Re-calibration of flow cytometry standards for plant genome size estimation DOI Creative Commons
Abhishek Soni, Robert J Henry

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

Abstract The evolution of long-read sequencing technologies has advanced the development genome assemblies that are now frequently presented as gap-free or nearly gapless, reflecting substantial improvements in accuracy and completeness. However, discrepancies between size estimates derived from flow cytometry create ambiguity regarding these complementary approaches. Accurate estimation via relies on use an internal standard with a known size. Historically, standards was often calibrated against incomplete non-plant genomes, such human male genome, which previously considered to be 7 pg but is around 6.15 after 20 years advancements. Calibrating plant references not recommended due differential staining properties. Therefore, we recalibrated five genomes commonly used reference cytometry, by utilizing recent telomere-to-telomere (T2T) assembly Nipponbare rice. Our results indicate significant overestimation 20% previous cytometry-based for Pisum sativum Nicotiana benthamiana , 10% Arabidopsis thaliana less than 5% Sorghum bicolor Gossypium hirsutum . close alignment GS recalculated different studies confirms their suitability more accurate measurement

Language: Английский

Role of Genome Sequences of Major and Minor Millets in Strengthening Food and Nutritional Security for Future Generations DOI Creative Commons
Theivanayagam Maharajan,

Thumadath Palayullaparambil Ajeesh Krishna,

Neenthamadathil Mohandas Krishnakumar

et al.

Agriculture, Journal Year: 2024, Volume and Issue: 14(5), P. 670 - 670

Published: April 25, 2024

Millets are small-seeded cereals belonging to the family Poaceae. They considered be climate-resilient and future nutritional food for humans. resistant biotic abiotic stressors compared other major thrive in low-quality soils with little maintenance less rainfall. The importance of millets is still not well known many people due lack popularity cultivation semi-arid tropics Asia Africa. United Nations has declared 2023 as International Year (IYM 2023) promote millet popularize their health benefits globally. A few years ago, application molecular biology was its infancy unavailability genome sequences. Genome sequences available most on NCBI Phytozome databases. In this review, we discuss details millets, candidate genes identified from native millets. current status quantitative trait loci genome-wide association studies also discussed. utilization functional genomics research translating information crop improvement will help non-millet survive harsh environments future. Such efforts strengthen security reduce malnutrition worldwide 2050.

Language: Английский

Citations

12
Gene mapping and candidate gene analysis of a sorghum sheathed panicle‐I mutant DOI Creative Commons

Jianling Ao,

Ruoruo Wang,

Wenzeng Li

et al.

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: March 1, 2025

Panicle exsertion is essential for crop yield and quality, understanding its molecular mechanisms crucial optimizing plant architecture. In this study, the sheathed panicle-I (shp-I) mutant was identified from ethyl methane sulfonate population of sorghum [Sorghum bicolor (L.) Moench] variety Hongyingzi (HYZ). While phenotypically similar to wild type during seedling stage, shp-I exhibits a significantly shorter peduncle internode at heading stage. Cytomorphological analysis revealed reduced parenchyma cell size within mutant's internode. Phytohormonal profiling showed lower levels indole-3-acetic acid higher concentrations brassinosteroid in compared Genetic confirmed that phenotype caused by recessive single-gene mutation. Through bulked segregant sequencing (BSA-seq) genetic mapping, causative locus localized 59.65-59.92 Mb interval on chromosome 10, which contains 28 putative genes. Additionally, gene SbiHYZ.10G230700, encodes BTB/POZ MATH (BPM) domain protein, as candidate gene. Further non-synonymous mutations were located domain, affecting 3D structure protein. summary, study provides new material genes future research into regulation length.

Language: Английский

Citations

1
Unlocking plant genetics with telomere-to-telomere genome assemblies DOI
Vanika Garg, Abhishek Bohra, Martin Mascher

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(9), P. 1788 - 1799

Published: July 24, 2024

Language: Английский

Citations

6
Brown-top millet: an overview of breeding, genetic, and genomic resources development for crop improvement DOI

P. Bhavani,

C. Nandini,

Theivanayagam Maharajan

et al.

Planta, Journal Year: 2024, Volume and Issue: 260(1)

Published: May 26, 2024

Language: Английский

Citations

4
Message from the Editor-in-Chief: Embracing challenges and opportunities in crop sciences in the New Year DOI Creative Commons
Jianmin Wan

The Crop Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0
Comparative analysis of microbial communities and flavor compounds in fermented grains from different sorghum varieties used in Sichuan Xiaoqu liquor DOI Creative Commons

Minghong Bian,

Yuli Fang,

Kailong Yang

et al.

LWT, Journal Year: 2025, Volume and Issue: unknown, P. 117640 - 117640

Published: March 1, 2025

Language: Английский

Citations

0
Genetic mechanisms, biological function, and biotechnological advance in sorghum tannins research DOI
Fu Wang, Qian Zhao, Shuyao Li

et al.

Biotechnology Advances, Journal Year: 2025, Volume and Issue: unknown, P. 108573 - 108573

Published: March 1, 2025

Language: Английский

Citations

0
Unraveling the regional environmental ecology dominated baijiu fermentation microbial community succession and associated unique flavor DOI Creative Commons
Xiaowei Wu, Xiaoli Zhao,

Li Wang

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Oct. 31, 2024

Chinese baijiu as one of the famous distilled liquor in which fermented open environments, with various microorganisms (i.e., bacteria, fungi, and yeast) involved their brewing process, created corresponding unique flavor. However, sources environmentally enriched microbial communities associated fermentation are still being characterized yet. Given dependence growth reproduction on environmental ecology, it is important to understand correlation between community surrounding ecology temperature, humidity, wind, precipitation). This study systematically overviewed Jiang-flavor-Baijiu system. The results showed that mold, lactic acid mainly originated from matrices, including air

Language: Английский

Citations

1
Re-calibration of flow cytometry standards for plant genome size estimation DOI Creative Commons
Abhishek Soni, Robert J Henry

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

Abstract The evolution of long-read sequencing technologies has advanced the development genome assemblies that are now frequently presented as gap-free or nearly gapless, reflecting substantial improvements in accuracy and completeness. However, discrepancies between size estimates derived from flow cytometry create ambiguity regarding these complementary approaches. Accurate estimation via relies on use an internal standard with a known size. Historically, standards was often calibrated against incomplete non-plant genomes, such human male genome, which previously considered to be 7 pg but is around 6.15 after 20 years advancements. Calibrating plant references not recommended due differential staining properties. Therefore, we recalibrated five genomes commonly used reference cytometry, by utilizing recent telomere-to-telomere (T2T) assembly Nipponbare rice. Our results indicate significant overestimation 20% previous cytometry-based for Pisum sativum Nicotiana benthamiana , 10% Arabidopsis thaliana less than 5% Sorghum bicolor Gossypium hirsutum . close alignment GS recalculated different studies confirms their suitability more accurate measurement

Language: Английский

Citations

0