Evolution of coastal forests based on a full set of mangrove genomes

He, Ziwen; Feng, Xiao; Chen, Qipian; Li, Liangwei; Li, Sen; Han, Kai; Guo, Zixiao; Wang, Jiayan; Liu, Min; Shi, Chengcheng; Xu, Shaohua; Shao, Shao; Liu, Xin; Mao, Xiaomeng; Xie, Wei; Wang, Xinfeng; Wei, Fei; Li, Guohong; Wu, Weihong; Zhang, Zheng; Zhong, Cairong; Duke, Norman C.; Boufford, David E.; Fan, Guangyi; Wu, Chung‐I; Ricklefs, Robert E.; Shi, Suhua

doi:10.1038/s41559-022-01744-9

Cited by 65 publications

(62 citation statements)

References 113 publications

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“…The longest scaffold, N50, and N90 were 12,839,107; 4,834,853; and 74,632 bp in length, respectively ( Table S1 ). The size of our R. apiculata genome (231 Mb) is similar to the size of the previously reported R. apiculata genomes (232 Mb) in China [ 37 , 62 ], which covered 84% of the estimated R. apiculata genome based on flow cytometry (274 Mb) [ 37 ]. The BUSCO (benchmarking universal single-copy orthologues) result revealed that all scaffolds (208 Mb, Table S1 ) covered approximately 97% of predicted R. apiculata genes ( Figure S1 ) [ 37 ].…”

Section: Resultssupporting

confidence: 81%

Assessment of the Genetic Diversity and Population Structure of Rhizophora apiculata Blume (Rhizophoraceae) in Thailand

Ruang-areerate

Naktang

Kongkachana

et al. 2022

Biology

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Rhizophora apiculata is one of the most widespread and economically important mangrove trees in the Indo-West Pacific region. Knowledge of the genetic variation of R. apiculata in Thailand is limited. Here, we generated a whole-genome sequence of R. apiculata using the 10× Genomics technology. R. apiculata genome assembly was 230.47 Mb. Based on its genome, 2640 loci of high-quality biallelic SNPs were identified from 82 R. apiculata accessions collected from 17 natural mangrove forests in Thailand to assess the genetic diversity and population structure among them. A moderate level of genetic diversity of R. apiculata was observed. The average observed heterozygosity (Ho = 0.48) was higher than the average expected heterozygosity (He = 0.36). Two subpopulations were observed and confirmed from three approaches: population structure, PCA, and phylogenetic analyses. They corresponded to the Gulf of Thailand and the Andaman Sea separated by the Malay Peninsula. AMOVA analyses indicated that genetic variation was attributable to 76.22% within populations and 23.78% among populations. A high level of genetic differentiation between the two subpopulations (FST = 0.24, p < 0.001) was observed. This study evaluated the genetic diversity and population structure of R. apiculata, providing useful information for sustainable mangrove management in Thailand.

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Section: Resultssupporting

confidence: 81%

Assessment of the Genetic Diversity and Population Structure of Rhizophora apiculata Blume (Rhizophoraceae) in Thailand

Ruang-areerate

Naktang

Kongkachana

et al. 2022

Biology

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“…Comparison of microsynteny revealed the presence of the S -locus remnant in other S-RNase -based self-incompatible species, including Chiococca alba 30 (Rubiaceae), Citrus clementina 31 (Rutaceae), Physalis pubescens 32 (Solanaceae), Prunus davidiana 33 (Rosaceae), but not in the syntenic regions of species outside Eudicotyledoneae, such as Oryza sativa (Poaceae). The distribution pattern also suggested that the S -locus emerged early right after the divergence of Eudicotyledoneae from with other Mesangiosperms.…”

Section: Resultsmentioning

confidence: 99%

The snapdragon genomes reveal the evolutionary dynamics of theSlocus supergene

Zhu

Zhang

Copsey

et al. 2022

Preprint

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Multi-allelic S-locus, containing pistil S-RNase and dozens of S-locus F-box (SLF), is known to take responsibility for genetic control of self-incompatibility (SI) in Plantaginaceae. Loss of SI is a prerequisite for mating system transition from self-incompatible to self-compatible, which is very frequent in flowering plants. The transition to selfing is excepted to have noticeable effects on adaptive potential and genome evolution. However, there have been limited comparative studies on the evolutionary shift and S-locus from genome-wide perspective due to lack of high-quality genomic data to date. The genus Antirrhinum has long been used as model plant to study self- incompatibility, here, through integrating sequencing data from multiple platforms, we present the chromosome-level reference and haplotype- resolved genome assembly of an A.hispanicum line, AhS7S8. Comparative genomics approach revealed that the self-incompatible A.hispanicum diverged from its self-compatible relative A.majus approximately 3.6 million years ago (Mya) just after Zanclean flood. The expanded gene families enriched in distinct functional terms implied quite different evolutionary trajectory of outcrossing and selfing snapdragon, and contributed to the adaptation of snapdragon with different mating system. Particularly, we successfully reconstructed two complete S-haplotypes spanning ∼1.2Mb, each consists of 32 SLFs and a S-RNase, as well as a pseudo S-haplotype from self-compatible A.majus. Multiple copies of SLFs derived from proximal or tandem duplication via retroelement-mediated way at a very early time, announcing the ancient history of S-locus. Furthermore, we detected a candidate cis-transcription factor associated with regulating SLFs expression, and two miRNAs may control expression of this TF in a higher position. In general, our abundant genomic data provide excellent resources to study mating system transition of snapdragon, and facilitate the functional genomics and evolutional research of S-RNase based self-incompatibility system.

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“…Methods used for genome sequencing, assembly, and annotation are detailed in Supplementary Note S1 in the supporting information. These genomes were sequenced as part of a project aiming to sequence most mangrove species worldwide (He et al., 2022).…”

Section: Methodsmentioning

confidence: 99%

Adaptation to a new environment with pre‐adaptive genomic features – Evidence from woody plants colonizing the land–sea interface

Guo

Xie

et al. 2022

The Plant Journal

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SUMMARY Adaptation to new environments is a key evolutionary process which presumably involves complex genomic changes. Mangroves, a collection of approximately 80 woody plants that have independently invaded intertidal zones >20 times, are ideal for studying this process. We assembled near‐chromosome‐scale genomes of three Xylocarpus species as well as an outgroup species using single‐molecule real‐time sequencing. Phylogenomic analysis reveals two separate lineages, one with the mangrove Xylocarpus granatum and the other comprising a mangrove Xylocarpus moluccensis and a terrestrial Xylocarpus rumphii. In conjunction with previous studies, we identified several genomic features associated with mangroves: (i) signals of positive selection in genes related to salt tolerance and root development; (ii) genome‐wide elevated ratios of non‐synonymous to synonymous substitution relative to terrestrial relatives; and (iii) active elimination of long terminal repeats. These features are found in the terrestrial X. rumphii in addition to the two mangroves. These genomic features, not being strictly mangrove‐specific, are hence considered pre‐adaptive. We infer that the coastal but non‐intertidal habitat of X. rumphii may have predisposed the common ancestor to invasion of true mangrove habitats. Other features including the preferential retention of duplicated genes and intolerance to pseudogenization are not found in X. rumphii and are likely true adaptive features in mangroves. In conclusion, by studying adaptive shift and partial shifts among closely related species, we set up a framework to study genomic features that are acquired at different stages of the pre‐adaptation and adaptation to new environments.

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Evolution of coastal forests based on a full set of mangrove genomes

Cited by 65 publications

References 113 publications

Assessment of the Genetic Diversity and Population Structure of Rhizophora apiculata Blume (Rhizophoraceae) in Thailand

Assessment of the Genetic Diversity and Population Structure of Rhizophora apiculata Blume (Rhizophoraceae) in Thailand

The snapdragon genomes reveal the evolutionary dynamics of theSlocus supergene

Adaptation to a new environment with pre‐adaptive genomic features – Evidence from woody plants colonizing the land–sea interface

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