Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations

Izuno, Ayako; Hatakeyama, Masaomi; Nishiyama, Tomoaki; Tamaki, Ichiro; Shimizu‐Inatsugi, Rie; Sasaki, Ryuta; Shimizu, Kentaro; Isagi, Yuji

doi:10.1007/s10265-016-0822-3

Cited by 22 publications

(19 citation statements)

References 64 publications

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“…The recognition site of MseI consists of only adenine and thymine (5 0 -T|TAA-3 0 ), whereas that of NlaIII consists of all nucleotides (5'-CATG|-3 0 ). Although the GC content in the whole genome is lower than 50% for many plants [50], Myrtaceae species also tend to exhibit low GC content [51,52]. Thus, these results showed that the varying number of integrated reads obtained when different restriction enzymes were used was reasonable.…”

Section: Effect Of Fragmentationmentioning

confidence: 80%

Microsatellite Capture Sequencing

Tanaka¹,

Ohtake²,

Yoshida³

et al. 2018

Genotyping

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Microsatellites (simple sequence repeats, SSRs) that consist of repetitive sequences of one to six bases are ubiquitous in most eukaryotic genomes. The use of molecular markers for this region is efficacious in molecular-assisted breeding, molecular phylogenetics, and population genetics. Recently, the detection of a number of SSRs using a high-throughput DNA sequencing assay has become possible. Particularly, microsatellite capture sequencing using our developed protocol can detect SSRs more effectively by enriching the DNA library using an SSR probe. Our protocol used in this study demonstrates the possibility of using low-input DNA (≥1 ng), and while the use of restriction enzymes was more suitable for identifying the heterozygous genotype than sonication was, sonication facilitated the detection of various SSR flanking regions with both species-specific and common characteristics more than restriction enzyme digestion did. Moreover, a simulation analysis using various scale reads estimated that a few thousand SSRs could be detected from 50 K reads per sample. Furthermore, we described an in silico polymorphic detection and phylogenetic analysis method based on microsatellite capture sequencing data.

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Section: Effect Of Fragmentationmentioning

confidence: 80%

Microsatellite Capture Sequencing

Tanaka¹,

Ohtake²,

Yoshida³

et al. 2018

Genotyping

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“…The reads were mapped to the genome sequences of M. polymorpha (Izuno et al . ; DDBJ Accession BCNH01000001–BCNH01036376) using bowtie 2 (ver. 2.2.4; Langmead & Salzberg ) with default parameter settings.…”

Section: Methodsmentioning

confidence: 99%

“…To enhance the genomewide studies of M. polymorpha (2 n = 22), we recently reported a genome assembly (Izuno et al . ). By sequencing two paired‐end and nine mate‐pair libraries (up to 24‐kb insertion size), we obtained 304‐Mbp genome sequences.…”

Section: Introductionmentioning

confidence: 97%

“…In this study, more than 1000 polymorphic DNA markers annotated with the assembled genome sequences (Izuno et al . ) were used to (i) reveal the population genetic structure of an array of individuals growing across an environmental gradient, (ii) estimate the demographic history of the genetic clusters found in the study sites and (iii) detect outlier loci, which show non‐neutral differentiation patterns and may play key roles in adaptation to various environments.…”

Section: Introductionmentioning

confidence: 99%

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The population genomic signature of environmental association and gene flow in an ecologically divergent tree speciesMetrosideros polymorpha(Myrtaceae)

et al. 2017

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Genomewide markers enable us to study genetic differentiation within a species and the factors underlying it at a much higher resolution than before, which advances our understanding of adaptation in organisms. We investigated genomic divergence in Metrosideros polymorpha, a woody species that occupies a wide range of ecological habitats across the Hawaiian Islands and shows remarkable phenotypic variation. Using 1659 single nucleotide polymorphism (SNP) markers annotated with the genome assembly, we examined the population genetic structure and demographic history of nine populations across five elevations and two ages of substrates on Mauna Loa, the island of Hawaii. The nine populations were differentiated into two genetic clusters distributed on the lower and higher elevations and were largely admixed on the middle elevation. Demographic modelling revealed that the two genetic clusters have been maintained in the face of gene flow, and the effective population size of the high-altitude cluster was much smaller. A F -based outlier search among the 1659 SNPs revealed that 34 SNPs (2.05%) were likely to be under divergent selection and the allele frequencies of 21 of them were associated with environmental changes along elevations, such as temperature and precipitation. This study shows a genomic mosaic of M. polymorpha, in which contrasting divergence patterns were found. While most genomic polymorphisms were shared among populations, a small fraction of the genome was significantly differentiated between populations in diverse environments and could be responsible for the dramatic adaptation to a wide range of environments.

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“…The first genome assembly of M. polymorpha (version 1.0 hereon) was reported as 304 Mb sequences, half of which were composed of 19 scaffolds with >5 Mbp (Izuno et al 2016). On the assembly, RepeatMasker (Smit et al 2013) identified 4.1% of the bases to be associated with repeated sequences and transposable elements (TEs), based on the homology with Arabidopsis thaliana repeat sequences.…”

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confidence: 99%

Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence

Izuno

Wicker

Hatakeyama

et al. 2019

G3 Genes|Genomes|Genetics

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Accurate feature annotation as well as assembly contiguity are important requisites of a modern genome assembly. They allow large-scale comparison of genomes across and within species and identification of polymorphisms, leading evolutionary and functional studies. We report an updated genome resource for Metrosideros polymorpha, the most dominant tree species in the Hawaiian native forests and a unique example of rapid and remarkable ecological diversification of woody species. Ninety-one percent of the bases in the sequence assembly (304 Mb) were organized into 11 pseudo-molecules, which would represent the chromosome structure of the species assuming the synteny to a close relative Eucalyptus. Our complementary approach using manual annotation and automated pipelines identified 11.30% of the assembly to be transposable elements, in contrast to 4.1% in previous automated annotation. By increasing transcript and protein sequence data, we predicted 27,620 gene models with high concordance from the supplied evidence. We believe that this assembly, improved for contiguity, and annotation will be valuable for future evolutionary studies of M. polymorpha and closely related species, facilitating the isolation of specific genes and the investigation of genome-wide polymorphisms associated with ecological divergence.

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Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations

Cited by 22 publications

References 64 publications

Microsatellite Capture Sequencing

Microsatellite Capture Sequencing

The population genomic signature of environmental association and gene flow in an ecologically divergent tree speciesMetrosideros polymorpha(Myrtaceae)

Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence

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