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Article ; Online: Genome-wide association of dry (Tamar) date palm fruit color.

Younuskunju, Shameem / Mohamoud, Yasmin A / Mathew, Lisa S / Mayer, Klaus F X / Suhre, Karsten / Malek, Joel A

2023 Volume 16, Issue 4, Page(s) e20373

Abstract: Date palm (Phoenix dactylifera) fruit (dates) are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. ... ...

Abstract	Date palm (Phoenix dactylifera) fruit (dates) are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. Genetic studies of some date palm traits have been performed, including sex determination, sugar content, and fresh fruit color. In this study, we used genome sequences and image data of 199 dry dates (Tamar) collected from 14 countries to identify genetic loci associated with the color of this fruit stage. Here, we find loci across multiple linkage groups (LG) associated with dry fruit color phenotype. We recover both the previously identified VIRESCENS (VIR) genotype associated with fresh fruit yellow or red color and new associations with the lightness and darkness of dry fruit. This study will add resolution to our understanding of date color phenotype, especially at the most commercially important Tamar stage.
MeSH term(s)	Phoeniceae/genetics ; Genome-Wide Association Study ; Genotype ; Phenotype
Language	English
Publishing date	2023-08-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2375444-8
ISSN	1940-3372 ; 0011-183X
ISSN (online)	1940-3372
ISSN	0011-183X
DOI	10.1002/tpg2.20373
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Article: Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm (

Torres, Maria F / Mohamoud, Yasmin A / Younuskunju, Shameem / Suhre, Karsten / Malek, Joel A

Frontiers in plant science

2021 Volume 12, Page(s) 634901

Abstract: ... The ... ...

Abstract	The genus
Language	English
Publishing date	2021-04-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711035-7
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2021.634901
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Article ; Online: Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit.

Malek, Joel A / Mathew, Sweety / Mathew, Lisa S / Younuskunju, Shameem / Mohamoud, Yasmin A / Suhre, Karsten

Plant direct

2020 Volume 4, Issue 5, Page(s) e00214

Abstract: The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across ... ...

Abstract	The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content, we analyzed date fruit metabolomics for association with genotype data from 120 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta-fructofuranosidase (invertase) gene in the reference Khalas genome, a low-sucrose fruit. High-sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains all copies of the gene in 3 other species of
Language	English
Publishing date	2020-05-27
Publishing country	England
Document type	Journal Article
ISSN	2475-4455
ISSN (online)	2475-4455
DOI	10.1002/pld3.214
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Article: Deletion of beta‐fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Malek, Joel A. / Mathew, Sweety / Mathew, Lisa S. / Younuskunju, Shameem / Mohamoud, Yasmin A. / Suhre, Karsten

Plant direct. 2020 May, v. 4, no. 5

2020

Abstract	The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content, we analyzed date fruit metabolomics for association with genotype data from 120 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta‐fructofuranosidase (invertase) gene in the reference Khalas genome, a low‐sucrose fruit. High‐sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end‐point sucrose content in date fruit may be used in selective breeding in the future.
Keywords	Phoenix dactylifera ; alleles ; beta-fructofuranosidase ; cultivars ; dates (fruit) ; diet ; flavor ; fructose ; fruits ; genomics ; glucose ; homozygosity ; metabolomics ; plant physiology ; sucrose ; texture ; Middle East ; Northern Africa
Language	English
Dates of publication	2020-05
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ISSN	2475-4455
DOI	10.1002/pld3.214
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Article: Holocene Selection for Variants Associated With General Cognitive Ability: Comparing Ancient and Modern Genomes.

Woodley, Michael A / Younuskunju, Shameem / Balan, Bipin / Piffer, Davide

Twin research and human genetics : the official journal of the International Society for Twin Studies

2017 Volume 20, Issue 4, Page(s) 271–280

Abstract: Human populations living during the Holocene underwent considerable microevolutionary change. It has been theorized that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favored via ... ...

Abstract	Human populations living during the Holocene underwent considerable microevolutionary change. It has been theorized that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favored via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes (Fst = 0.013), using three different cognitive polygenic scores (130 SNP, 9 SNP and 11 SNP). Significant differences favoring the modern genomes were found for all three polygenic scores (odds ratios = 0.92, p = 001; .81, p = 037; and .81, p = .02 respectively). These polygenic scores also outperformed the majority of scores assembled from random SNPs generated via a Monte Carlo model (between 76.4% and 84.6%). Furthermore, an indication of increasing positive allele count over 3.25 kyr was found using a subsample of 66 ancient genomes (r = 0.22, pone-tailed = .04). These observations are consistent with the expectation that GCA rose during the Holocene.
Language	English
Publishing date	2017-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2182682-1
ISSN	1839-2628 ; 1832-4274
ISSN (online)	1839-2628
ISSN	1832-4274
DOI	10.1017/thg.2017.37
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Article ; Online: Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing.

Mohamoud, Yasmin A / Mathew, Lisa S / Torres, Maria F / Younuskunju, Shameem / Krueger, Robert / Suhre, Karsten / Malek, Joel A

BMC genomics

2019 Volume 20, Issue 1, Page(s) 498

Abstract: Background: The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near ... ...

Abstract	Background: The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. Results: To better understand the origins of date palm cultivation we sequenced and analyzed over 200 mitochondrial and chloroplast genomes from a geographically diverse set of date palms. Here we show that, based on mitochondrial and chloroplast genome-wide genotyping data, the most common cultivated date palms contain 4 haplotypes that appear associated with geographical region of cultivar origin. Conclusions: These data suggest at least 3 and possibly 4 original maternal contributions to the current date palm population and doubles the original number. One new haplotype was found mainly in Tunisia, Algeria and Egypt and the second in Iraq, Iran and Oman. We propose that earliest date palm cultivation occurred independently in at least 3 distinct locations. This discovery will further inform understanding of the history and origins of cultivated date palm.
MeSH term(s)	Base Sequence ; Haplotypes/genetics ; Organelles/genetics ; Phoeniceae/classification ; Phoeniceae/genetics ; Whole Genome Sequencing
Language	English
Publishing date	2019-06-17
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-019-5834-7
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Article: Two prolonged viremic SARS-CoV-2 infections with conserved viral genome for two months

Infection, genetics, and evolution. 2021 Mar., v. 88

2021

Abstract: We document two cases of viremic and prolonged active infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) where the viral genome was conserved for two months, but infection was with little or no symptoms. The first infection ... ...

Abstract	We document two cases of viremic and prolonged active infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) where the viral genome was conserved for two months, but infection was with little or no symptoms. The first infection persisted for 80 days and the second for 62 days. Clearance of infection occurred 40 and 41 days, respectively, after development of detectable antibodies. Both cases were identified incidentally in an investigation of reinfection in a cohort of 133,266 laboratory-confirmed infected persons.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; evolution ; infection ; viral genome
Language	English
Dates of publication	2021-03
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104684
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Article ; Online: Two prolonged viremic SARS-CoV-2 infections with conserved viral genome for two months.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2020 Volume 88, Page(s) 104684

Abstract	We document two cases of viremic and prolonged active infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) where the viral genome was conserved for two months, but infection was with little or no symptoms. The first infection persisted for 80 days and the second for 62 days. Clearance of infection occurred 40 and 41 days, respectively, after development of detectable antibodies. Both cases were identified incidentally in an investigation of reinfection in a cohort of 133,266 laboratory-confirmed infected persons.
MeSH term(s)	Adult ; Antibodies, Viral/blood ; Asymptomatic Diseases ; COVID-19/diagnosis ; COVID-19/immunology ; COVID-19/virology ; COVID-19 Testing ; Enzyme-Linked Immunosorbent Assay ; Female ; Genome, Viral ; Humans ; Infectious Disease Incubation Period ; Male ; RNA, Viral/blood ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/genetics ; SARS-CoV-2/growth & development ; SARS-CoV-2/immunology ; Time Factors ; Viremia/diagnosis ; Viremia/immunology ; Viremia/virology
Chemical Substances	Antibodies, Viral ; RNA, Viral
Language	English
Publishing date	2020-12-24
Publishing country	Netherlands
Document type	Case Reports ; Journal Article
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104684
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Article ; Online: SARS-CoV-2 antibody-positivity protects against reinfection for at least seven months with 95% efficacy.

Abu-Raddad, Laith J / Chemaitelly, Hiam / Coyle, Peter / Malek, Joel A / Ahmed, Ayeda A / Mohamoud, Yasmin A / Younuskunju, Shameem / Ayoub, Houssein H / Al Kanaani, Zaina / Al Kuwari, Einas / Butt, Adeel A / Jeremijenko, Andrew / Kaleeckal, Anvar Hassan / Latif, Ali Nizar / Shaik, Riyazuddin Mohammad / Abdul Rahim, Hanan F / Nasrallah, Gheyath K / Yassine, Hadi M / Al Kuwari, Mohamed Ghaith /

Al Romaihi, Hamad Eid / Al-Thani, Mohamed H / Al Khal, Abdullatif / Bertollini, Roberto

EClinicalMedicine

2021 Volume 35, Page(s) 100861

Abstract: Background: Reinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented, raising public health concerns. SARS-CoV-2 reinfections were assessed in a cohort of antibody-positive persons in Qatar.: Methods: All ... ...

Abstract	Background: Reinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented, raising public health concerns. SARS-CoV-2 reinfections were assessed in a cohort of antibody-positive persons in Qatar. Methods: All SARS-CoV-2 antibody-positive persons from April 16 to December 31, 2020 with a PCR-positive swab ≥14 days after the first-positive antibody test were investigated for evidence of reinfection. Viral genome sequencing was conducted for paired viral specimens to confirm reinfection. Incidence of reinfection was compared to incidence of infection in the complement cohort of those who were antibody-negative. Findings: Among 43,044 antibody-positive persons who were followed for a median of 16.3 weeks (range: 0-34.6), 314 individuals (0.7%) had at least one PCR positive swab ≥14 days after the first-positive antibody test. Of these individuals, 129 (41.1%) had supporting epidemiological evidence for reinfection. Reinfection was next investigated using viral genome sequencing. Applying the viral-genome-sequencing confirmation rate, the incidence rate of reinfection was estimated at 0.66 per 10,000 person-weeks (95% CI: 0.56-0.78). Incidence rate of reinfection versus month of follow-up did not show any evidence of waning of immunity for over seven months of follow-up. Meanwhile, in the complement cohort of 149,923 antibody-negative persons followed for a median of 17.0 weeks (range: 0-45.6), incidence rate of infection was estimated at 13.69 per 10,000 person-weeks (95% CI: 13.22-14.14). Efficacy of natural infection against reinfection was estimated at 95.2% (95% CI: 94.1-96.0%). Reinfections were less severe than primary infections. Only one reinfection was severe, two were moderate, and none were critical or fatal. Most reinfections (66.7%) were diagnosed incidentally through random or routine testing, or through contact tracing. Interpretation: Reinfection is rare in the young and international population of Qatar. Natural infection appears to elicit strong protection against reinfection with an efficacy ~95% for at least seven months. Funding: Biomedical Research Program, the Biostatistics, Epidemiology, and Biomathematics Research Core, and the Genomics Core, all at Weill Cornell Medicine-Qatar, the Ministry of Public Health, Hamad Medical Corporation, and the Qatar Genome Programme.
Language	English
Publishing date	2021-04-28
Publishing country	England
Document type	Journal Article
ISSN	2589-5370
ISSN (online)	2589-5370
DOI	10.1016/j.eclinm.2021.100861
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Article ; Online: Introduction and expansion of the SARS-CoV-2 B.1.1.7 variant and reinfections in Qatar: A nationally representative cohort study.

Abu-Raddad, Laith J / Chemaitelly, Hiam / Ayoub, Houssein H / Coyle, Peter / Malek, Joel A / Ahmed, Ayeda A / Mohamoud, Yasmin A / Younuskunju, Shameem / Tang, Patrick / Al Kanaani, Zaina / Al Kuwari, Einas / Butt, Adeel A / Jeremijenko, Andrew / Kaleeckal, Anvar Hassan / Latif, Ali Nizar / Shaik, Riyazuddin Mohammad / Abdul Rahim, Hanan F / Nasrallah, Gheyath K / Yassine, Hadi M /

Al Kuwari, Mohamed Ghaith / Al Romaihi, Hamad Eid / Al-Thani, Mohamed H / Al Khal, Abdullatif / Bertollini, Roberto

PLoS medicine

2021 Volume 18, Issue 12, Page(s) e1003879

Abstract: Background: The epidemiology of the SARS-CoV-2 B.1.1.7 (or Alpha) variant is insufficiently understood. This study's objective was to describe the introduction and expansion of this variant in Qatar and to estimate the efficacy of natural infection ... ...

Abstract	Background: The epidemiology of the SARS-CoV-2 B.1.1.7 (or Alpha) variant is insufficiently understood. This study's objective was to describe the introduction and expansion of this variant in Qatar and to estimate the efficacy of natural infection against reinfection with this variant. Methods and findings: Reinfections with the B.1.1.7 variant and variants of unknown status were investigated in a national cohort of 158,608 individuals with prior PCR-confirmed infections and a national cohort of 42,848 antibody-positive individuals. Infections with B.1.1.7 and variants of unknown status were also investigated in a national comparator cohort of 132,701 antibody-negative individuals. B.1.1.7 was first identified in Qatar on 25 December 2020. Sudden, large B.1.1.7 epidemic expansion was observed starting on 18 January 2021, triggering the onset of epidemic's second wave, 7 months after the first wave. B.1.1.7 was about 60% more infectious than the original (wild-type) circulating variants. Among persons with a prior PCR-confirmed infection, the efficacy of natural infection against reinfection was estimated to be 97.5% (95% CI: 95.7% to 98.6%) for B.1.1.7 and 92.2% (95% CI: 90.6% to 93.5%) for variants of unknown status. Among antibody-positive persons, the efficacy of natural infection against reinfection was estimated to be 97.0% (95% CI: 92.5% to 98.7%) for B.1.1.7 and 94.2% (95% CI: 91.8% to 96.0%) for variants of unknown status. A main limitation of this study is assessment of reinfections based on documented PCR-confirmed reinfections, but other reinfections could have occurred and gone undocumented. Conclusions: In this study, we observed that introduction of B.1.1.7 into a naïve population can create a major epidemic wave, but natural immunity in those previously infected was strongly associated with limited incidence of reinfection by B.1.1.7 or other variants.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Basic Reproduction Number ; COVID-19/epidemiology ; COVID-19/virology ; Child ; Female ; Humans ; Immunity, Innate ; Male ; Middle Aged ; Models, Theoretical ; Polymerase Chain Reaction ; Qatar/epidemiology ; Reinfection/epidemiology ; Reinfection/virology ; Retrospective Studies ; SARS-CoV-2 ; Time Factors ; Young Adult
Language	English
Publishing date	2021-12-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2185925-5
ISSN	1549-1676 ; 1549-1277
ISSN (online)	1549-1676
ISSN	1549-1277
DOI	10.1371/journal.pmed.1003879
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