The Chinese pine genome and methylome unveil key features of conifer evolution

Niu, Shihui; Jiang, Li; Bo, Wenhao; Yang, Weifei; Zuccolo, Andrea; Giacomello, Stefania; Chen, Xi; Han, Fangxu; Yang, Junhe; Song, Yitong; Nie, Yumeng; Zhou, Biao; Wang, Peiyi; Zuo, Quan; Zhang, Hui; Ma, Jingjing; Wang, Jun; Wang, Lvji; Zhu, Qianya; Zhao, Huanhuan; Liu, Zhanmin; Zhang, Xuemei; Liu, Tao; Pei, Surui; Li, Zhimin; Hu, Yue; Yang, Ya-Chien; Li, Wenzhao; Zan, Yanjun; Zhou, Linghua; Lin, Jun; Yuan, Tong‐Qi; Li, Wei; Li, Yue; Wei, Hairong; Wu, Huaxing

doi:10.1016/j.cell.2021.12.006

Cited by 183 publications

(218 citation statements)

References 118 publications

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“…Conifers and other gymnosperms provide unique opportunities to test key questions of plant mating system evolution and evolutionary conflict from a novel angle, especially now that their genomic resources are no longer seriously hindered by their large genome sizes (e.g. Niu et al 2022). From the empirical perspective, large seed size and gametophytic tissue allow easy identification of maternal haplotypes and alleles.…”

Section: Discussionmentioning

confidence: 99%

Reproductive compensation and selection among viable embryos drive the evolution of polyembryony

Brandvain

Harkness

Pyhäjärvi

2020

Preprint

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Simple polyembryony – where a single gametophyte produces multiple embryos with different sires but the same maternal haplotype – is common in conifers, ferns, horsetails and other vascular plants. Polyembryony could be favored as a mechanism of reproductive compensation, providing a backup for inviable embryos, or as a mechanism of embryo competition and eliminating plants with low fitness, perhaps acting as a mechanism of Self-Incompatibility (SI). However as the evolution of polyembryony from monoembryony has not been modeled these long standing verbal models have not been evaluated. We develop an infinite-site, forward population genetics model to test how these factors can favor the evolution of polyembryony, and how these underlying benefits of polyembryony shape the genetic load under a range of selfing rates, dominance, and selection coefficients. We find that the benefit of reproductive compensation strongly favors the evolution of polyembryony, while the benefits of embryo competition are much weaker. Importantly, when embryo competition favors the evolution of polyembryony it increases embryo competitiveness, but does not act as an SI mechanism, as it does not effectively trade low-fitness selfed offspring for high fitness outcrossed offspring. We find that the impact of polyembryony on the genetic load depends on its function – increasing the embryo load when acting as a mechanism of embryo compensation and decreasing the embryo load when acting as a mechanism of competition.

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Section: Discussionmentioning

confidence: 99%

Reproductive compensation and selection among viable embryos drive the evolution of polyembryony

Brandvain

Harkness

Pyhäjärvi

2020

Preprint

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“…Based on the P. tabuliformis genome database [ 40 ], a total of 43 putative TCP transcription factors were identified (Table S 1 ). With the online program SMART and NCBi CDD, we identified all proteins that contained a conserved TCP domain (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Homologs of clock genes have been identified and they are very conserved in conifer [ 38 ]. In the P. tabuliformis genome project, the photoperiodic pathway is the one of the most conserved pathways during the seed plant evolution [ 40 ]. In present study, we monitored PtCCA1 , PtTOC , PtLWD1 , PtGI , PtZTL , PtCOL2 and PtCOL3 from P. tabuliformis and we monitored their diurnal cycle expression profiles and annual cycle expression profiles twice a month for two years by RNA-seq (Table S 5 , Fig S 3 , Fig S 4 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis

Nie

Han

et al. 2022

BMC Plant Biol

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Background Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood. Results In the present study, 43 TCP genes were identified from P. tabuliformis genome database. Based on the phylogeny tree and sequence similarity, the 43 TCP genes were classified into four groups. The motif results showed that different subfamilies indeed contained different motifs. Clade II genes contain motif 1, clade I genes contain motif 1, 8, 10 and clade III and IV contain more motifs, which is consistent with our grouping results. The structural analysis of PtTCP genes showed that most PtTCPs lacked introns. The distribution of clade I and clade II on the chromosome is relatively scattered, while clade III and clade IV is relatively concentrated. Co-expression network indicated that PtTCP2, PtTCP12, PtTCP36, PtTCP37, PtTCP38, PtTCP41 and PtTCP43 were co-expressed with clock genes in annual cycle and their annual cycle expression profiles both showed obvious seasonal oscillations. PtTCP2, PtTCP12, PtTCP37, PtTCP38, PtTCP40, PtTCP41, PtTCP42 and PtTCP43 were co-expressed with clock genes in diurnal cycle. Only the expression of PtTCP42 showed diurnal oscillation. Conclusions The TCP gene family, especially clade II, may play an important role in the regulation of the season and circadian rhythm of P. tabuliformis. In addition, the low temperature in winter may affect the diurnal oscillations.

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“…Conifers have large genomes, which complicates genetic studies of these species (e.g., 25.4 Gb for Pinus tabuliformis 19 and ~20 Gb for Pinus taeda 20 ).…”

Section: Introductionmentioning

confidence: 99%

“…Conifers have large genomes, which complicates genetic studies of these species (e.g., 25.4 Gb for Pinus tabuliformis 19 and ∼20 Gb for Pinus taeda 20 ). Flowering trait analyses are particularly problematic due to the necessity of large fields for keeping materials for segregation analyses, as well as a wait time of several years until the flowering stage can be examined 21 .…”

Section: Introductionmentioning

confidence: 99%

Single-nucleotide substitution determines pollen production in Japanese cedar

Kakui

Ujino‐Ihara

Hasegawa

et al. 2022

Preprint

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Pollinosis, also known as pollen allergy or hay fever, is a global problem caused by pollen produced by various plant species. The wind-pollinated Japanese cedar (Cryptomeria japonica) is the largest contributor to severe pollinosis in Japan, where increasing proportions of people have been affected in recent decades. The MS4 (MALE STERILITY 4) locus of Japanese cedar controls pollen production, and its homozygous mutants (ms4/ms4) show abnormal pollen development after the tetrad stage and produce no mature pollen. In this study, we narrowed down the MS4 locus by fine mapping in Japanese cedar and found TKPR1 (TETRAKETIDE α-PYRONE REDUCTASE) gene in this region. Transformation experiments using Arabidopsis thaliana showed that single-nucleotide substitution of CjTKPR1 determines pollen production. Broad conservation of TKPR1 beyond plant division could lead to the creation of pollen-free plant not only for Japanese cedar but also for broader plant species.

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The Chinese pine genome and methylome unveil key features of conifer evolution

Cited by 183 publications

References 118 publications

Reproductive compensation and selection among viable embryos drive the evolution of polyembryony

Reproductive compensation and selection among viable embryos drive the evolution of polyembryony

Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis

Single-nucleotide substitution determines pollen production in Japanese cedar

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