Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load

Tao, Tongzhou; Milne, Richard I.; Li, Jialiang; Yang, Huohai; Wang, Shiyang; Chen, Sihan; Mao, Kangshan

doi:10.1016/j.pld.2023.06.005

Cited by 4 publications

(1 citation statement)

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“…The identification of abundant ultra-conserved genes (~1000) between M. lotungensis and M. sinica , with extremely low sequence divergence, further highlights the high degree of evolutionary conservation among closely related species, which suggests a deficiency in the emergence of novel genes during the processes of species divergence and independent evolution. This lack of genetic innovation may hinder the species’ ability to adapt to changing environmental conditions and contribute to its endangered status [ 47 , 48 , 49 ]. Our findings emphasize the importance of sequence conservation in the biology of M. lotungensis and provide compelling evidence that the paucity of new genes arising from adaptive evolution is a key factor underlying its threatened status.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis

Shi,

Xie,

Guan

et al. 2024

Genes

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Magnolia lotungensis is an extremely endangered endemic tree in China. To elucidate the genetic basis of M. lotungensis, we performed a comprehensive transcriptome analysis using a sample integrating the plant’s bark, leaves, and flowers. De novo transcriptome assembly yielded 177,046 transcripts and 42,518 coding sequences. Notably, we identified 796 species-specific genes enriched in organelle gene regulation and defense responses. A codon usage bias analysis revealed that mutation bias appears to be the primary driver of selection in shaping the species’ genetic architecture. An evolutionary analysis based on dN/dS values of paralogous and orthologous gene pairs indicated a predominance of purifying selection, suggesting strong evolutionary constraints on most genes. A comparative transcriptomic analysis with Magnolia sinica identified approximately 1000 ultra-conserved genes, enriched in essential cellular processes such as transcriptional regulation, protein synthesis, and genome stability. Interestingly, only a limited number of 511 rapidly evolving genes under positive selection were detected compared to M. sinica and Magnolia kuangsiensis. These genes were enriched in metabolic processes associated with adaptation to specific environments, potentially limiting the species’ ability to expand its range. Our findings contribute to understanding the genetic architecture of M. lotungensis and suggest that an insufficient number of adaptive genes contribute to its endangered status.

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Section: Discussionmentioning

confidence: 99%