Plant genome evolution in the genusEucalyptusis driven by structural rearrangements that promote sequence divergence

Genome Research, Journal Year: 2024, Volume and Issue: unknown

Published: April 8, 2024

Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression reproduction. Despite the need to conserve genome architecture, high level structural variation has been observed species. As species separate diverge, also diverges, becoming increasingly poorly conserved as divergence time increases. However, plant genomes, processes are not well described. Here we use long-read sequencing de novo assembly 33 phylogenetically diverse, wild naturally evolving Eucalyptus species, covering 1–50 million years diverging evolution measure architectural conservation describe divergence. The investigation these genomes revealed following lineage divergence, fragmented by rearrangements. continue accumulation mutations subsequent beyond recognition rearrangements become primary driver loss syntenic regions contribute but at slower pace than We hypothesize duplications translocations potentially greatest contributors

Language: Английский

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Progress in Plant Genome Sequencing

Applied Biosciences, Journal Year: 2022, Volume and Issue: 1(2), P. 113 - 128

Published: July 4, 2022

The genome sequence of any organism is key to understanding the biology and utility that organism. Plants have diverse, complex sometimes very large nuclear genomes, mitochondrial genomes much smaller more highly conserved chloroplast genomes. Plant sequences underpin our plant serve as a platform for genetic selection improvement crop plants achieve food security. development technology can capture volumes data at low costs with high accuracy has driven acceleration sequencing advancements. More recently, long read been advance supporting accurate assembly chromosome-level This review explored progress in outcomes date. support conservation biodiversity, adaptations climate change improvements sustainability agriculture, which nutritional

Language: Английский

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Integrative Pre-Breeding for Biotic Resistance in Forest Trees

Plants, Journal Year: 2021, Volume and Issue: 10(10), P. 2022 - 2022

Published: Sept. 26, 2021

Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations’ persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of resistance in tree species. Specifically, we first discuss how assessing genomic architecture stress enables us recognize a more polygenic nature trait typically regarded Mendelian, an expectation Fisherian runaway pathogen–host concerted arms-race model. Secondly, outline innovative pipelines capture harness natural pre-adaptations stresses by merging tools ecology, phylo-geography, omnigenetics fields within predictive platform. Promoting integrative studies promises better understanding co-evolutionary interactions, as well efficient utilization resistant phenotypes.

Language: Английский

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Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(6), P. 1271 - 1287

Published: July 10, 2022

Abstract Synteny, the ordering of sequences within homologous chromosomes, must be maintained genomes sexually reproducing species for sharing alleles and production viable, offspring. However, when closely related are compared, a loss synteny is often observed. Unequal recombination primary mechanism behind loss, occurring more in transposon rich regions, resulting formation chromosomal rearrangements. To examine patterns among three related, interbreeding, wild Eucalyptus species, we assembled their using long‐read DNA sequencing de novo assembly. We identify syntenic rearranged regions between these estimate that ~48% our remain while ~36% rearranged. observed rearrangements highly fragment microsynteny. Our results suggest primarily lost through small‐scale rearrangements, not sequence gain, or divergence. Further examination identified suggests may altering phenotypes species. study also underscores use single reference genomic variation studies could lead to bias, especially given scale at which show potentially adaptive loci have diverged, deleted, duplicated and/or This provides an unbiased framework look potential speciation rapidly radiating foundation woodland trees free from selective breeding seen most crop

Language: Английский

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A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

GigaScience, Journal Year: 2022, Volume and Issue: 12

Published: Dec. 28, 2022

Abstract Background Melaleuca quinquenervia (broad-leaved paperbark) is a coastal wetland tree species that serves as foundation in eastern Australia, Indonesia, Papua New Guinea, and Caledonia. While extensively cultivated for its ornamental value, it has also become invasive regions like Florida, USA. Long-lived trees face diverse pest pathogen pressures, plant stress responses rely on immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family. However, comprehensive annotation of NLR encoding genes been challenging due to their clustering arrangement chromosomes highly repetitive domain structure; expansion family driven largely tandem duplication. Additionally, allelic diversity remains unexplored outcrossing species, many genomes are presented haploid, collapsed state. Results We assembled chromosome-level pseudo-phased genome M. described NLRs using novel FindPlantNLRs pipeline. Analysis reveals variation number each haplotype, distinct patterns, differences types numbers integrated domains. Conclusions The high-quality assembly establishes new framework functional evolutionary studies this significant species. Our findings suggest maintaining within crucial enabling environmental stress, particularly long-lived plants.

Language: Английский

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E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 28, 2023

Abstract Background Eucalyptus urophylla × grandis , an economically important forest tree, provides raw material for energy and reduces damage to native forests. However, the absence of a high-quality E. reference genome has significantly hindered its evolution genetic analysis. Results We successfully presented (545.75 Mb; scaffold N50, 51.62 Mb) using combination Illumina, PacBio HiFi, Hi-C sequencing platforms. A total 34,502 genes 58.56% repetitive sequences in this were annotated. Using analyses, we identified recent whole-genome duplication (WGD) event . further found that gene families associated with starch sucrose metabolism, flavonoid biosynthesis, plant–pathogen interaction expanded Moreover, comparative genomic evolutionary analyses showed large structural variations among different chromosomes 34 accessions, which divided into six clades. Conclusions Overall, our findings provide valuable resource expanding understanding evolution, improvement, biology.

Language: Английский

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Redefining Eucalyptus cultivation in South America: adaptive strategies under future climate scenarios

New Forests, Journal Year: 2025, Volume and Issue: 56(4)

Published: May 23, 2025

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The terpene synthase genes of Melaleuca alternifolia (tea tree) and comparative gene family analysis among Myrtaceae essential oil crops

Plant Systematics and Evolution, Journal Year: 2023, Volume and Issue: 309(3)

Published: April 6, 2023

Abstract Terpene synthases (TPS) are responsible for the terminal biosynthetic step of terpenoid production. They encoded by a highly diverse gene family believed to evolve tandem duplication in response adaptive pressures. Taxa Myrtaceae renowned their diversity terpenoid-rich essential oils, and among them, tribe Eucalypteae has largest TPS found any plant (> 100 ). In this study, comparative analysis Melaleuca alternifolia (tea tree), from related Melaleuceae, revealed some have smaller families, as total 58 putatively functional full-length genes, 21 pseudogenes were identified manual annotation newly released long-read assembly genome. The TPS-a TPS-b2 subfamilies that synthesise secondary compounds often mediating plant-environment interactions more diminutive than those eucalypts, probably reflecting key differences evolutionary histories two lineages. Of TPS-b1 , 13 clustered into region around 400 kb on one scaffold. organisation these suggested was instrumental evolution terpene chemistry . Four likely catalyse synthesis three monoterpenoid components used classify tea tree chemotypes within single small 87 larger cluster raising possibility coregulation linkage may lead behaviour locus, providing an explanation categorical inheritance complex multiple-component taxon.

Language: Английский

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A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species

Gigabyte, Journal Year: 2021, Volume and Issue: 2021, P. 1 - 15

Published: Aug. 9, 2021

The economically important Melaleuca alternifolia (tea tree) is the source of a terpene-rich essential oil with therapeutic and cosmetic uses around world. Tea tree has been cultivated bred in Australia since 1990s. It extensively studied for genetics biochemistry terpene biosynthesis. Here, we report high quality de novo genome assembly using Pacific Biosciences Illumina sequencing. was assembled into 3128 scaffolds total length 362 Mb (N50 = 1.9 Mb), significantly higher contiguity than previous 8.7 Kb). Using homology-based, RNA-seq evidence-based ab initio prediction approach, 37,226 protein-coding genes were predicted. Genome annotation exhibited completeness scores 98.1% 89.4%, respectively. Sequence sufficient to reveal extensive gene order conservation chromosomal rearrangements alignments Eucalyptus grandis Corymbia citriodora genomes. This new advances currently available resources investigate structure family evolution M. alternifolia. will enable further comparative genomic studies Myrtaceae elucidate genetic foundations valuable traits this crop.

Language: Английский

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Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization

Horticulture Research, Journal Year: 2023, Volume and Issue: 10(11)

Published: Oct. 13, 2023

Water caltrop (

Language: Английский

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