A high-quality genome assembly and annotation of the gray mangrove,<i>Avicennia marina</i>

Friis, Guillermo; Vizueta, Joel; Nelson, David R.; Khraiwesh, Basel; Qudeimat, Enas; Salehi‐Ashtiani, Kourosh; Ortega, Alejandra; Marshell, Alyssa; Duarte, Carlos M.; Burt, John A.

doi:10.1101/2020.05.30.124800

Cited by 7 publications

(10 citation statements)

References 51 publications

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“…Large subunit of ribosomal proteins rpl2, 14,16,20,22,23,32,33,36 Small subunit of ribosomal proteins rps2, 3, 4, 7, 8, 11, 12, 14,15 , 16, 18, 19 DNA (37) were found in the C. nutans and the lowest number of forward repeats (16) were found in the A. paniculate and S. cusia. Similarly, the highest tandem repeats (62) and the lowest number of tandem repeats (14) were found in the A. knappiae, E. lofouensis and E. longzhouensis.…”

Section: Self-replicationmentioning

confidence: 99%

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Asaf

Khan

Numan

et al. 2021

Sci Rep

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Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

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Section: Self-replicationmentioning

confidence: 99%

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Asaf

Khan

Numan

et al. 2021

Sci Rep

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“…The first mangrove genome sequence ( Rhizophora apiculata ) was published in 2017 (Xu et al, 2017). More recently, a number of genome assemblies from several mangrove species have been reported, including Rhizophora mucronata , Rhizophora stylosa , Rhizophora mangle (He et al, 2020), Kandelia obovata (Hu et al, 2020) and Bruguiera gymnorrhiza (Miryeganeh et al, 2021) from the Rhizophoraceae family, Avicenna marina (Friis et al, 2021; Natarajan et al, 2021) from the Acanthaceae family, Sonneratia alba and Sonneratia caseolaris (He et al, 2020) from the Lythraceae family and Aegiceras corniculatum (Feng et al, 2021; Ma et al, 2021) from the Primulaceae family. Transcriptome sequencing has also been reported in various mangrove species (Yamanaka et al, 2009; Yang, Yang, Li, Deng, et al, 2015; Yang, Yang, Li, Li, et al, 2015; Krishnamurthy et al, 2017; Xu et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

A chromosome‐scale reference genome assembly of yellow mangrove (Bruguiera parviflora) reveals a whole genome duplication event associated with the Rhizophoraceae lineage

Pootakham

Sonthirod

Naktang

et al. 2022

Molecular Ecology Resources

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Mangrove forest ecosystems support a diverse flora and fauna of marine and terrestrial species and have important direct and indirect economic, ecological and social values to mankind. Yellow mangrove (Bruguiera parviflora) belongs to the Rhizophoraceae family and is widely distributed in the intertidal zones along sheltered coastal areas in tropical latitudes. Here, we present a high‐quality, chromosome‐level assembly of the B. parviflora genome. We employed the 10x Genomics linked‐read technology to obtain a preliminary assembly, which was subsequently scaffolded using the long‐range chromatin contact mapping technique (HiC) to obtain a final assembly containing 213,026,782 bases in 10,045 scaffolds with an N50 length of 10,906,948 bases. Our gene prediction recovered 96.5% of the highly conserved orthologues in the Embryophyta lineage based on the Benchmarking Universal Single‐Copy Orthologues (BUSCO) analysis. We analysed the transversion rate at fourfold‐degenerate sites from orthologous gene pairs and discovered evidence supporting a recent whole‐genome duplication event in B. parviflora and other Rhizophoreae members. Comparative studies based on single‐copy orthologous genes indicated that B. parviflora and Bruguiera gymnorrhiza diverged approximately 24.1 million years ago. The population structure analysis revealed that 63 B. parviflora accessions from different geographical regions in Thailand were an admixture of two subpopulations. The examination of alternative splicing events in B. parviflora showed that the most prevalent splicing mechanism was intron retention. This high‐quality genome assembly together with the genetic diversity information obtained from the germplasm provide useful genomic resources for future studies on comparative phylogenetics and evolution of adaptive traits in mangrove species.

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“…Trimming and quality filtering treatment was conducted using Trim Galore version 0.6.6 (Krueger, 2015) with parameters --stringency 1 --clip_R1 12 --clip_R2 12 --length 90, resulting in a set of reads ranging between 90 and 138 bp long. Reads were then mapped against the previously published reference genome for A. marina (Friis et al, 2020) SNPs (Table 1 and Table S2) with a per-individual average coverage of 16.8 and a missing data rate of 0.11. The program KING version 2.2.7 (Manichaikul et al, 2010) was used to confirm the absence of close relatives in our set of sampled individuals.…”

Section: Genome Resequencing and Variant Callingmentioning

confidence: 99%

Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula

Friis,

Smith,

Lovelock

et al. 2024

Molecular Ecology

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Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic‐environment association analyses revealed high levels of adaptive divergence and detected signs of multi‐loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.

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A high-quality genome assembly and annotation of the gray mangrove,Avicennia marina

Cited by 7 publications

References 51 publications

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

A chromosome‐scale reference genome assembly of yellow mangrove (Bruguiera parviflora) reveals a whole genome duplication event associated with the Rhizophoraceae lineage

Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula

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