The Metasequoia genome and evolutionary relationships among redwoods

Fu, Fangfang; Song, Chi; Wen, Cheng; Guo, Ying; Yang, Xiaoming; Shu, Ziqiang; Li, Xiaodong; Feng, Youzhi; Liu, Bingshuang; Sun, Mingsheng; Zhong, Yang; Chen, Li; Ning, Yan; Chen, Jie; Wang, Guibin; Yin, Tongming; Chen, Shilin; Xue, Liang‐Jiao; Cao, Fuliang

doi:10.1016/j.xplc.2023.100643

Cited by 8 publications

(4 citation statements)

References 75 publications

(103 reference statements)

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“…To determine the covariance of GbPAL family individual genes among other species, A. thaliana and Metasequoia glyptostroboides 27 were analyzed with the PAL family in ginkgo. ( Figure 5(b) ).…”

Section: Resultsmentioning

confidence: 99%

Expression profiling of the phenylalanine ammonia-lyase ( PAL ) gene family in ginkgo biloba L.

Gao,

Hu,

et al. 2023

Plant Signaling & Behavior

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The PAL gene family plays an important role in plant growth, development, and response to abiotic stresses and has been identified in a variety of plants. However, a systematic characterization is still lacking in Ginkgo biloba . Using a bioinformatics approach, 11 GbPAL members of the PAL gene family identified in ginkgo were identified in this study. The protein structure and physicochemical properties indicated that the GbPAL genes were highly similar. Based on their exon-intron structures, they can be classified into three groups. A total of 62 cis-elements for hormone, light, and abiotic stress responses were identified in the promoters of GbPAL genes, indicating that PAL is a multifunctional gene family. GbPAL genes were specifically expressed in different tissues and ploidy of ginkgo. These results provide a theoretical basis for further studies on the functional expression of the GbPAL genes.

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Section: Resultsmentioning

confidence: 99%

Expression profiling of the phenylalanine ammonia-lyase ( PAL ) gene family in ginkgo biloba L.

Gao,

Hu,

et al. 2023

Plant Signaling & Behavior

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“…These results suggest that tandem duplication is important to expand the VQ family gene in gymnosperms. While wholegenome duplication (WGD) played a critical role in adaptive evolution in angiosperms [43], few recent WGD events were found in extant gymnosperms [36][37][38][39][40]44], which indicates that these duplicate VQ gene pairs were evolved from independent duplication events or derived from older ancestors.…”

Section: Gene Duplication and Collinearity Analysis Of Vq Genes In Gy...mentioning

confidence: 99%

“…Among all VQ gene pairs mentioned above (n = 17), only one VQ gene (GbVQ29, TcVQ13, and PtVQ38) was shared by these three gymnosperms. In order to better see the conservatism of these VQ genes in different gymnosperms, we introduced the collinearity comparison with another two gymnosperms: Cycas panzhihuaensis [38] and Metasequoia glyptostroboides [40]. We found that this VQ gene and its related collinear block also existed in Metasequoia glyptostroboides and Cycas panzhihuaensis.…”

Section: Gene Duplication and Collinearity Analysis Of Vq Genes In Gy...mentioning

confidence: 99%

“…Many gymnosperms have large genomes and numerous repetitive sequences, making it difficult to assemble a complete genome. But, in recent years, with the advancement in technology, some gymnosperms have gradually completed genome sequencing and assembly [36][37][38][39][40]. In view of the prominent role of VQ genes in the growth and development and the responses to environmental stress in angiosperms such as Arabidopsis and rice, VQ genes may also participate in various life processes in gymnosperms.…”

Section: Introductionmentioning

confidence: 99%

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Large-Scale Identification and Characterization Analysis of VQ Family Genes in Plants, Especially Gymnosperms

Tian,

Zhang,

Francis

2023

IJMS

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VQ motif-containing (VQ) proteins are a class of transcription regulatory cofactors widely present in plants, playing crucial roles in growth and development, stress response, and defense. Although there have been some reports on the member identification and functional research of VQ genes in some plants, there is still a lack of large-scale identification and clear graphical presentation of their basic characterization information to help us to better understand this family. Especially in gymnosperms, the VQ family genes and their evolutionary relationships have not yet been reported. In this study, we systematically identified 2469 VQ genes from 56 plant species, including bryophytes, gymnosperms, and angiosperms, and analyzed their molecular and evolutionary features. We found that amino acids are only highly conserved in the VQ domain, while other positions are relatively variable; most VQ genes encode relatively small proteins and do not have introns. The GC content in Poaceae plants is the highest (up to 70%); these VQ proteins can be divided into nine subgroups. In particular, we analyzed the molecular characteristics, chromosome distribution, duplication events, and expression levels of VQ genes in three gymnosperms: Ginkgo biloba, Taxus chinensis, and Pinus tabuliformis. In gymnosperms, VQ genes are classified into 11 groups, with highly similar motifs in each group; most VQ proteins have less than 300 amino acids and are predicted to be located in nucleus. Tandem duplication is an important driving force for the expansion of the VQ gene family, and the evolutionary processes of most VQ genes and duplication events are relatively independent; some candidate VQ genes are preliminarily screened, and they are likely to be involved in plant growth and stress and defense responses. These results provide detailed information and powerful references for further understanding and utilizing the VQ family genes in various plants.

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Nearly complete genome assembly of a critically endangered pine illuminates evolution and conservation of conifers

Zhang,

Liu,

Shu

et al. 2024

Preprint

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Conifers are dominant in most temperate and boreal forest ecosystems, and are the most widely distributed of the gymnosperms. Despite this, many conifer species are threatened with extinction, and in particular the genetic mechanisms underlying their endangerment remain largely unknown.Pinus squamata, which harbors an extremely large diploid genome and conservation significance, is among the 100 most endangered species (plants and animals) globally, and has been designated as ‘Critically Endangered’ on the IUCN Red List. In this study, we report an almost complete genome sequence forP. squamatagenerated by a suite of sequencing technologies, with an assembly of 29.2 Gb, a scaffold N50 length of 2.5 Gb, and a remarkable contig N50 length of 915.4 Mb. This represents the largest and most high-quality gymnosperm genome sequenced to date. The genome is characterized by an ultra-low rate of heterozygosity, is dominated by transposable elements, and contains 55,413 protein-coding genes. Our study provides the first detailed examination of chromosome organization inP. squamata, revealing Rabl configurations and distinctive centromere signatures. This genomic milestone not only deepens our understanding of gymnosperm genetics and evolution but also lays a solid foundation for the development of effective conservation measures, ensuring the survival of this rare species in the face of environmental challenges.

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The Metasequoia genome and evolutionary relationships among redwoods

Cited by 8 publications

References 75 publications

Expression profiling of the phenylalanine ammonia-lyase ( PAL ) gene family in ginkgo biloba L.

Expression profiling of the phenylalanine ammonia-lyase ( PAL ) gene family in ginkgo biloba L.

Large-Scale Identification and Characterization Analysis of VQ Family Genes in Plants, Especially Gymnosperms

Nearly complete genome assembly of a critically endangered pine illuminates evolution and conservation of conifers

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