Chromosome-Scale Genome Assembly of the Resurrection Plant <i>Acanthochlamys bracteata</i> (Velloziaceae)

Zhang-hai, LI; Lin, Dong-Liang; Jin, Xiao‐Hua

doi:10.1093/gbe/evab147

Cited by 6 publications

(5 citation statements)

References 42 publications

(46 reference statements)

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“…The preliminary genome was further assembled using a Hi‐C (in vitro fixation of chromosomes) library. The final assembly contained 20 pseudomolecules (Figure 2a,b), which is consistent with the results of a recently published genome assembly (Gao et al, 2021). The final reference assembly was 191.61 Mb in length and included 50 scaffolds (scaffold N50 = 8.62 Mb) and 20 pseudochromosomes.…”

Section: Resultssupporting

confidence: 88%

“…The preliminary genome was further assembled using a Hi-C (in vitro fixation of chromosomes) library. The final assembly contained 20 pseudomolecules (Figure 2a,b), which is consistent with the results of a recently published genome assembly (Gao et al, 2021)…”

Section: Genome Sequencing and Assemblysupporting

confidence: 88%

“…The 20 pseudochromosomes covered 187,720,221 bases or 97.97% of the 191.61‐Mb A . bracteata assembly, which is higher than that of Gao et al (2021) (183.84/197.97 Mb: 92.82%).…”

Section: Resultscontrasting

confidence: 62%

“…To assess the Hi-C assembly quality, we determined the completeness of our primary assembly of A. bracteata and the Hi-C assembly (Table 1). Whilst this work was under revision, a genome assembly of A. bracteata was published by Gao et al (2021) and we have also included comparisons with this assembly, which has a slightly lower completeness score (92.8%). A linear comparison of the chromosomes in our assembly and that of Gao et al (2021) showed good colinearity (Figure S4).…”

Section: Evaluation Of Assembly Qualitymentioning

confidence: 99%

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Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

Liao

Deng

et al. 2021

Molecular Ecology Resources

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The Hengduan Mountains region is an important hotspot of alpine plant diversity and endemism. Acanthochlamys bracteata is a species of a threatened monotypic genus endemic to the Hengduan Mountains. In this study, we present a high‐quality, chromosome‐level reference genome for A. bracteata, constructed using long reads, short reads and Hi‐C technology. We characterized its genetic diversity, population structure, demographic history and gene flow by resequencing individuals collected across its distribution. Comparative genomics analyses based on sequence information from single‐copy orthologous genes revealed that A. bracteata and Dioscorea rotundata diverged ~104.5 million years ago. Whole‐genome resequencing based on population genetic analysis revealed that the division of the 14 populations into 10 distinct clusters reflected geographical divergence, and three separate high levels of gene flow occurred sequentially between isolated populations of the Hengduan Mountains, a finding which is consistent with the turnover between ice ages and interglacial periods. Our findings indicate that Quaternary climatic changes played an important role in shaping the genetic structure and demographic trajectories of A. bracteata, and provide critical insights into the genetic status and evolutionary history of this poorly understood species, and possibly other alpine plants with a similar distribution. This study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes and identifying conservation units for the conservation and management of threatened species. Our high‐quality genome represents a valuable resource for future studies of the underlying molecular mechanisms of adaptive evolution and provides insight for further comparative genomic analysis with other Velloziaceae species.

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Section: Resultssupporting

confidence: 88%

Section: Genome Sequencing and Assemblysupporting

confidence: 88%

“…The 20 pseudochromosomes covered 187,720,221 bases or 97.97% of the 191.61‐Mb A . bracteata assembly, which is higher than that of Gao et al (2021) (183.84/197.97 Mb: 92.82%).…”

Section: Resultscontrasting

confidence: 62%

Section: Evaluation Of Assembly Qualitymentioning

confidence: 99%

See 2 more Smart Citations

Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

Liao

Deng

et al. 2021

Molecular Ecology Resources

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“…Genes encoding LEA proteins and ELIPs, acting further downstream the stress network, were among the most responsive in this experiment, and they were upregulated in all cases. Both families are typically associated with desiccation [ 63 , 64 ], but here it is shown that some representatives are induced by low temperatures as well. The transcripts of some of the ELIPs, as well as LEA D-29, accumulate in all stress conditions, while the LEAs D-34 and SLE2 remain unchanged only during freezing and chilling + freezing.…”

Section: Resultsmentioning

confidence: 97%

The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments

Gupta,

Petrov,

Garg

et al. 2024

Cell. Mol. Life Sci.

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Haberlea rhodopensis, a resurrection species, is the only plant known to be able to survive multiple extreme environments, including desiccation, freezing temperatures, and long-term darkness. However, the molecular mechanisms underlying tolerance to these stresses are poorly studied. Here, we present a high-quality genome of Haberlea and found that ~ 23.55% of the 44,306 genes are orphan. Comparative genomics analysis identified 89 significantly expanded gene families, of which 25 were specific to Haberlea. Moreover, we demonstrated that Haberlea preserves its resurrection potential even in prolonged complete darkness. Transcriptome profiling of plants subjected to desiccation, darkness, and low temperatures revealed both common and specific footprints of these stresses, and their combinations. For example, PROTEIN PHOSPHATASE 2C (PP2C) genes were substantially induced in all stress combinations, while PHYTOCHROME INTERACTING FACTOR 1 (PIF1) and GROWTH RESPONSE FACTOR 4 (GRF4) were induced only in darkness. Additionally, 733 genes with unknown functions and three genes encoding transcription factors specific to Haberlea were specifically induced/repressed upon combination of stresses, rendering them attractive targets for future functional studies. The study provides a comprehensive understanding of the genomic architecture and reports details of the mechanisms of multi-stress tolerance of this resurrection species that will aid in developing strategies that allow crops to survive extreme and multiple abiotic stresses.

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Integrating Genomic and Cytogenetic Data to Study the Evolutionary History of Arapaimas and Arowanas in the Neotropics

Perez,

Toma,

Souza

et al. 2023

Conservation Genetics in the Neotropics

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Chromosome-Scale Genome Assembly of the Resurrection Plant Acanthochlamys bracteata (Velloziaceae)

Cited by 6 publications

References 42 publications

Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments

Integrating Genomic and Cytogenetic Data to Study the Evolutionary History of Arapaimas and Arowanas in the Neotropics

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