Complete chloroplast genomes of three Alseodaphne species reconstructed
Alseodaphne is a genus of timber trees (ca. 40 spp.) belonging to the Persea group of the Lauraceae.
The genus Alseodaphne is confined to tropical and subtropical Asia, with 10 of the 40 known species in China. Alseodaphne is part of the Persea group of the Lauraceae and appears to be polyphyletic as currently constituted, although the precise generic boundaries and species delineations based on morphological characters are currently unclear
Researchers from Xishuangbanna Tropical Botanical Garden (XTBG) selected three species of Alseodaphne (i.e. Alseodaphne huanglianshanensis , A. gracilis, and A. semecarpifolia) to sequencethe complete chloroplast genomes. They then used the entire chloroplast genomes to perform comparative analyses of Alseodaphne and a phylogenomic study with other Lauraceae.
By Illumina high-throughput sequencing, the researchers obtained three complete chloroplast genomes for woody plants in the genus Alseodaphne. The sizes of the three Alseodaphne plastomes are very similar to each other, with lengths from 153 051 bp to 153 099 bp. They have similar genome size and are very different with previously published plastomes of Lauraceae in length.
Through comparative genomics analysis, the researchers identified two main reasons for the size differences. First, one copy of the ycf2 gene with a length of 6834 bp was complete in both Endiandra plastomes but truncated to 3162 bp in the other 10 plastomes, contributing almost 3700 bp to the length difference. Second, the lengths of the truncated ycf1 genes varied from 1875 bp to 1374 bp among the 12 plastomes, which contributed around 250 bp to the length difference.
The two genes ycf1 and ycf2 are located at the boundaries between the IR regions and the LSC or SSC regions, and the length mutations are responsible for the contraction of the IR regions in the plastomes.
Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPersea group comprising species of Alseodaphne, Phoebe, Persea and Machilus.
The study entitled “Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae” has been published in Holzforschung.
TAN Yunhong Principal Investigator
Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China