The multiple fates of gene duplications: deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation

JA Birchler, H Yang - The Plant Cell, 2022 - academic.oup.com
Gene duplications have long been recognized as a contributor to the evolution of genes with
new functions. Multiple copies of genes can result from tandem duplication, from …

One hundred years of gene balance: how stoichiometric issues affect gene expression, genome evolution, and quantitative traits

JA Birchler, RA Veitia - Cytogenetic and Genome Research, 2022 - karger.com
A century ago experiments with the flowering plant Datura stramonium and the fruit fly
Drosophila melanogaster revealed that adding an extra chromosome to a karyotype was …

The supernumerary B chromosome of maize: drive and genomic conflict

JA Birchler, H Yang - Open Biology, 2021 - royalsocietypublishing.org
The supernumerary B chromosome of maize is dispensable, containing no vital genes, and
thus is variable in number and presence in lines of maize. In order to be maintained in …

A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning‐expressed …

K Laosuntisuk, A Vennapusa, IM Somayanda… - The Plant …, 2024 - Wiley Online Library
SUMMARY RNA‐Sequencing is widely used to investigate changes in gene expression at
the transcription level in plants. Most plant RNA‐Seq analysis pipelines base the …

Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize

H Yang, X Shi, C Chen, J Hou, T Ji, J Cheng… - The Plant …, 2021 - academic.oup.com
The phenotypic consequences of the addition or subtraction of part of a chromosome is
more severe than changing the dosage of the whole genome. By crossing diploid trisomies …

MicroRNAs play regulatory roles in genomic balance

X Shi, H Yang, JA Birchler - BioEssays, 2023 - Wiley Online Library
Classic genetics studies found that genomic imbalance caused by changing the dosage of
part of the genome (aneuploidy) has more detrimental effects than altering the dosage of the …

Effect of aneuploidy of a non‐essential chromosome on gene expression in maize

X Shi, H Yang, C Chen, J Hou, T Ji, J Cheng… - The Plant …, 2022 - Wiley Online Library
The non‐essential supernumerary maize (Zea mays) B chromosome (B) has recently been
shown to contain active genes and to be capable of impacting gene expression of the A …

[HTML][HTML] Consequences of chromosome loss: why do cells need each chromosome twice?

NK Chunduri, K Barthel, Z Storchova - Cells, 2022 - mdpi.com
Aneuploidy is a cellular state with an unbalanced chromosome number that deviates from
the usual euploid status. During evolution, elaborate cellular mechanisms have evolved to …

Gene-dosage issues: a recurrent theme in whole genome duplication events

RA Veitia, JA Birchler - Trends in Genetics, 2022 - cell.com
Two recent studies have addressed the long-term consequences of whole genome
duplications (WGD). Specifically, they analyzed transcriptomes of the plant Arabidopsis …

[HTML][HTML] Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy

S Zhang, R Wang, X Zhu, L Zhang, X Liu, L Sun - Iscience, 2023 - cell.com
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to
organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions …