Evidence map›Paper›PMID 38359907›Full record

ArticleAnnals of botany2024

Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae).

Shiyun Han, Sijia Zhang, Ran Yi, De Bi, Hengwu Ding, Jianke Yang, Yuanxin Ye, Wenzhong Xu, Longhua Wu, Renying Zhuo and 1 more

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Article in Annals of botany, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

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6citing papers in PubMed
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1 · What the graph read from it

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3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

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  2. PhytoKeys · 2026
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4 · The record

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5 · Who and what money

Authors and funding

11 authors.

Shiyun HanAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.ORCID 0000-0001-6834-502X
Sijia ZhangAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
Ran YiAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
De BiSuzhou Polytechnic Institute of Agriculture, Suzhou 215000, China.
Hengwu DingAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
Jianke YangSchool of Basic Medical Sciences, Wannan Medical College, Wuhu 241000, China.
Yuanxin YeAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
Wenzhong XuKey Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Longhua WuCAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
Renying ZhuoState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
Xianzhao KanAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China.ORCID 0000-0002-9225-407X

Funding

Basic Research Program of Natural Science Foundation of Jiangsu Province of China BK20211078Doctoral Enhancement Program of Suzhou Polytechnic Institute of Agriculture BS2101Key Laboratory of Heavy Metal Pollution Prevention & Control, Ministry of Agriculture and Rural Affairs NEL&MARA-003Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies
6 · The paper itself

Abstract

BACKGROUND AND

aimsKalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale 'barcodes' (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes.

methodsTo explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes). KEY

resultsSignificant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic.

conclusionsThis study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.

Indexed as

CrassulaceaePhylogenyBiological EvolutionEvolution, MolecularGenome, PlastidPlastidsChloroplast tRNAcodon aversionCrassulaceaeEukalanchoeindelsKalanchoideaephylogenyycf1

Identifiers

PMID38359907
PMCPMC11037489

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.