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Plastid genome evolution in subtribe Gentianinae (Gentianaceae)

Citation

Fu, Pengcheng (2021), Plastid genome evolution in subtribe Gentianinae (Gentianaceae), Dryad, Dataset, https://doi.org/10.5061/dryad.h70rxwdgw

Abstract

We investigated plastome evolution in Subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae as well as all 14 sections of the species-rich genus Gentiana. Here, we upload (1) original alignments, Gblock alignments and tree topology file in phylogenetic analysis, and (2) results about a 5 kb insertion in Gentiana cuneibarba, including Sanger sequencing results which verified its two boundaries as well as the middle, and annotation results.

Methods

1. alignments

Sequences of all protein coding genes were extracted from each plastome in PhyloSuite (Zhang et al. 2020) and aligned respectively using MAFFT (Katoh et al. 2002). A protein-coding matrix was constructed where we excluded genes that were absent in some species, or that showed high-sequence variability that made alignment difficult. We examined the matrix and removed the most rapidly evolving sites using Gblocks (Talavera & Castresana, 2007) using default setting.

2. tree topology file

Phylogenetic analyses were performed with IQ-TREE (Nguyen et al. 2014) implemented in PhyloSuite (Zhang et al. 2020) using the maximum likelihood (ML) method with 1000 rapid bootstrap replicates. The substitution model was chosen using ModelFinder (Kalyaanamoorthy et al., 2017).

3. Sanger sequencing results

 One 5 kb insertion was detected in Gentiana cuneibarba. We designed three pairs of primers to verified its two boundaries as well as the middle via PCR and Sanger sequencing.

4. Alignment descriptions of the 5kb insertion

The 5kb insertion in Gentiana cuneibarba is BLAST with default settings. The top 100 alignment descriptions are provided.

 

Usage Notes

1 Phylogeny_64_genes_Original_alignments.fasta: Original alignment of 64 protein coding genes in Subtribe Gentianinae.

2 Phylogeny_64_genes_Gblocks_alignments.fasta: Gblocks alignment of 64 protein coding genes in Subtribe Gentianinae.

3 ML tree IQTREE.contree: ML tree file  in Subtribe Gentianinae

4 G.cuneibarba insertion sequence.txt: The insertion sequence of the insertion in Gentiana cuneibarba.

5 Gcun1_F2.P91104845.ab1: Sanger suquencing result of primer Gcun1, verifying the first boundary.

6 Gcun2_F1.P91104847.ab1: Sanger suquencing result of primer Gcun2, verifying the middle of the insertion.

7 Gcun3_F2.P91104848.ab1: Sanger suquencing result of primer Gcun3, verifying the end boundary.

8 Insertion-Alignment-Descriptions.xls: The top 100 alignment descriptions of the insertion sequence by BLAST.

Funding

National Natural Science Foundation of China, Award: 31600296