showed similar kind of microbial composition between inner and edge sabkha, while outer sabkha samples show different microbial composition. At phylum level, Bacteroidetes (~ 22 to 34%), Euryarchaeota (~ 18 to ~ 30%), unclassified bacteria (~ 24 to ~ 35%), Actinobacteria (~ 0.01 to ~ 11%) and Cyanobacteria (less than 1%) are predominantly found in both inside and edge sabkha regions, whereas Proteobacteria (~ 92 to ~ 97%) and Parcubacteria (~ 1 to ~ 2%) are predominately found in outer sabkha. Our 225 metagenomes assembly from this study showed similar bacterial community profile as observed in 16S rDNA-based analysis. From the assembled genomes, we found important genes that are involved in biogeochemical cycles and secondary metabolite biosynthesis. We observed a dynamic, thriving ecosystem that engages in metabolic activity that shapes biogeochemical structure via carbon fixation, nitrogen, and sulfur cycling. Our results show varying degrees of horizontal gene transfers (HGT) and homologous recombination, which correlates with the observed high diversity for these populations. Moreover, our pairwise population differentiation (Fst) for the abundance of species across the salinity gradient of sabkhas identified genes with strong allelic differentiation, lower diversity and elevated nonsynonymous to synonymous ratio of variants, which suggest selective sweeps for those gene variants. We conclude that the process of HGT, combined with recombination and gene specific selection, constitute the driver of genetic variation in bacterial population along a salinity gradient in the unique sabkha ecosystem.
MeSH term(s)	Bacteroidetes/genetics ; Cyanobacteria/genetics ; DNA, Ribosomal ; Ecosystem ; Salinity ; Sodium Chloride ; Sodium Chloride, Dietary
Chemical Substances	DNA, Ribosomal ; Sodium Chloride, Dietary ; Sodium Chloride (451W47IQ8X)
Language	English
Publishing date	2022-07-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-15347-8
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Article ; Online: The Genome of the Mimosoid Legume

Sudalaimuthuasari, Naganeeswaran / Ali, Rashid / Kottackal, Martin / Rafi, Mohammed / Al Nuaimi, Mariam / Kundu, Biduth / Al-Maskari, Raja Saeed / Wang, Xuewen / Mishra, Ajay Kumar / Balan, Jithin / Chaluvadi, Srinivasa R / Al Ansari, Fatima / Bennetzen, Jeffrey L / Purugganan, Michael D / Hazzouri, Khaled M / Amiri, Khaled M A

International journal of molecular sciences

2022 Volume 23, Issue 15

Abstract: The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The ... ...

Abstract	The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The tree
MeSH term(s)	Disease Resistance/genetics ; Fabaceae/genetics ; Genes, Plant ; Genome, Plant ; Prosopis/genetics ; Trees/genetics
Language	English
Publishing date	2022-07-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23158503
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Article: Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population

Aljasmi, Fatma A / Vijayan, Ranjit / Sudalaimuthuasari, Naganeeswaran / Souid, Abdul-Kader / Karuvantevida, Noushad / Almaskari, Raja / Mohammed Abdul Kader, Hidaya / Kundu, Biduth / Michel Hazzouri, Khaled / Amiri, Khaled M. A

Genes. 2020 Aug. 01, v. 11, no. 8

2020

Abstract: In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of ... ...

Abstract	In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity. We identified 968 mtDNA variants and high-resolution 15 haplogroups. Our results show that the UAE population received enough gene flow from Africa represented by the haplogroups L, U6, and M1, and that 16.8% of the population has an eastern provenance, depicted by the U haplogroup and the M Indian haplogroup (12%), whereas western Eurasian and Asian haplogroups (R, J, and K) represent 11 to 15%. Interestingly, we found an ancient migration present through the descendant of L (N1 and X) and other sub-haplogroups (L2a1d and L4) and (L3x1b), which is one of the oldest evolutionary histories outside of Africa. Our demographic analysis shows no population structure among populations, with low diversity and no population differentiation. In addition, we show that the transmission of mtDNA in the UAE population is under purifying selection with hints of diversifying selection on ATP8 gene. Last, our results show a population bottleneck, which coincides with the Western European contact (1400 ybp). Our study of the UAE mitogenomes suggest that several maternal lineage migratory episodes liking African–Asian corridors occurred since the first modern human emerges out of Africa.
Keywords	demography ; females ; gene flow ; genes ; genetic variation ; humans ; maternal lineage ; mitochondrial DNA ; mitochondrial genome ; nationalities and ethnic groups ; population dynamics ; population structure ; provenance ; Africa ; United Arab Emirates
Language	English
Dates of publication	2020-0801
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11080876
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