Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

Zhang, Guojin; Yang, Junbo; Zhang, Caifei; Jiao, Bohan; Panero, José L.; Cai, Jie; Zhang, Zhi-Rong; Gao, Lian-Ming; Gao, Tiangang; Ma, Hong

doi:10.1016/j.xplc.2024.100851

Plant Communications

2024

DOI: 10.1016/j.xplc.2024.100851

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Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

Guojin Zhang,

Junbo Yang,

Caifei Zhang

et al.

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2024

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Cited by 3 publications

References 120 publications

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A New Pattern of Phytomelanin Deposition in Cypselae of Bahieae (Asteraceae, Heliantheae Alliance)

Mathur,

Pandey

2024

Feddes Repertorium

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Phytomelanin is the dark and highly inert substance found in the fruit walls of the Heliantheae alliance clade within Asteroideae (Asteraceae). Phytomelanin deposition pattern in the cypselar wall was studied in two taxa of the Bahieae—Bahia pedata A. Gray and Palafoxia arida B. L. Turner. The pericarp anatomy studies have revealed that the phytomelanin deposits in the schizogenous space between the hypodermis and fiber layer. Our findings reveal that phytomelanin deposition is associated with fiber and has also brought out a new pattern of phytomelanin deposition between inner (fibrous zone) and outer sclerified layers (hypodermal) in the schizogenous space. The study recorded a first‐time report of a second layer of phytomelanin outer to the sclerified hypodermal cells at maturity. Our observations point to phytomelanin precursors being synthesized as pliable fluid substances associated with fiber cells and solidifies later in the intercellular space. The study also recorded the first report for the occurrence of tracheoidal cells in the pericarp wall of the Bahieae within the Heliantheae alliance. Our study has provided insights to decipher evolutionary patterns and the significance of phytomelanin in the phytomelanic fruit clade (PFC), and it could help to resolve long‐standing debates on deposition patterns and the site of synthesis of phytomelanin.

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A New Pattern of Phytomelanin Deposition in Cypselae of Bahieae (Asteraceae, Heliantheae Alliance)

Mathur,

Pandey

2024

Feddes Repertorium

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AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research

Liu,

Luo,

Dai

et al. 2024

Nucleic Acids Research

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As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies. To address these gaps, we introduce the Asteraceae Multi-omics Information Resource (AMIR; https://yanglab.hzau.edu.cn/AMIR/), a multi-omics hub for the Asteraceae plant community. AMIR integrates diverse omics data from 74 species, encompassing 132 genomes, 4 408 432 genes annotated across seven different perspectives, 3897 transcriptome sequencing samples spanning 131 organs, tissues and stimuli, 42 765 290 unique variants and 15 662 metabolites genes. Leveraging these data, AMIR establishes the first pan-genome, comparative genomics and transcriptome system for the Asteraceae family. Furthermore, AMIR offers user-friendly tools designed to facilitate extensive customized bioinformatics analyses. Two case studies demonstrate AMIR’s capability to provide rapid, reproducible and reliable analysis results. In summary, by integrating multi-omics data of Asteraceae species and developing powerful analytical tools, AMIR significantly advances functional genomics research and contributes to breeding practices of Asteraceae.

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Complete chloroplast genomes of two Ainsliaea species and the phylogenetic analysis in the tribe Pertyeae

Chen,

Feng,

et al. 2024

Front. Genet.

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The genus Ainsliaea DC. is one of the major groups within the tribe Pertyeae (Asteraceae). It comprises several important Chinese medicinal species. However, the phylogenetic position has undergone a long process of exploration. The complete chloroplast (cp) genome sequences data has not been employed in species identification and phylogeny of Ainsliaea. In this study, the complete cp genomes of two Ainsliaea species (A. gracilis and A. henryi) were reported, followed by structural, comparative, and phylogenetic analyses within the tribe Peryteae. Both cp genomes displayed a typical quadripartite circular structure, with the LSC and SSC regions separated by the IR regions. The genomes were 152,959 (A. gracilis) and 152,805 (A. henryi) base pairs (bp) long, with a GC content of 37.6%. They were highly conserved, containing 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1). Moreover, thirteen highly polymorphic regions (e.g., trnK-UUU, trnG-UCC, trnT-GGU, accD-psaI, and rpl22-rps19) were identified, indicating their potential as DNA barcodes. The phylogenetic analysis confirmed the placement of Ainsliaea in the tribe Pertyeae, revealing close relationships with the genera Myripnois and Pertya. In comparison with Ainsliaea, Myripnois was more closely related to Pertya. This study lays a theoretical foundation for future research on species identification, population genetics, resource conservation, and sustainable utilization within Ainsliaea and Pertyeae.

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Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

Cited by 3 publications

References 120 publications

A New Pattern of Phytomelanin Deposition in Cypselae of Bahieae (Asteraceae, Heliantheae Alliance)

A New Pattern of Phytomelanin Deposition in Cypselae of Bahieae (Asteraceae, Heliantheae Alliance)

AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research

Complete chloroplast genomes of two Ainsliaea species and the phylogenetic analysis in the tribe Pertyeae

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