Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

Zhou, Ran; Macaya-Sanz, David; Schmutz, Jeremy; Jenkins, Jerry W.; Tuskan, Gerald A.; DiFazio, Stephen P.

doi:10.3390/genes11080843

Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

Journal Article · Fri Jul 24 00:00:00 EDT 2020 · Genes

DOI:https://doi.org/10.3390/genes11080843· OSTI ID:1648902

Zhou, Ran ^[1]; Macaya-Sanz, David ^[1]; ^[2]; Jenkins, Jerry W. ^[3]; ^[4]; ^[1]

West Virginia Univ., Morgantown, WV (United States)
HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725

OSTI ID:: 1648902

Journal Information:: Genes, Journal Name: Genes Journal Issue: 8 Vol. 11; ISSN 2073-4425

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 3 of Repeated turnovers keep sex chromosomes young in willows Wang, Deyan; Li, Yiling; Li, Mengmeng figshare https://doi.org/10.6084/m9.figshare.21200824.v1	dataset	January 2022
Additional file 1 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim Hu, Xiu-qin; Song, Han; Li, Na figshare https://doi.org/10.6084/m9.figshare.22599281.v1	dataset	January 2023
Additional file 3 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim Hu, Xiu-qin; Song, Han; Li, Na figshare https://doi.org/10.6084/m9.figshare.22599287	dataset	January 2023
Additional file 4 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim Hu, Xiu-qin; Song, Han; Li, Na figshare https://doi.org/10.6084/m9.figshare.22599290.v1	dataset	January 2023
Additional file 5 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim Hu, Xiu-qin; Song, Han; Li, Na figshare https://doi.org/10.6084/m9.figshare.22599293	dataset	January 2023
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Characterization of a large sex determination region in Salix purpurea L. (Salicaceae)

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