Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

doi:10.1111/1755-0998.13347

. 2021 Jul;21(5):1593-1607.

doi: 10.1111/1755-0998.13347. Epub 2021 Mar 8.

Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

Dongna Ma¹, Zejun Guo¹, Qiansu Ding¹, Zhizhu Zhao¹, Zhijun Shen¹, Mingyue Wei¹, Changhao Gao¹, Ludan Zhang¹, Huan Li¹, Shan Zhang¹, Jing Li¹, Xueyi Zhu¹, Hai-Lei Zheng¹

Affiliations

PMID: 33550674
DOI: 10.1111/1755-0998.13347

Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

Dongna Ma et al. Mol Ecol Resour. 2021 Jul.

. 2021 Jul;21(5):1593-1607.

doi: 10.1111/1755-0998.13347. Epub 2021 Mar 8.

Authors

Dongna Ma¹, Zejun Guo¹, Qiansu Ding¹, Zhizhu Zhao¹, Zhijun Shen¹, Mingyue Wei¹, Changhao Gao¹, Ludan Zhang¹, Huan Li¹, Shan Zhang¹, Jing Li¹, Xueyi Zhu¹, Hai-Lei Zheng¹

Affiliation

¹ Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.

PMID: 33550674
DOI: 10.1111/1755-0998.13347

Abstract

Aegiceras corniculatum is a major mangrove plant species adapted to waterlogging and saline conditions, grows in the coastal intertidal zone of tropical and subtropical regions. Here, we present a chromosome-level genome assembly of A. corniculatum by incorporating PacBio long-read sequencing and Hi-C technology. The results showed that the PacBio draft genome size is 906.63 Mb. Hi-C scaffolding anchored 885.06 Mb contigs (97.62% of draft assembly) onto 24 pseudochromosomes. The contig N50 and scaffold N50 were 7.1 Mb and 37.74 Mb, respectively. Out of 40,727 protein-coding genes predicted in the study, 89% have functional annotations in public databases. We also showed that of the 603.93 Mb repetitive sequences predicted in the assembled genome, long terminal repeat retrotransposons constitute 41.52%. The genome evolution analysis showed that the A. corniculatum genome experienced two whole-genome duplication events and shared the ancient γ whole-genome triplication event. A comparative genomic analysis revealed an incidence of expansion in 1,488 gene families associated with essential metabolism and biosynthetic pathways, including photosynthesis, oxidative phosphorylation, phenylalanine, glyoxylate, dicarboxylate metabolism, and DNA replication, which probably constitute adaptation traits that allow the A. corniculatum to survive in the intertidal zone. Also, the systematic characterization of genes associated with flavonoid biosynthesis pathway and the AcNHX gene family conducted in this study will provide insight into the adaptation mechanism of A. corniculatum to intertidal environments. The high-quality genome reported here can provide historical insights into genomic transformations that support the survival of A. corniculatum under harsh intertidal habitats.

Keywords: Aegiceras corniculatum; adaptive evolution; mangrove; whole-genome duplication; whole-genome sequencing.

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References

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[1] Abrusan, G., Grundmann, N., DeMester, L., & Makalowski, W. (2009). TEclass - A tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics, 25(10), 1329-1330. https://doi.org/10.1093/bioinformatics/btp084

[2] Abrusan, G., Grundmann, N., DeMester, L., & Makalowski, W. (2009). TEclass - A tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics, 25(10), 1329-1330. https://doi.org/10.1093/bioinformatics/btp084

[3] Albalat, R., & Cañestro, C. (2016). Evolution by gene loss. Nature Reviews Genetics, 17(7), 379-391. https://doi.org/10.1038/nrg.2016.39

[4] Albalat, R., & Cañestro, C. (2016). Evolution by gene loss. Nature Reviews Genetics, 17(7), 379-391. https://doi.org/10.1038/nrg.2016.39

[5] Alongi, D. M. (2002). Present state and future of the world's mangrove forests. Environmental Conservation, 29(3), 331-349. https://doi.org/10.1017/s0376892902000231

[6] Alongi, D. M. (2002). Present state and future of the world's mangrove forests. Environmental Conservation, 29(3), 331-349. https://doi.org/10.1017/s0376892902000231

[7] Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. https://doi.org/10.1038/75556

[8] Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. https://doi.org/10.1038/75556

[9] Bairoch, A., & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research, 28(1), 45-48. https://doi.org/10.1093/nar/21.13.3093

[10] Bairoch, A., & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research, 28(1), 45-48. https://doi.org/10.1093/nar/21.13.3093

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Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

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Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

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