The complete chloroplast genome sequence of Achimenes cettoana (Gesneriaceae)

Abstract

Achimenes Pers. is well known for its floral diversity and widely used in horticulture, but its phylogenetic position is still poorly understood. And most research about the complete chloroplast genome sequence focused on the Old World species; therefore, we think it is necessary to examine taxa of the New World in more detail. This study determined the complete chloroplast genome of Achimenes cettoana H.E. Moore. The cp genome was 153,011 bp in a total length containing two inverted repeats (IRs) of 25,162 bp separated by a large single-copy (LSC) region of 84,669 bp and a small single-copy (SSC) region of 18,018 bp. The whole cp genome of A. cettoana contains 112 genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. This plastid genome is firstly reported in the New World Gesneriaceae, which will be a valuable resource for future studies on breeding, conservation genetics, and phylogeny of Gesneriaceae.

Full text

MITOGENOME ANNOUNCEMENT
The complete chloroplast genome sequence of Achimenes cettoana
(Gesneriaceae)
Shu Li
a,b
, Rui Liao
c
, Zi-Bing Xin
a,b
, Zhang-Jie Huang
a,b
, Stephen Maciejewski
b,d
and Fang Wen
a,b
a
Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang
Autonomous Region and Chinese Academy of Sciences, Guilin, PR China;
b
Gesneriad Conservation Center of China, Guilin Botanical Garden,
Chinese Academy of Sciences, Guilin, PR China;
c
Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm
in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Science, South-Central
University for Nationalities, Wuhan, PR China;
d
The Gesneriad Society, Philadelphia, PA, USA
ABSTRACT
Achimenes Pers. is well known for its floral diversity and widely used in horticulture, but its phylogen-
etic position is still poorly understood. And most research about the complete chloroplast genome
sequence focused on the Old World species; therefore, we think it is necessary to examine taxa of the
New World in more detail. This study determined the complete chloroplast genome of Achimenes
cettoana H.E. Moore. The cp genome was 153,011 bp in a total length containing two inverted repeats
(IRs) of 25,162 bp separated by a large single-copy (LSC) region of 84,669bp and a small single-copy
(SSC) region of 18,018 bp. The whole cp genome of A. cettoana contains 112 genes, including 79 pro-
tein-coding genes, 29 tRNA genes, and four rRNA genes. This plastid genome is firstly reported in the
New World Gesneriaceae, which will be a valuable resource for future studies on breeding, conserva-
tion genetics, and phylogeny of Gesneriaceae.
ARTICLE HISTORY
Received 21 July 2020
Accepted 3 November 2020
KEYWORDS
Achimenes; chloroplast
genome; phylogenetics
Based on molecular phylogenetic studies, the first detailed
and overall classification of Gesneriaceae was made by
Weber et al. (2013), three subfamilies were recognized:
Sanangooideae (monospecific with Sanango racemosum G.S.
Bunting & J.A. Duke), Gesnerioideae, and Didymocarpoideae.
Both Subfam. Sanangooideae and Subfam. Gesnerioideae are
distributed in the New World (Titanotrichum Soler. excluded),
and Subfam. Didymocarpoideae is distributed in the Old
World. Achimenes Pers. (belonging to the Subfam.
Gesnerioideae) is an herbaceous genus of about 24 species
(IPNI 2020; Tropicos 2020), distributed from southern Mexico
through Central America (Roa et al. 2002; Roalson and
Roberts 2016).
The DNA sequence of the chloroplast genome can be
used as a valuable resource for future studies on breeding,
conservation genetics and phylogeny. Within Gesneriaceae,
all chloroplast genomes reported belong to Subfam.
Didymocarpoideae and no complete chloroplast sequence for
the New World Gesneriaceae have been published to date.
The members of the Gesneriad Society collected seeds of
Achimenes cettoana, which grows on rocks in the stream of a
shaded ravine, from Chiapas, Mexico (GPS: 16.74 N, 92.69 W).
Then seeds were shared to GCCC, and were being cultivated
in the nursery of GCCC since 2015. Achimenes cettoana is a
compact plant and adapts well to cultivation (Moore 1961),
especially for a windowsill or under artificial light. The vou-
cher specimen (HZJ001) was deposited at the Herbarium of
Guangxi Institute of Botany, CAS (IBK). The chloroplast DNA
of A. cettoana was extracted by the CTAB method (Doyle and
Doyle 1987) and sequenced using the Illumina Hiseq 4000
sequencing platform (Majorbio Company (http://www.major-
bio.com/, China). We used Map to Reference function in
Geneious R11 (Kearse et al. 2012) to exclude nuclear and
mitochondrial reads using the plastid genome of Petrocodon
jingxiensis (GenBank-MK887172) as reference. Putative chloro-
plast reads were used for de novo assembling construction
using Geneious R11. Generated contigs were concatenated
into larger ones using the Repeat Finder function in
Geneious R11. The original data were again mapped to the
larger contigs to extend their boundaries until all contigs
were able to concatenate to one contig. The inverted repeat
(IR) region was determined using the Repeat Finder function
in Geneious R11 and was inverted and copied to obtain the
complete chloroplast sequence. DOGMA program was used
for annotation of the complete chloroplast genome (Wyman
et al. 2004) and the annotation was corrected with Geneious
R11 (Kearse et al. 2012). The complete chloroplast genome of
A. cettoana was 153,011 bp in length (MT627324), and the GC
content was 38.2%. Large single-copy (LSC) and small single-
copy (SSC) contained 84,669 bp and 18,018 bp, while IRs were
CONTACT Fang Wen wenfang760608@139.com Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute
of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, PR China
ß2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
MITOCHONDRIAL DNA PART B
2021, VOL. 6, NO. 3, 705–707
https://doi.org/10.1080/23802359.2020.1847607

25,162 bp in length. The plastid genome included 79 protein-
coding genes, 29 tRNA genes, and four rRNA genes.
To analyze the phylogenetic position of A. cettoana, the
concatenated sequences of protein-coding genes of A. cet-
toana and 11 other species from Gesneriaceae were aligned
using MAFFT version 7.307 (Katoh and Standley 2013) and 3
species from Labiatae and Acanthaceae were selected as out-
group. A phylogenetic tree (Figure 1) was constructed with
the maximum likelihood (ML) method and the TVM þFþR2
evolutionary model using RAxML (Stamatakis 2014). The
result was congruent with previous studies that established
that Achimenes is a member of the New World Gesneriaceae
(Clark et al. 2012; Weber et al. 2013). The topology of this
molecular tree supports the division of this subfamily and
shows that A. cettoana is a representative of Subtr.
Gloxiniinae and is a sister group of Gesneriinae (Clark et al.
2012). The newly reported chloroplast genome of A. cettoana
allows developing markers for further studies on resolving
the relationship within the Subfam. Gesnerioideae and par-
ticularly, the genus Achimenes.
Acknowledgments
We would like to thank Michael LoFurno (Adjunct Professor, Temple
University, Philadelphia, PA, USA) for his editorial assistance.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Funding
This study was supported by Guilin Science and Technology Foundation.
[20170107-2/20180107-6], Guangxi Science and Technology Project
[Guike AD20159091], Basal Research Fund of GXIB [Guizhiye20009], 21st
Talent project of ‘Ten-Hundred-Thousand’in Guangxi, and the
Foundation of Guangxi Key Laboratory of Plant Conservation and
Restoration Ecology in Karst Terrain [19-050-6].
Data availability statement
The data that support the findings of this study are openly available in
GenBank of NCBI at https://www.ncbi.nlm.nih.gov, reference num-
ber MT627324.
References
Clark JL, Funke MM, Duffy AM, Smith JF. 2012. Phylogeny of a neotrop-
ical clade in the Gesneriaceae: more tales of convergent evolution. Int
J Plant Sci. 173(8):894–916.
Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quan-
tities of fresh leaf material. Phytochem Bull. 19:11–15.
IPNI. 2020. The international plant names index [accessed 3 July 2020].
http://www.ipni.org.
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment soft-
ware version 7: improvements in performance and usability. Mol Biol
Evol. 30(4):772–780.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S,
Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic:
an integrated and extendable desktop software platform for the
organization and analysis of sequence data. Bioinformatics. 28(12):
1647–1649.
Moore HE. 1961. Achimenes cettoana (Gesneriaceae). Baileya. 8:144.
Figure 1. Phylogenetic tree reconstructed by maximum likelihood (ML) analysis based on concatenated sequences of protein-coding genes from 15 taxa of
Lamiales, numbers upon branches are assessed by ML bootstrap.
706 S. LI ET AL.

Roa AR, Skog LE, Ramirez A. 2002. Novae Gesneriaceae neotropicarum X:
a new species of Achimenes from Mexico. Novon. 12(3):382–384.
Roalson EH, Roberts WR. 2016. Distinct processes drive diversification in
different clades of Gesneriaceae. Syst Biol. 65(4):662–684.
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and
post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313.
Tropicos. 2020. Tropicos.org. Missouri botanical garden. [accessed 3 July
2020]. http://www.tropicos.org.
Weber A, Clark JL, M€
oller M. 2013. A new formal classification of
Gesneriaceae. Selbyana. 31(2):68–94.
Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of
organellar genomes with DOGMA. Bioinformatics. 20(17):
3252–3255.
Xin ZB, Fu LF, Fu ZX, Li S, Wei YG, Wen F. 2019. Complete chloroplast
genome sequence of Petrocodon jingxiensis (Gesneriaceae).
Mitochondrial DNA Part B. 4(2):2771–2772.
MITOCHONDRIAL DNA PART B 707