The plastid genome of winter cropping plants Ficus tinctoria (Moraceae)

Abstract

Ficus tinctoria subsp. gibbosa (Blume) Corner is a hemiepiphytic dioecious fig species of the genus Ficus in the family Moraceae. To better determine its phylogenetic location with respect to the other Ficus species, the complete plastid genome of F. tinctoria was sequenced. The whole plastome is 160,342 bp in length, consisting of a pair of inverted repeat (IR) regions of 25,859 bp, one large single-copy (LSC) region of 88,526 bp, and one small single-copy (SSC) region of 20,098 bp. The overall GC content of the whole plastome is 35.9%. Further, maximum likelihood (ML) phylogenetic analyze was conducted using 23 complete fig plastomes, which support close relationships among F. tinctoria, F. heteropleura, F. obscura, and F. deltoidea.

Keywords:

• Ficus tinctoria
• chloroplast genome
• phylogenetic analysis

Ficus tinctoria subsp. gibbosa (Blume) Corner, a hemiepiphytic species distributed in tropical and subtropical areas of much of Asia, was assigned to subgenus Sycidium in the family Moraceae (Berg and Corner 2005). In contrast to other figs of seasonal climates, which have low production in winter, both sexes of F. tinctoria produce major crops at the coldest time of the year (Chen et al. 2015). This unique phenological strategy has evolved to maximize seed dispersal and establishment in seasonal climate (Chen et al. 2015). For a better understanding of the relationships of F. tinctoria and other fig species, it is necessary to reconstruct a phylogenetic tree based on high-throughput sequencing approaches.

Fresh young leaves of F. tinctoria in Xishuangbanna (Yunnan, China; Long. 101.2611 E, Lat. 21.9275 N, 555 m) were picked for DNA extraction (Doyle and Dickson1987). The voucher was deposited at the Biodiversity Research Group of Xishuangbanna Tropical Botanical Garden (Accession Number: XTBG-BRG-10002). The whole plastid genome was sequenced following Zhang et al. (2016), and their 15 universal primer pairs were used to perform long-range PCR for next-generation sequencing. The contigs were aligned with the cp genomes of relatively related species and annotated in Geneious version 4.8.

The plastome of F. tinctoria (LAU10102), with a length of 160,342 bp, was 869 bp larger than that of F. racemosa (159,473 bp, KT368151). It was also 32, 260, and 285 bp smaller than that of F. hirta (160,374 bp, MN364706), F. carica (160,602 bp, KY635880), and F. religiosa (160,627 bp, KY416513). The length of the inverted repeats (IRs), large single-copy (LSC), and small single-copy (SSC) regions of F. altissima was 25,859, 88,526, and 20,098 bp, respectively. The overall G + C content is 35.9% (LSC, 33.6%; SSC, 2.9%; IR, 42.6%).

Furthermore, based on 23 published plastid genome sequences (Bruun-Lund et al. 2017), we reconstructed a phylogenetic tree (Figure 1) to confirm the evolutionary relationship between F. tinctoria and other species with published plastomes in Ficus. Maximum likelihood (ML) phylogenetic analyses were performed base on GTR + F+R2 model in the iqtree version 1.6.7 program with 1000 bootstrap replicates (Nguyen et al. 2015). The ML phylogenetic tree with 42–100% bootstrap values at each node supported that F. tinctoria was closely related to and F. heteropleura, F. obscura, and F. deltoidea.

Figure 1. The ML phylogenetic tree for F. tinctoria based on other 22 species plastid genomes.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the finding of this study are openly available in Moraceae Chloroplast Genome Database (http://lcgdb.wordpress.com). Accession number is LAU10102.

Additional information

Funding

This work was supported by [Yunnan Agricultural Foundation Projects] under grant [Number: 2017FG001 (-051)]; [The Project of Key Laboratory of Insect Resources Conservation and Utilization in Western Yunnan] under grant [Number: YJF(2019)No.57].