Assembly of the Salt-secreting Mangrove Avicennia Rumphiana

Overview

Journal PLoS One

Date 2025 Feb 5

PMID 39908310

Authors

Jeremy R Shearman

Chaiwat Naktang

Chutima Sonthirod

Wasitthee Kongkachana

Sonicha U-Thoomporn

Nukoon Jomchai

Chatree Maknual

Suchart Yamprasai

Poonsri Wanthongchai

Wirulda Pootakham

Sithichoke Tangphatsornruang

Affiliations

Soon will be listed here.

Abstract

Avicennia rumphiana, also known as Avicennia marina var. rumphiana or Avicennia lanata, is a mangrove species that has high salt tolerance and is one of the few species that secretes salt through the leaves, similar to Avicennia marina. We sequenced and assembled the A. rumphiana genome into 24,094 Supernova-scaffolds totalling 499.6 Mb. Sequence comparison showed that 68.7% of the A. rumphiana genome aligned to A. marina sequence, covering 72% of the A. marina genome at an average nucleotide identity of 87.7%, showing that A. marina is closely related to A. rumphiana and, thus, suitable for reference based scaffolding of the A. rumphiana Supernova-scaffolds. Reference based scaffolding produced 32 chromosome-level scaffolds containing 447.3 Mb, with 52.3 Mb of sequence unplaced. Annotation of this genome assembly resulted in 37,347 genes with 22,414 of those contained within chromosome scaffolds. A total of 671 genes matched to genes that are linked to salt tolerance. Genome comparison shows that A. rumphiana is quite different to A. marina and should, therefore, not be referred to as a variant of A. marina.

References

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Weisenfeld N, Kumar V, Shah P, Church D, Jaffe D . Direct determination of diploid genome sequences. Genome Res. 2017; 27(5):757-767. PMC: 5411770. DOI: 10.1101/gr.214874.116. View

Gotz S, Garcia-Gomez J, Terol J, Williams T, Nagaraj S, Nueda M . High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008; 36(10):3420-35. PMC: 2425479. DOI: 10.1093/nar/gkn176. View

Yang Z . PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007; 24(8):1586-91. DOI: 10.1093/molbev/msm088. View

Natarajan P, Murugesan A, Govindan G, Gopalakrishnan A, Kumar R, Duraisamy P . A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina. Commun Biol. 2021; 4(1):851. PMC: 8266904. DOI: 10.1038/s42003-021-02384-8. View

Gordon S, Contreras-Moreira B, Woods D, Des Marais D, Burgess D, Shu S . Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat Commun. 2017; 8(1):2184. PMC: 5736591. DOI: 10.1038/s41467-017-02292-8. View

Ma D, Ding Q, Guo Z, Xu C, Liang P, Zhao Z . The genome of a mangrove plant, Avicennia marina, provides insights into adaptation to coastal intertidal habitats. Planta. 2022; 256(1):6. DOI: 10.1007/s00425-022-03916-0. View

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck F . RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019; 20(1):224. PMC: 6816165. DOI: 10.1186/s13059-019-1829-6. View

10.

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

11.

Marks P, Garcia S, Martinez Barrio A, Belhocine K, Bernate J, Bharadwaj R . Resolving the full spectrum of human genome variation using Linked-Reads. Genome Res. 2019; 29(4):635-645. PMC: 6442396. DOI: 10.1101/gr.234443.118. View

12.

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

13.

Serrote C, Reiniger L, Silva K, Rabaiolli S, Stefanel C . Determining the Polymorphism Information Content of a molecular marker. Gene. 2019; 726:144175. DOI: 10.1016/j.gene.2019.144175. View

14.

Lei L, Goltsman E, Goodstein D, Wu G, Rokhsar D, Vogel J . Plant Pan-Genomics Comes of Age. Annu Rev Plant Biol. 2021; 72:411-435. DOI: 10.1146/annurev-arplant-080720-105454. View

15.

Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, Antonescu C . Versatile and open software for comparing large genomes. Genome Biol. 2004; 5(2):R12. PMC: 395750. DOI: 10.1186/gb-2004-5-2-r12. View

16.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

17.

Shearman J, Naktang C, Sonthirod C, Kongkachana W, U-Thoomporn S, Jomchai N . Assembly of a hybrid mangrove, Bruguiera hainesii, and its two ancestral contributors, Bruguiera cylindrica and Bruguiera gymnorhiza. Genomics. 2022; 114(3):110382. DOI: 10.1016/j.ygeno.2022.110382. View

18.

Rhie A, Walenz B, Koren S, Phillippy A . Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020; 21(1):245. PMC: 7488777. DOI: 10.1186/s13059-020-02134-9. View

19.

Huang X, Adams M, Zhou H, Kerlavage A . A tool for analyzing and annotating genomic sequences. Genomics. 1997; 46(1):37-45. DOI: 10.1006/geno.1997.4984. View

20.

Shearman J, Naktang C, Sonthirod C, Kongkachana W, U-Thoomporn S, Jomchai N . De novo assembly and analysis of Sonneratia ovata genome and population analysis. Genomics. 2024; 116(3):110837. DOI: 10.1016/j.ygeno.2024.110837. View