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BMC Genomics. 2017 Dec 8;18(1):956. doi: 10.1186/s12864-017-4319-9.

Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution.

Author information

1
Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
2
University of Chinese Academy of Sciences, Beijing, 100049, China.
3
Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
4
Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Edinburgh, Scotland, EH9 3JH, UK.
5
Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. dzl@mail.kib.ac.cn.
6
University of Chinese Academy of Sciences, Beijing, 100049, China. dzl@mail.kib.ac.cn.
7
Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. dzl@mail.kib.ac.cn.
8
Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. gaolm@mail.kib.ac.cn.

Abstract

BACKGROUND:

The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies.

RESULTS:

All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified.

CONCLUSIONS:

Phylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants.

KEYWORDS:

Alignment; Cornales; Gene loss; Partitioning schemes; Phylogenomics; Plastid genome

PMID:
29216844
PMCID:
PMC5721659
DOI:
10.1186/s12864-017-4319-9
[Indexed for MEDLINE]
Free PMC Article

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