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Novel B-chromosome-specific transcriptionally active sequences are present throughout the maize B chromosome

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Abstract

Supernumerary B chromosomes are dispensable parts of the nuclear genome and occur in all eukaryotic groups. They differ from the normal A chromosomes in morphology, genetic behavior, and inheritance. Because they are nonessential for individual development, B chromosomes are considered to be genetically inert and to lack functional genes. However, the maize B chromosome carries control elements that direct its behavior and affects A chromosomes during cell division. Therefore, the maize B chromosome might contain genic regions that differ from the genic regions of A chromosomes. Yet, only a few B-specific transcript sequences have been isolated. To identify more B-specific transcriptionally active sequences, we constructed de novo transcriptome assemblies for maize B73 inbred lines with 0B (+0B) and 2B (+2B). Comparative analysis of the B73 + 0B and B73 + 2B assemblies revealed that unigenes annotated to 201 gene ontology terms were differentially expressed. Using RT-PCR analysis of novel transcript sequences specific to B73 + 2B, we identified 32 novel B-related transcript sequences, and most sequences showed consistent B-specific transcription in different inbred lines. Moreover, 20 of those novel B-related transcript sequences were further confirmed to be located only on the B chromosome by genomic PCR analysis. A total of 19 novel B-specific transcript sequences were mapped to various positions along the B chromosome using B-10L translocations. Taken together, our results suggest that the maize B chromosome indeed affects the expression of A-located genes and that a substantial amount of novel B-specific transcriptionally active sequences are present throughout the maize B chromosome. Therefore, the maize B chromosome seems not to be genetically inert.

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Data availability

We deposited the B73 + 0B and B73 + 2B RNA-Seq libraries in the Sequence Read Archive (SRA) database under accession PRJNA482010.

Abbreviations

cDNA-AFLP:

Complementary DNA-amplified fragment length polymorphism

CK:

Centromeric knob

DE:

Distal euchromatin

DH:

Distal heterochromatin

DPE:

Distal portion of proximal euchromatin

FISH:

Fluorescence in situ hybridization

FPKM:

Fragments per kilobase of transcript per million mapped reads

GO:

Gene ontology

InDel:

Insertion/deletion

NCBI:

National Center for Biotechnology Information

PAGE:

Parametric analysis of gene set enrichment

PE:

Proximal euchromatin

PPE:

Proximal portion of proximal euchromatin

RAPD:

Random amplified polymorphic DNA

RNA-Seq:

RNA-sequencing

RT-PCR:

Reverse transcriptase-polymerase chain reaction

SNP:

Single nucleotide polymorphism

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Acknowledgements

We are thankful to the reviewers for the very helpful suggestions and corrections for improving the paper.

Funding

This study was funded by the Ministry of Science and Technology of Taiwan (Grant numbers: MOST 104-2311-B-005-012-MY3 and MOST 107-2311-B-005-003).

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Author notes

  1. Zi-Jie Hong and Jun-Xiang Xiao contributed equally to this work.

Authors and Affiliations

  1. Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan

    Zi-Jie Hong, Jun-Xiang Xiao & Ya-Ming Cheng

  2. Department of Medical Research, China Medical University Hospital, Taichung, Taiwan

    Shu-Fen Peng

  3. Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan

    Yao-Pin Lin

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  1. Zi-Jie Hong
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  2. Jun-Xiang Xiao
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Correspondence to Ya-Ming Cheng.

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Hong, ZJ., Xiao, JX., Peng, SF. et al. Novel B-chromosome-specific transcriptionally active sequences are present throughout the maize B chromosome. Mol Genet Genomics 295, 313–325 (2020). https://doi.org/10.1007/s00438-019-01623-2

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