Chromosome-scale assembly of the Kandelia obovata genome

Hu, Min; Sun, Wei; Tsai, Wen Chieh; Lai, Xing Kai; Chen, De Qiang; Liu, Xue Die; Wang, Yi Fan; Le, Yi Xun; Chen, Si Ming; Zhang, Di Yang; Xia, Yu; Hu, Wen; Zhou, Zhuang; Chen, Yan Qiong; Zou, Shuang Quan; Liu, Zhong‐Jian

doi:10.1038/s41438-020-0300-x

Cited by 42 publications

(68 citation statements)

References 71 publications

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“…The candidate sequences of the MADS-box and SAUR genes of A. thaliana were downloaded from TAIR ( https://www.arabidopsis.org/index.jsp ). The HMM profiles of the MADS (PF00319) 84 , GH3 auxin-responsive promoter (PF03321) 85 , and SAUR (PF02519) 86 gene families were obtained from Pfam ( http://pfam.xfam.org/ ). Each protein of the gene families of P. bournei and C. kanehirae was separately searched with the HMMER 3.2.1 (with default parameters) 87 and BLASTP ( E -value of e −5 ) 53 methods in the P. bournei and C. kanehirae genomes.…”

Section: Methodsmentioning

confidence: 99%

The Phoebe genome sheds light on the evolution of magnoliids

et al. 2020

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Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46-and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.

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Section: Methodsmentioning

confidence: 99%

The Phoebe genome sheds light on the evolution of magnoliids

et al. 2020

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“…This event is known to have led to the divergence of mangroves from its terrestrial Rhizophoraceae ancestor family ( Guo et al., 2017 ). Similarly, phylogenetic analysis on Aegiceras corniculatum and Kandelia obovata genome indicated the WGD event as a turning point in adaptive evolution and mangrove emergence from Myrsinaceae and Rhizophoraceae, respectively ( Feng et al., 2021 ; Hu et al., 2020 ). WGD is often followed by fractionation by which most of the gene duplicates created are lost.…”

Section: Evolution Of Mangroves and Their Adaptations To Intertidal Environmentsmentioning

confidence: 99%

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

2022

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Mangroves are halophytic plants belonging to diverse angiosperm families that are adapted to highly stressful intertidal zones between land and sea. They are special, unique, and one of the most productive ecosystems that play enormous ecological roles and provide a large number of benefits to the coastal communities. To thrive under highly stressful conditions, mangroves have innovated several key morphological, anatomical, and physio-biochemical adaptations. The evolution of the unique adaptive modifications might have resulted from a host of genetic and molecular changes and to date we know little about the nature of these genetic and molecular changes. Although slow, new information has accumulated over the last few decades on the genetic and molecular regulation of the mangrove adaptations, a comprehensive review on it is not yet available. This review provides up-to-date consolidated information on the genetic, epigenetic, and molecular regulation of mangrove adaptive traits.

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“…A recent, whole-genome structure analysis performed in Rhizophoreae mangrove plant Kandelia obovata revealed two whole-genome duplication events with an expansion in 459 gene families, including "structural constituent of cytoskeleton" and "structural constituent of the ribosome." The successful generation of whole-genome sequence assembly resources for mangrove plants will serve as an essential reference for studying the molecular mechanisms that promote the intertidal adaptation in mangrove species to enhance the selection and breeding of coastal shelterbelts (Hu et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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

Guo

Ding

et al. 2021

Molecular Ecology Resources

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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 wholegenome 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.

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Chromosome-scale assembly of the Kandelia obovata genome

Cited by 42 publications

References 71 publications

The Phoebe genome sheds light on the evolution of magnoliids

The Phoebe genome sheds light on the evolution of magnoliids

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

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

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