Telomere-to-telomere genome of the model plant<i>Physcomitrium patens</i>

Bi, Guoan; Zhao, Shijun; Yao, Jianhua; Wang, Huan; Zhao, Mengkai; Sun, Yuhan; Hou, Xueren; Jiao, Yuling; Ma, Yingxin; Yan, Jianbin; Dai, Junbiao

doi:10.1101/2023.05.19.541548

Cited by 4 publications

(1 citation statement)

References 113 publications

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“…Inodorus (Wei et al, 2023)), Mangifera indica 'Irwin' (Henry et al preprint), Musa acuminata Wild type and Cavendish , Oryza sativa ZS97RS3 and MH63RS3 , Mycrica rubra (Supplemental Table S1). However, assembled telomere sequence is often used as a means to an end in confirming a complete assembly; their details are often relegated to supplemental materials or in many cases not clearly reported at all (Belser et al, 2021;Bao et al, 2023;Sun et al, 2023;Wang et al, 2023;Bi et al, 2024;Z. Wang et al, 2024).…”

Section: Discussionmentioning

confidence: 99%

Telomere Length in Plants Estimated with Long Read Sequencing

Colt,

Petrus,

Abramson

et al. 2024

Preprint

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Telomeres play an important role in chromosome stability and their length is thought to be related to an organism's lifestyle and lifespan. Telomere length is variable across plant species and between cultivars of the same species, possibly conferring adaptive advantage. However, it is not known whether telomere length is related to lifestyle or life span across a diverse array of plant species due to the lack of information on telomere length in plants. Here we leverage genomes assembled with long read sequencing data to estimate telomere length by chromosome. We find that long read assemblies based on Oxford Nanopore Technologies (ONT) accurately predict telomere length in the two model plant species Arabidopsis thaliana and Oryza sativa matching lab-based length estimates. We then estimate telomere length across an array of plant species with different lifestyles and lifespans and find that in general gymnosperms have shorter telomeres compared to eudicots and monocots. Crop species frequently have longer telomeres than their wild relatives, and species that have been maintained clonally such as hemp have long telomeres possibly reflecting that this lifestyle requires long term chromosomal stability.

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Section: Discussionmentioning

confidence: 99%

Telomere Length in Plants Estimated with Long Read Sequencing

Colt,

Petrus,

Abramson

et al. 2024

Preprint

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Molecular breakthroughs in modern plant breeding techniques

Abdul Aziz,

Masmoudi

2024

Horticultural Plant Journal

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The ancestral chromatin landscape of land plants

Hisanaga

Axelsson

et al. 2022

Preprint

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SummaryIn mammals and flowering plants chromatin is modified by DNA methylation (5mC) and methylation of lysine residues of the N-terminal tail of histone H3 that reflect transcriptional activity in three chromosomal domains: euchromatin comprising transcribed genes, facultative heterochromatin comprising repressed genes, and constitutive heterochromatin comprising transposons. Yet recent studies have shown that the correlation between chromatin modifications and transcriptional regulation of transposons and genes vary among different lineages of eukaryotes including the bryophytes that diverged from vascular plants 510-480 mya. The monophyletic bryophytes comprise mosses, liverworts and hornworts. The chromatin landscapes of mosses and liverworts are different, leaving open the question regarding the identity of the chromatin landscape of all bryophytes.Here we assembled the chromatin landscape of the model hornwortAnthoceros agrestis. By comparing chromatin landscapes between mosses, liverworts and hornworts we define the common chromatin landscape of the ancestor of extant bryophytes. The constitutive heterochromatin of bryophytes is characterized by the absence of gene body DNA methylation, low levels of non-CG DNA methylation and the absence of segregation of transposons in a few well defined chromosomal compartments. In addition, whereas histone modifications of euchromatin and facultative heterochromatin are primarily associated with genes in angiosperms and mosses, nearly half of the hornwort transposons are associated with facultative heterochromatin and euchromatin. Hence the ancestral genome of bryophytes was likely a patchwork of interspersed small units of euchromatin, facultative and constitutive heterochromatin. Each unit contained a few transposons and genes that share the same chromatin state. We propose that in bryophytes, this specific type of genome organization prevented the recruitment of transposons to form constitutive heterochromatin around point centromeres observed in the genomes of angiosperms.

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Telomere-to-telomere genome of the model plantPhyscomitrium patens

Cited by 4 publications

References 113 publications

Telomere Length in Plants Estimated with Long Read Sequencing

Telomere Length in Plants Estimated with Long Read Sequencing

Molecular breakthroughs in modern plant breeding techniques

The ancestral chromatin landscape of land plants

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