Dataset Information

Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae).

ABSTRACT: Recent plastid genome (plastome) studies of legumes (family Fabaceae) have shown that this family has undergone multiple atypical plastome evolutions from each of the major clades. The tribe Desmodieae belongs to the Phaseoloids, an important but systematically puzzling clade within Fabaceae. In this study, we investigated the plastome evolution of Desmodieae and analyzed its phylogenetic signaling. We sequenced six complete plastomes from representative members of Desmodieae and from its putative sister Phaseoloid genus Mucuna. Those genomes contain 128 genes and range in size from 148,450 to 153,826 bp. Analyses of gene and intron content revealed similar characters among the members of Desmodieae and Mucuna. However, there were also several distinct characters identified. The loss of the rpl2 intron was a feature shared between Desmodieae and Mucuna, whereas the loss of the rps12 intron was specific to Desmodieae. Likewise, gene loss of rps16 was observed in Mucuna but not in Desmodieae. Substantial sequence variation of ycf4 was detected from all the sequenced plastomes, but pseudogenization was restricted to the genus Desmodium. Comparative analysis of gene order revealed a distinct plastome conformation of Desmodieae compared with other Phaseoloid legumes, i.e., an inversion of an approximately 1.5-kb gene cluster (trnD-GUC, trnY-GUA, and trnE-UUC). The inversion breakpoint suggests that this event was mediated by the recombination of an 11-bp repeat motif. A phylogenetic analysis based on the plastome-scale data set found the tribe Desmodieae is a highly supported monophyletic group nested within the paraphyletic Phaseoleae, as has been found in previous phylogenetic studies. Two subtribes (Desmodiinae and Lespedezinae) of Desmodieae were also supported as monophyletic groups. Within the subtribe Lespedezinae, Lespedeza is closer to Kummerowia than Campylotropis.

SUBMITTER: Jin DP

PROVIDER: S-EPMC6590825 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae).

Jin Dong-Pil DP Choi In-Su IS Choi Byoung-Hee BH

PloS one 20190624 6

Recent plastid genome (plastome) studies of legumes (family Fabaceae) have shown that this family has undergone multiple atypical plastome evolutions from each of the major clades. The tribe Desmodieae belongs to the Phaseoloids, an important but systematically puzzling clade within Fabaceae. In this study, we investigated the plastome evolution of Desmodieae and analyzed its phylogenetic signaling. We sequenced six complete plastomes from representative members of Desmodieae and from its putati ...[more]

PMID: 31233545

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Project description:Traditionally, the tribe Sophoreae sensu lato has been considered a basal but also heterogeneous taxonomic group of the papilionoid legumes. Phylogenetic studies have placed Sophoreae sensu stricto (s.s.) as a member of the core genistoids. The recently suggested new circumscription of this tribe involved the removal of traditional members and the inclusion of Euchresteae and Thermopsideae. Nonetheless, definitions and inter- and intra-taxonomic issues of Sophoreae remain unclear. Within the field of legume systematics, the molecular characteristics of a plastid genome (plastome) have an important role in helping to define taxonomic groups. Here, we examined the plastome of Maackia fauriei, belonging to Sophoreae s.s., to elucidate the molecular characteristics of Sophoreae. Its gene contents are similar to the plastomes of other typical legumes. Putative pseudogene rps16 of Maackia and Lupinus species imply independent functional gene loss from the genistoids. Our overall examination of that loss among legumes suggests that it is common among all major clades of Papilionoideae. The M. fauriei plastome has a novel 24-kb inversion in its large single copy region, as well as previously recognized 50-kb and 36-kb inversions. The 36-kb inversion is shared by the core genistoids. The 24-kb inversion is present in the eight genera belonging to three tribes: Euchresteae, Sophoreae s.s., and Thermopsideae. The phylogenetic distribution of this 24-kb inversion strongly supports the monophyly of members of Sophoreae s.s. with Euchresteae and Thermopsideae. Hence, it can be used as a putative synapomorphic characteristic for the newly circumscribed Sophoreae, including Euchresteae and Thermopsideae. However, plastome conformation suggests a slightly narrower taxonomic group because of heterogeneous results from Bolusanthus and Dicraeopetalum. The phylogenetic analysis, based on plastome sequences from 43 legumes, represents well our understanding of legume systematics while resolving the genistoid clade as a sister group to an Old World clade. It also demonstrates the value that plastomes are powerful marker for systematic studies of basal papilionoid legumes.

Project description:BackgroundAmpelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights.ResultsWe sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa.ConclusionsOur results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.

Dataset Information

Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae).

Publications

Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae).

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