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Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

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 pro...

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Autores principales: Zhou, Ran, Macaya-Sanz, David, Schmutz, Jeremy, Jenkins, Jerry W., Tuskan, Gerald A., DiFazio, Stephen P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465354/
https://www.ncbi.nlm.nih.gov/pubmed/32722098
http://dx.doi.org/10.3390/genes11080843
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author Zhou, Ran
Macaya-Sanz, David
Schmutz, Jeremy
Jenkins, Jerry W.
Tuskan, Gerald A.
DiFazio, Stephen P.
author_facet Zhou, Ran
Macaya-Sanz, David
Schmutz, Jeremy
Jenkins, Jerry W.
Tuskan, Gerald A.
DiFazio, Stephen P.
author_sort Zhou, Ran
collection PubMed
description 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.
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spelling pubmed-74653542020-09-04 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. Genes (Basel) Article 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. MDPI 2020-07-24 /pmc/articles/PMC7465354/ /pubmed/32722098 http://dx.doi.org/10.3390/genes11080843 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhou, Ran
Macaya-Sanz, David
Schmutz, Jeremy
Jenkins, Jerry W.
Tuskan, Gerald A.
DiFazio, Stephen P.
Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
title Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
title_full Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
title_fullStr Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
title_full_unstemmed Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
title_short Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
title_sort sequencing and analysis of the sex determination region of populus trichocarpa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465354/
https://www.ncbi.nlm.nih.gov/pubmed/32722098
http://dx.doi.org/10.3390/genes11080843
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