Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

MA Chapman, Y He, M Zhou - New Phytologist, 2022 - Wiley Online Library
Underutilized crops are, by definition, under‐researched compared to staple crops yet come
with traits that may be especially important given climate change and the need to feed a …

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

P Novák, L Ávila Robledillo, A Koblížková… - Nucleic acids …, 2017 - academic.oup.com
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly
arranged repeat copies that form contiguous arrays up to megabases in length. This type of …

Genomics and evolution in traditional medicinal plants: road to a healthier life

DC Hao, PG Xiao - Evolutionary Bioinformatics, 2015 - journals.sagepub.com
Medicinal plants have long been utilized in traditional medicine and ethnomedicine
worldwide. This review presents a glimpse of the current status of and future trends in …

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

J Macas, P Novák, J Pellicer, J Čížková, A Koblížková… - PloS one, 2015 - journals.plos.org
The differential accumulation and elimination of repetitive DNA are key drivers of genome
size variation in flowering plants, yet there have been few studies which have analysed how …

The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads

Q Liu, X Li, X Zhou, M Li, F Zhang, T Schwarzacher… - BMC plant biology, 2019 - Springer
Background Repetitive DNA motifs–not coding genetic information and repeated millions to
hundreds of times–make up the majority of many genomes. Here, we identify the nature …

B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)

W Huang, Y Du, X Zhao, W Jin - BMC Plant Biology, 2016 - Springer
Abstract Background The dispensable maize (Zea mays L.) B chromosome is highly
heterochromatic and widely believed to be devoid of functional genes. Although low-copy B …

Evolution and domestication footprints uncovered from the genomes of Coix

H Liu, J Shi, Z Cai, Y Huang, M Lv, H Du, Q Gao, YI Zuo… - Molecular plant, 2020 - cell.com
Coix lacryma-jobi, a plant species closely related to Zea and Sorghum, is an important food
and medicinal crop in Asia. However, no reference genome of this species has been …

Cyto-molecular characterization of rDNA and chromatin composition in the NOR-associated satellite in Chestnut (Castanea spp.)

N Islam-Faridi, GL Hodnett, T Zhebentyayeva… - Scientific reports, 2024 - nature.com
Abstract The American chestnut (Castanea dentata, 2 n= 2 x= 24), once known as the “King
of the Appalachian Forest”, was decimated by chestnut blight during the first half of the …

Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.)

Q He, Z Cai, T Hu, H Liu, C Bao, W Mao, W Jin - BMC plant biology, 2015 - Springer
Abstract Background Radish (Raphanus sativus L., 2n= 2x= 18) is a major root vegetable
crop especially in eastern Asia. Radish root contains various nutritions which play an …

The Coix genome provides insights into Panicoideae evolution and papery hull domestication

C Guo, Y Wang, A Yang, J He, C Xiao, S Lv, F Han… - Molecular plant, 2020 - cell.com
Coix is a grass crop domesticated as early as the Neolithic era. It is still widely cultivated for
both highly nutritional food and medicinal use. However, the genetic study and breeding of …