Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range
While most of the species in Goodeniaceae family, excluding the <i>Scaevola</i> genus, are endemic to Australasia, <i>S. taccada</i> and <i>S. hainanensis</i> have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. <...
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MDPI AG
2023-04-01
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| Series: | International Journal of Molecular Sciences |
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| author | Sen Li Xiaomeng Mao Ziwen He Shaohua Xu Zixiao Guo Suhua Shi |
| author_facet | Sen Li Xiaomeng Mao Ziwen He Shaohua Xu Zixiao Guo Suhua Shi |
| author_sort | Sen Li |
| collection | DOAJ |
| description | While most of the species in Goodeniaceae family, excluding the <i>Scaevola</i> genus, are endemic to Australasia, <i>S. taccada</i> and <i>S. hainanensis</i> have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. <i>S. taccada</i> appears to be highly adapted to coastal sandy lands and cliffs, and it has become invasive in places. <i>S. hainanensis</i> is found mainly in salt marshes near mangrove forests, and is at risk of extinction. These two species provide a good system to investigate adaptive evolution outside the common distribution range of this taxonomic group. Here, we report their chromosomal-scale genome assemblies with the objective of probing their genomic mechanisms related to divergent adaptation after leaving Australasia. The scaffolds were assembled into eight chromosome-scale pseudomolecules, which covered 90.12% and 89.46% of the whole genome assembly for <i>S. taccada</i> and <i>S. hainanensis</i>, respectively. Interestingly, unlike many mangroves, neither species has undergone whole-genome duplication. We show that private genes, specifically copy-number expanded genes are essential for stress response, photosynthesis, and carbon fixation. The gene families that are expanded in <i>S. hainanensis</i> and contracted in <i>S. taccada</i> might have facilitated adaptation to high salinity in <i>S. hainanensis</i>. Moreover, the genes under positive selection in <i>S. hainanensis</i> have contributed to its response to stress and its tolerance of flooding and anoxic environments. In contrast, compared with <i>S. hainanensis</i>, the more drastic copy number expansion of <i>FAR1</i> genes in <i>S. taccada</i> might have facilitated its adaptation to the stronger light radiation present in sandy coastal lands. In conclusion, our study of the chromosomal-scale genomes of <i>S. taccada</i> and <i>S. hainanensis</i> provides novel insights into their genomic evolution after leaving Australasia. |
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| spelling | doaj.art-88b1e54ff43f4a8c9f68ddd59150b7a42023-11-17T19:39:10ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-04-01248735510.3390/ijms24087355Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common RangeSen Li0Xiaomeng Mao1Ziwen He2Shaohua Xu3Zixiao Guo4Suhua Shi5State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaWhile most of the species in Goodeniaceae family, excluding the <i>Scaevola</i> genus, are endemic to Australasia, <i>S. taccada</i> and <i>S. hainanensis</i> have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. <i>S. taccada</i> appears to be highly adapted to coastal sandy lands and cliffs, and it has become invasive in places. <i>S. hainanensis</i> is found mainly in salt marshes near mangrove forests, and is at risk of extinction. These two species provide a good system to investigate adaptive evolution outside the common distribution range of this taxonomic group. Here, we report their chromosomal-scale genome assemblies with the objective of probing their genomic mechanisms related to divergent adaptation after leaving Australasia. The scaffolds were assembled into eight chromosome-scale pseudomolecules, which covered 90.12% and 89.46% of the whole genome assembly for <i>S. taccada</i> and <i>S. hainanensis</i>, respectively. Interestingly, unlike many mangroves, neither species has undergone whole-genome duplication. We show that private genes, specifically copy-number expanded genes are essential for stress response, photosynthesis, and carbon fixation. The gene families that are expanded in <i>S. hainanensis</i> and contracted in <i>S. taccada</i> might have facilitated adaptation to high salinity in <i>S. hainanensis</i>. Moreover, the genes under positive selection in <i>S. hainanensis</i> have contributed to its response to stress and its tolerance of flooding and anoxic environments. In contrast, compared with <i>S. hainanensis</i>, the more drastic copy number expansion of <i>FAR1</i> genes in <i>S. taccada</i> might have facilitated its adaptation to the stronger light radiation present in sandy coastal lands. In conclusion, our study of the chromosomal-scale genomes of <i>S. taccada</i> and <i>S. hainanensis</i> provides novel insights into their genomic evolution after leaving Australasia.https://www.mdpi.com/1422-0067/24/8/7355genome assembly<i>Scaevola taccada</i><i>Scaevola hainanensis</i>evolutionadaptation<i>FAR1</i> |
| spellingShingle | Sen Li Xiaomeng Mao Ziwen He Shaohua Xu Zixiao Guo Suhua Shi Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range International Journal of Molecular Sciences genome assembly <i>Scaevola taccada</i> <i>Scaevola hainanensis</i> evolution adaptation <i>FAR1</i> |
| title | Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range |
| title_full | Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range |
| title_fullStr | Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range |
| title_full_unstemmed | Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range |
| title_short | Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range |
| title_sort | chromosomal scale genome assemblies of two coastal plant species i scaevola taccada i and i s hainanensis i insight into adaptation outside of the common range |
| topic | genome assembly <i>Scaevola taccada</i> <i>Scaevola hainanensis</i> evolution adaptation <i>FAR1</i> |
| url | https://www.mdpi.com/1422-0067/24/8/7355 |
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