Sabiha Parweeen

Postdoctoral Fellows

PostDoctoral Fellow.

Current

Location:

3216_ws05

Social Profile:

Selected Publications

 Publications from KAUST 
1. Host genome and bacterial taxa shape the Arabidopsis seed microbiome.Sabiha 
Parween, Naheed Tabassum ,Kirti Shekhawat, Bruno Gnannt , Waad Alzayed , Rewaa 
Jalal ,Heribert Hirt.10.1038/s44319-025-00635-x. EMBOR-2025-62320V1 (Accepted)
2. Darwin21 Genome Database: A Curated Whole-Genome Repository of Endophytic 
Bacteria from Desert Plants. Sabiha Parween, Arun Prasanna Nagarajan, Amal K 
Alghamdi, Abdul Aziz Eida, Feras F Lafi, Luma Albanna, Nida Salem, Barakat AbuIrmaileh, Zaid A Pirzada, Shahid Siddique, Ruben Garrido-Oter, Paul Schulze-Lefert, Maged 
M Saad, Heribert Hirt.
MS ID#: BIORXIV/2025/672100 (Under review)
3. The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in 
Arabidopsis thaliana. Rolli, E., de Zélicourt, A., Alzubaidy, H., Karampelias, M., Parween, S.,
Rayapuram, N., Han, B., Froehlich, K., Abulfaraj, A.A., Alhoraibi, H., Mariappan, K., AndrésBarrao, C., Colcombet, J. and Hirt, H. (2022), Environ Microbiol, 24: 223-239. 
https://doi.org/10.1111/1462-2920.15839
4. Analysis of the Arabidopsis coilin mutant reveals a positive role of AtCOILIN in plant 
immunity. Aala A Abulfaraj, Hanna M Alhoraibi, Kiruthiga Mariappan, Jean Bigeard, Huoming
Zhang, Marilia Almeida-Trapp, Olga Artyukh, Fatimah Abdulhakim, Sabiha Parween, Delphine
Pflieger, Ikram Blilou, Heribert Hirt, Naganand Rayapuram, Plant Physiology, Volume 190, 
Issue 1, September 2022, Pages 745–761, https://doi.org/10.1093/plphys/kiac280
5. Complete genome sequence analysis of plant growth-promoting bacterium, Isoptericola 
sp. AK164 isolated from the rhizosphere of Avicennia marina growing at the Red Sea 
coast. Amal Khalaf Alghamdi, Sabiha Parween, Heribert Hirt & Maged M. Saad. Arch 
Microbiol 205, 341 (2023). https://doi-org.kaust.idm.oclc.org/10.1007/s00203-023-03687-6
6. Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome.
Naheed Tabassum, Hanin Ibrahim Ahmed, Sabiha Parween, Arsheed H. Sheikh, Maged M. 
Saad, Simon G. Krattinger & Heribert Hirt.Microbiome 12, 11 (2024). 
https://doi.org/10.1186/s40168-023-01725-5
7. Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting
bacterium isolated from Avicennia marina. BMC Genomics.Alghamdi AK, Parween S, Hirt 
H, Saad MM. BMC Genomics 25, 672 (2024). https://doi.org/10.1186/s12864-024-10555-0
8. Microbe-induced coordination of plant iron-sulfur metabolism enhances high light stress 

tolerance of Arabidopsis. Plant Communications. Shekhawat, Kirti & Veluchamy, Alaguraj

& Fatima, Anam & García-Ramírez, Gabriel & Reichheld, Jean-Philippe & Artyukh, Olga & 
Fröhlich, Katja & Polussa, Alexander & Parween, Sabiha & Nagarajan, Arun & Rayapuram, 
Naganand & Hirt, Heribert. Plant Communications, Volume 5, Issue 11, 101012
9. Unveiling the bacterial diversity and potential of the Avicennia marina ecosystem for 
enhancing plant resilience to saline conditions. Alghamdi, A.K., Parween, S., Hirt, H. et al. 
Environmental Microbiome 19, 101 (2024). https://doi.org/10.1186/s40793-024-00642-w
10.Switch From Soil to Plant Host Lifestyle Is Mediated by rpoS Mutations in Bacterial 
Endophyte. Alsharif, W., Andrés-Barrao, C., Parween, S., Hashim, A., Shekhawat, K., Abrouk, 
M., Wang, J.Y., Marasco, R., Krattinger, S.G., Daffonchio, D., Al-Babili, S., Saad, M.M. and 
Hirt, H. (2025),. Plant, Cell & Environment, 48: 8068-8085. https://doi.org/10.1111/pce.70101
11.Plant growth promotion and pathogen protection by the desert endophyte Pseudomonas 
grandensis R4-79. Alghanmi, L., Elhady, A., Parween, S. et al. BMC Microbiol 25, 690 (2025).
https://doi.org/10.1186/s12866-025-04431-4
12. Mangrove-Derived Endophytic Bacteria Enhance Growth, Yield, and Stress Resilience in 
Rice. Alghamdi, A.K.; Rawat, A.; Alzayed, W.; Parween, S.; Nagarajan, A.P.; Saad, M.M.; Hirt, 
H. Int. J. Mol. Sci. 2025, 26, 9317. https://doi.org/10.3390/ijms26199317
13.Comprehensive Mapping of EZ-Tn5 Transposon Insertion Sites in Pseudomonas 
argentinensis SA190 Using RATE-PCR. Elkatmis B, Han B, Parween S, Kopriva S, Hirt H,
Saad MM. Bio Protoc. 2025 Jul 20;15(14):e5389. doi: 10.21769/BioProtoc.5389. PMID: 
40741398; PMCID: PMC12304473.
14.Differential influence of water and early vegetation on desert soil microbiome 
abundance and interaction. A Elhady, B Schroeter, S Parween, M Saad, A Naegel, H,Hirt. 
https://doi.org/10.21203/rs.3.rs-7411547/v1 (Under review)
15.Impact of Strigolactone Analogs on Soil Microbial Community Dynamics and 
Functional Enrichment. Maged M. Saad*
, Sabiha Parween*
, Muhammad Jamil, Jian You 
Wang, Tadao Asami, Salim Al-Babili, Heribert Hirt.
Submission ID cff52191-b2ce-4fcd-9c36 (Submitted)
 Others:
16.Galactinol synthase across evolutionary diverse taxa: Functional preference for higher
plants? Sonali Sengupta ,Sritama Mukherjee, Sabiha Parween, Arun Lahiri Majumder.
Division of Plant Biology, Bose Institute (Centenary Building), P-1/12, C I T Scheme VII
M,Kolkata 700 054, India (FEBS letter)
17.An advanced draft genome assembly of a desi type chickpea (Cicer arietinumL.) Sabiha 
Parween * , Kashif Nawaz *,Riti Roy * , Anil K. Pole, B. Venkata Suresh, Gopal Misra,Mukesh
Jain, Gitanjali Yadav, Swarup K. Parida, Akhilesh K. Tyagi, Sabhyata Bhatia &Debasis 
Chattopadhyay.Scientific Reports 5, Article number:12806 (2015):10.1038/srep12806

18.Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta 
rabiei provides insight into the necrotrophic effector repertoire Dr. Sandhya Verma , Mr. 
Rajesh Gazara , Dr. Shadab Nizam , Miss Sabiha Parween , Dr. Debasis Chattopadhyay.Sci 
Rep. 2016 Apr 19;6:24638. doi: 10.1038/srep24638.
19.Draft genome of Cicer reticulatum L., the wild progenitor of chickpea provides insigt into 
the domesticationprocess.
Gupta, Sonal*; Nawaz, Kashif*; Parween, Sabiha*; Roy, Riti; Sahu, Kamlesh; Pole, Anil; 
Khandal, Hitaishi; Srivastava, Rishi; Parida, Swarup; Chattopadhyay, Debasis.DNA Res. 2017 
Feb 1;24(1):1-10. doi: 10.1093/dnares/dsw042.
20.MicroRNA profiling provides insights into post-transcriptional regulation of gene 
expression in chickpea root apex under salinity and water deficiency.Khandal, Hitaishi & 
Parween, Sabiha & Roy, Riti & Meena, Mukesh & Chattopadhyay, Debasis.(2017). Scientific 
Reports. 7. 10.1038/s41598-017-04906-z.
21.Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis Vito M. 
Butardo Jr. , Roslen Anacleto , Sabiha Parween, Irene Samson, Krishna de Guzman, Crisline 
Mae Alhambra, Gopal Misra, and Nese Sreenivasulu. Grain Quality and Nutrition Center, Plant 
Breeding Division, International Rice Research 11 Institute, Los Baños, Laguna, Philippines. 
Plant Physiol. 2017 Jan;173(1):887-906. doi: 10.1104/pp.16.01248. Epub 2016 Nov 23.
22.Investigating glycemic potential of rice by unraveling compositional variations in mature 
grain and starch mobilization patterns during seed germination. Maria Krishna de 
Guzman,Sabiha Parween,Vito M. Butardo, Crisline Mae Alhambra, Roslen Anacleto,Christiane 
Seiler,Anthony R. Bird,Chung-Ping Chow & Nese Sreenivasulu. Scientific Reports volume 7, 
Article number:5854 (2017) :10.1038/s41598-017-06026-0
23.Integrating a genome‐wide association study with a large‐scale transcriptome analysis to 
predict genetic regions influencing the glycaemic index and texture in rice. 
Anacleto,R.,Badoni,S.,Parween, S.,Butardo, V. M.,Misra, G.,Cuevas, R. P.,Kuhlmann, 
M.,Trinidad, T. P.,Mallillin, A. C.,Acuin, C.,Bird, A. R.,Morell, M. KandSreenivasulu, N.(2019)
Plant Biotechnol. J.,https://doi.org/10.1111/pbi.13051.
24.Laser Microdissection-Based Tissue-Specific Transcriptome Analysis Reveals a Novel 
Regulatory Network of Genes Involved in Heat-Induced Grain Chalk in Rice 
Endosperm.Tsutomu Ishimaru, Sabiha Parween, Yuhi Saito, Takanari Shigemitsu, Hiromoto 
Yamakawa, Mikio Nakazono, Takehiro Masumura, Naoko K Nishizawa,MotohikoKondo,Nese 
Sreenivasulu. Plant and Cell Physiology, Volume 60, Issue 3, March 2019, Pages 626–642, 

https://doi.org/10.1093/pcp/pcy233

25.Balancing the double‐edged sword effect of increased resistant starch content and its 
impact on rice texture: Its genetics and molecular physiological mechanisms. Parween, S.*,
Anonuevo, J. J., Butardo, V. M., Misra, G., Anacleto, R., Llorente, C., Kosik, O., Romero, M. 
V., Bandonill, E. H., Mendioro, M. S., Lovegrove, A.,Fernie,A. R., Brotman, Y.and 
Sreenivasulu, N. ( 2020) Plant Biotechnol. J., https://doi.org/10.1111/pbi.13339 
26.The genetics underlying metabolic signatures in a brown rice diversity panel and their 
vital role in human nutrition.Nese Sreenivasulu, Yariv Brotman, Cindy Llorente-Wiegand, 
Glenn Oyong, Saurabh Badoni, Gopal Misra, Roslen Anacleto, Sabiha Parween, Erstelle Pasion,
Rhowell N. Tiozon Tiozon, Joanne Anonuevo, Maria deGuzman, Saleh Alseekh, Edwige 
Mbanjo, Lesley Boyd, and Alisdair Fernie. Plant J, 106: 507-525. 
https://doi.org/10.1111/tpj.15182
27.Genome-wide association coupled gene to gene interaction studies unveil novel epistatic 
targets among major effect loci impacting rice grain chalkiness. Misra, Gopal; Badoni, 
Saurabh; Parween, Sabiha; Sreenivasulu, Nese.Plant Biotechnol J. 2021 May;19(5):910-925. 
doi: 10.1111/pbi.13516. Epub 2020 Dec 9. PMID: 33220119; PMCID: PMC8131057
28.OsTPR boosts the superior grains through increase in upper secondary rachis branches 
without incurring a grain quality penalty.Pasion, Erstelle; Misra, Gopal; Anacleto, Roslen; 
Parween, Sabiha; Kohli, Ajay; Sreenivasulu, Nese.Plant Biotechnol. J., 
https://doi.org/10.1111/pbi.13560
29.Systems seed biology to understand and manipulate rice grain quality and 
nutrition.Saurabh Badoni, Sabiha Parween, Robert J. Henry & Nese 
Sreenivasulu(2022),Critical Reviews in Biotechnology,DOI: 10.1080/07388551.2022.2058460
30.Laser microdissection transcriptome data derived gene regulatory networks of developing
rice endosperm revealed tissue- and stage-specific regulators modulating starch 
metabolism. Ishimaru, T., Parween, S., Saito, Y. et al. Plant Mol Biol 108, 443–467 (2022). 
https://doi.org/10.1007/s11103-021-01225-w

Education

 PhD, Molecular Biology and Biotechnology,University of Philippines (International Rice Research
Institute).
 M.Sc., Bioinformatics, Birla Institute of Technology,Mesra. India.
 B.Sc., Botany, University of Ranchi, India.
 Higher Secondary, CBSE-New Delhi, Ranchi, India.
 Secondary, CBSE-New Delhi, Ranchi , India

Professional Profile

Consultant (December, 2020-July, 2022); Postdoc Bioinformatics (August, 2022 upto present)
King Abdullah University of Science and Technology, Saudi Arab.
Establish a global knowledge base of microbes associated with desert plants and leverage this resource
to restore sustainable agricultural systems in arid regions. Integrate genomics, transcriptomics,
epigenomics, metagenomics, and amplicon data from desert plant species and micro biota across
diverse geographies to resolve the genetic basis of microbial traits and plant–microbe–environment
interactions. Layer this with predictive and mechanistic modeling to identify, prioritize, and deploy
consortia that enhance plant growth under drought, heat, salinity, and pathogen pressure.
 Consultant- Bioinformatics (November, 2019-November,2020)
International Rice Research Institute, Strategic Innovation Platform,Philippines.
My work centered on transcriptomics to map the gene-regulatory cascades underlying key rice
nutritional traits amylose:amylopectin ratio, grain chalkiness, dietary fibre, and micronutrient content. I
integrated multi-omics RNA-seq, epigenomic marks (DNA methylation/histone), long non-coding
RNAs, and structural-variant NGS to build multi-layer gene regulatory networks and applied systemsbiology modeling to prioritize causal candidate genes.
PhD (January, 2016-October, 2019)
Grain Quality and Nutrition Center, International Rice Research Institute, Philippines and Universit 
of Philippines.
Thesis entitled . “Elucidation of the Genetic and Molecular basis of Resistant Starch formation in
rice for optimal Nutritional and Textural attributes”
Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a
substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS
contributes to a lower glycemic index. Using a 281-line indica panel (~2.2M SNPs), we mapped lowto-intermediate resistant starch (RS) variation by GWAS and targeted gene tests, uncovering loci in
amylopectin biosynthesis/degradation (notably SSIIa). Deep phenotyping of SSIIa allele groups
(medium vs low RS) integrated transcriptomics, metabolomics, dietary fiber chemistry, starch structure,
and texture. Networks flagged a protein phosphatase with starch-metabolism genes; metabolite hubs
(carboxylic acids, sugars, polyamines) characterized medium-RS lines. Moderate RS gains coincided
with higher amylose I/II, while texture remained comparable to IR64—supporting breeding for higherRS, low-GI rice without major quality penalties.
 Senior Research fellow (November, 2012-November, 2014)
National Institute of Plant Genome Research (NIPGR), New Delhi, India
Project title: “Chickpea genome sequence analysis and its alignment to genetic map of Next 
Generation Challenge program on Chickpea Genomics”
Chickpea (Cicer arietinum L.) is an important pulse legume crop. We reported an advanced version of
the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an
improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and
substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated
gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes
encoding potential transcription factors (TF) and resistance gene homologs, respectively. Pairwise
comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier)
chickpea assemblies showed an extensive local collinearity. This reference desi genome assembly could
serve as an efficient genomic resource for mining SNPs at a genome-wide scale in diverse desi and
kabuli genotypes and thus would expedite genomics-assisted breeding applications and genetic
enhancement targeting multiple qualitative and quantitative traits in chickpea.
 Intern (September, 2011-February,2012)
Project title:“Insilico Designing of siRNA tool.” Department of Biotechnology, India.
siRNA mediated gene silencing by RNA interference is a powerful mechanism which can be used in
certain aspects of functional and medical genomic research and also therapeutics. Using bioinformatics
approaches many tools are developed to design siRNAs against a particular gene which is to be
silenced. We tried to develop an innovative siRNA design algorithm for a new siRNA design tool using
algorithms from present literature as well as developing new rules based on vast statistical studies and
machine learning approaches.