High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres

Chang, Xing; He, Xin; Li, Jianying; Liu, Zhenping; Pi, Ruizhen; Luo, Xuanxuan; Wang, Ruipeng; Hu, Xiubao; Lu, Sifan; Zhang, Xianlong; Wang, Maojun

doi:10.1016/j.xplc.2023.100722

Cited by 10 publications

(4 citation statements)

References 109 publications

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“…In addition, centromeric Gypsy was dominated by Tekay, Angela and centromeric retrotransposons of maize ( CRM ) (Supplemental Figure 8A). Notably, CRM appeared more frequently in centromeric regions rather in non-centromeric, consistent with previous reports for maize and cotton (Chang et al, 2023; Chen et al, 2023). Phylogenetic analysis of Gypsy demonstrated that centromeric CRM s formed a unique clade, suggesting centromeric CRM expansion without non-centromeric CRM (Supplemental Figure 8B).…”

Section: Resultssupporting

confidence: 92%

The complete genome of lettuce reveals centromere landscape and empowers breeding

Wang,

Jin,

Wang

et al. 2024

Preprint

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Lettuce (Lactuca sativa L.) is a globally grown vegetable crop as the most popular salad ingredient. Lettuce breeding is crucial to enhancing yield, nutrition and disease resistance, but impeded by lacking a high-quality genome resource. In addition, the released genomes remain fragmented (with hundreds of gaps) and incomplete with omitting pivotal centromeres and telomeres. Here, we report a 2.59 Gb complete telomere-to-telomere (T2T) genome assembly for lettuce. T2T genome analysis revealed the unique genetic and epigenetic architectures of centromere repeats dominated by retrotransposons and satellites. The complete genome and annotation facilitate the identification of candidate disease resistance (NLR) genes induced during grey mold infection. The genomic resources, and biological insights into genetic and epigenetic landscape of centromeres not only advance lettuce research and breeding, but also propel the biology and evolution of centromeres across plant kingdom.

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Section: Resultssupporting

confidence: 92%

The complete genome of lettuce reveals centromere landscape and empowers breeding

Wang,

Jin,

Wang

et al. 2024

Preprint

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“…Gene duplication events, which produce new functional genes and promote species development, occurred in all the species. Upland cotton is a heterotetraploid cotton species composed of the A t subgenome and D t subgenome [49]. As expected, orthologs of almost all the GhANNs were found in G. arboreum and G. raimondii, which is consistent with the findings in closely related species.…”

Section: Discussionsupporting

confidence: 89%

Genome-Wide Identification of the GhANN Gene Family and Functional Validation of GhANN11 and GhANN4 under Abiotic Stress

Luo,

Li,

et al. 2024

IJMS

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Annexins (ANNs) are a structurally conserved protein family present in almost all plants. In the present study, 27 GhANNs were identified in cotton and were unevenly distributed across 14 chromosomes. Transcriptome data and RT-qPCR results revealed that multiple GhANNs respond to at least two abiotic stresses. Similarly, the expression levels of GhANN4 and GhANN11 were significantly upregulated under heat, cold, and drought stress. Using virus-induced gene silencing (VIGS), functional characterization of GhANN4 and GhANN11 revealed that, compared with those of the controls, the leaf wilting of GhANN4-silenced plants was more obvious, and the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) were lower under NaCl and PEG stress. Moreover, the expression of stress marker genes (GhCBL3, GhDREB2A, GhDREB2C, GhPP2C, GhRD20-2, GhCIPK6, GhNHX1, GhRD20-1, GhSOS1, GhSOS2 and GhSnRK2.6) was significantly downregulated in GhANN4-silenced plants after stress. Under cold stress, the growth of the GHANN11-silenced plants was significantly weaker than that of the control plants, and the activities of POD, SOD, and CAT were also lower. However, compared with those of the control, the elasticity and orthostatic activity of the GhANN11-silenced plants were greater; the POD, SOD, and CAT activities were higher; and the GhDREB2C, GhHSP, and GhSOS2 expression levels were greater under heat stress. These results suggest that different GhANN family members respond differently to different types of abiotic stress.

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“…To calculate the age of the full-length LTR retrotransposons, divergence (K) was estimated based on the divergence between two LTR copies. The Jukes–Cantor model [ 71 ] was applied for correction, and then the ages of each copy were estimated using T = K / r , in which r is the nucleotide mutation rate ( r = 9 × 10 −9 ) [ 72 ].…”

Section: Methodsmentioning

confidence: 99%

Pangenome analysis reveals transposon-driven genome evolution in cotton

He,

Qi,

Liu

et al. 2024

BMC Biol

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Background Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution. Results Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes. Conclusions Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.

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High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres

Cited by 10 publications

References 109 publications

The complete genome of lettuce reveals centromere landscape and empowers breeding

The complete genome of lettuce reveals centromere landscape and empowers breeding

Genome-Wide Identification of the GhANN Gene Family and Functional Validation of GhANN11 and GhANN4 under Abiotic Stress

Pangenome analysis reveals transposon-driven genome evolution in cotton

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