Apocynaceae, the dogbane family, is one of the ten largest angiosperm families, comprising 378 genera and more than 5,000 species. However, the backbone phylogeny of the family is less well supported, and the evolutionary pattern of plastomes in this large family is much less clear.
To gain a better understanding of the phylogenetic relationships and plastome evolutionary pattern of Apocynaceae, researchers from the Wuhan Botanical Garden of the Chinese Academy of Sciences (CAS) obtained a total of 101 complete plastomes, representing 26 out of 27 tribes of Apocynaceae, to perform comparative plastome analyses. Phylogenetic trees were also reconstructed using maximum likelihood and Bayesian inference methods.
The 101 complete Apocynaceae plastomes showed a typical quadripartite structure, including a large single copy (LSC) region, a small single copy (SSC) region, and two inverted repeated (IR) regions. Plastome lengths ranged from 150,897 bp in Apocynum venetum L. to 178,616 bp in Hoya exilis Schltr., with a difference of 27,719 bp. Six types of IR/SC boundaries were found in the 101 Apocynaceae plastomes.
In addition, different sizes of IR expansion were found in three lineages (Alyxieae, Ceropegieae and Marsdenieae), suggesting that IR expansions have occurred independently at least three times in Apocynaceae. Two clades within Marsdenieae showed different trends in IR expansion direction: the 'Cosmopolitan Clade' expanded towards the LSC, while the 'Asia-Pacific Clade' expanded towards both the LSC and the SSC.
Five non-coding regions and six protein-coding genes were found to be highly diverse: accD, ccsA-ndhD, clpP, matK, ndhF, ndhG-ndhI, trnG(GCC)-trnfM(CAU), trnH(GUG)-psbA, trnY(GUA)-trnE(UUC), ycf1, and ycf2. They can be used as promising candidate markers for shallow phylogenetic analyses and DNA barcoding.
Maximum likelihood and Bayesian phylogenetic analyses yielded almost identical tree topologies. A total of 15 consecutive dichotomies were identified along the backbone. The subfamily Periplocoideae were nested in the Apocynoid grade and were sister to a clade of Echiteae-Odontadenieae-Mesechiteae clade with strong support.
The placement of Periplocoideae and the non-monophyletic Willughbeieae, Melodineae, Hoya, and Ceropegia, as well as these conflicting relationships on the nuclear phylogeny, suggest that there is much room for improvement in the phylogeny and taxonomy of Apocynaceae at ranks above genus.
This study assembled the largest plastome dataset to date for Apocynaceae, studied the plastome evolution across the family for the first time, and reconstructed a phylogeny with a well-resolved backbone.
Results have been published in Molecular Phylogenetics and Evolution entitled "Evolution of 101 Apocynaceae plastomes and phylogenetic implications".
The research was supported by the Biological Resources Program of CAS, the China National Plant Specimen Resource Center, the International Partnership Program of CAS, and the Sino-Africa Joint Research Center of CAS.
