A systematic comparison of eight new plastome sequences from Ipomoea L

Sampling and DNA extraction

Total genomic DNA was extracted from eight species for sequencing (Table 1). The seeds of I. trifida (CIP 460377) were provided by the International Potato Center (Lima, Peru), those of I. triloba (NCNSP0323) were provided by North Carolina State University, and the rest were provided by the US National Plant Germplasm System (images of three species are shown in Supplementary Figures). Plants were grown in the greenhouse of the Xuzhou Sweet Potato Research Centre in China. Young leaves were collected from one plant of each species and were subsequently frozen in liquid nitrogen and stored at −80 °C until further use. Total genomic DNA was extracted using the Takara miniBEST plant genomic DNA extraction kit (Dalian, China). The integrity of genomic DNA was assessed by performing gel electrophoresis using a 1% agarose gel.

Chloroplast genome assembling and annotation

We constructed genomic libraries using the TruSeq DNA Nano kit with a DNA insert size of 350 bp. Sequencing was conducted on the Illumina X Ten platform, which generated at least 21 Gb raw data from each species. Sequence data were quality trimmed using SOAPnuke (with the options: -n 0.1 -| 20 –q 0.1 -5 1) (Chen et al., 2018). Sequences were assembled into contigs according to the protocol described by Hahn, Bachmann & Chevreux (2013) using MIRA sequence assembler software (default settings) with the reference genome I. trifida (accession number: KF242476.1). The reads were blasted into contigs with perl scripts and contigs were extended to obtain the complete sequence. Finally, we blasted the reads to the complete sequence, detected the coverage of reads and manually corrected the sequence. The services of library construction, sequencing, and assembly were provided by Macrogen (http://www.macrogencn.com/sy, Shenzhen, China).

The eight chloroplast genome sequences were initially annotated using the online CpGAVAS (Liu et al., 2012) software with default settings, and then manually corrected using Genious 11.0.5. The circular chloroplast genome maps were constructed using the OrganellarGenome DRAW tool (Lohse, Drechsel & Bock, 2007).

Repeat structure analysis

Simple sequence repeats (SSRs) were detected using MISA-web (Beier et al., 2017). Thresholds of 10, six, and four repeat units for mono-, di-, and trinucleotides were used, respectively; while a threshold of three was used for tetra-, penta-, and hexanucleotides, respectively. REPuter (Kurtz et al., 2001) was used to visualize forward, palindrome, reverse, and complementary sequences, with a minimum repeat size of 30 bp and a sequence identity >90%.

Divergence hotspot identification

In order to study the differences among these genomes, the chloroplast genome sequences were aligned using MAFFT v7.307 (Katoh & Toh, 2010) including whole chloroplast genomes, then sliding window analysis was conducted. To calculate the proportion of mutational events, we used a modified formula previously described by Gielly & Taberlet (1994): proportion of mutational events = [(NS + ID)/L] × 100%, where NS, number of nucleotide substitutions; ID, number of indels; L, length of sequence. The step size was set to 400 bp, with an 800 bp window (Fu et al., 2017).

Phylogenetic analysis

We downloaded 32 published Ipomoea chloroplast genomes, and Merremia quinquefolia (KF242501) and Operculina macrocarpa (KF242502) were included in the analysis as the outgroup taxa to perform the phylogenetic analyses (Table S1). Before maximum-likelihood (ML) analyses, 42 chloroplast genomes were aligned using the MAFFT plugin in Geneious 11.0.5. The gaps in the alignment were stripped. ML analyses were performed using RAxML-HPC2 on XSEDE with 1,000 bootstrap replicates and the GTRGAMMA model on CPIRES Science Gateway (Miller, Pfeiffer & Schwartz, 2010) (https://www.phylo.org/).

Genome sequencing and assembly

At least 21 Gb of raw data from each species were generated using Illumina sequencing technology, then through filtering, we obtained 12.58–17.77 Gb of clean data. Using the I. trifida (accession number: KF242476.1) genome as a reference, we obtained the mapped reads. Finally, there were 0.59–1.28 Gb remaining bases and we assembled the chloroplast genomes of eight Ipomoea species using these data. The coverage of chloroplast genomes in each species ranged from 3,664 (in I. splendor-sylvae) to 7,941 (in I. cordatotriloba) (Table S2). All eight newly-sequenced chloroplast genomes were submitted to GenBank (accession numbers: MH173253; MH173254; MH173257; MH173259–MH173263) (Table 1).

Genome features

Genome size and GC content

The chloroplast genome size of the eight Ipomoea species ranged from 161,225 (I. tabascana) to 161,721 bp (I. splendor-sylvae) (Table 2; Fig. 1). These genomes displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,940 bp) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine content is approximately 40.5% in the IR regions, 36.1% in the LSC region, 32.2% in the SSC region, and 37.5% in the entire sequence of all plastomes (Table 2).

Table 2:

The chloroplast genome features of eight newly sequenced Ipomoea species.

	Ipomoea trifida	Ipomoea cynanchifolia	Ipomoea splendor-sylvae	Ipomoea cordatotriloba	Ipomoea lacunosa	Ipomoea X leucantha	Ipomoea tabascana	Ipomoea triloba
Total cpDNA size	161,531	161,386	161,721	161,242	161,446	161,296	161,225	161,269
Length of LSC region	87,606	87,591	88,004	87,581	87,575	87,598	87,583	87,625
Proportion of LSC (%)	54.23	54.27	54.42	54.32	54.24	54.31	54.32	54.33
Length of IR region	30,940	30,882	30,833	30,806	30,910	30,840	30,798	30,810
Proportion of IRs (%)	38.31	38.27	38.13	38.21	38.29	38.24	38.20	38.21
Length of SSC region	12,045	12,031	12,051	12,049	12,051	12,018	12,046	12,024
Proportion of SSC (%)	7.46	7.45	7.45	7.47	7.46	7.45	7.47	7.46
Total GC content (%)	37.52	37.53	37.52	37.55	37.53	37.55	37.55	37.54
LSC	36.1	36.1	36.1	36.2	36.2	36.1	36.1	36.1
IR	40.48	40.52	40.58	40.57	40.5	40.57	40.58	40.58
SSC	32.29	32.32	32.23	32.29	32.28	32.3	32.26	32.24
Total number of genes	121	121	121	121	121	121	121	121
Protein encoding	80	80	80	80	80	80	80	80
tRNA	37	37	37	37	37	37	37	37
rRNA	4	4	4	4	4	4	4	4

DOI: 10.7717/peerj.6563/table-2

Boundary between LSC/SSC and IRs

The junctions of LSC/IRa, SSC/IRa, and LSC/IRb regions are located in the IGS region between rpl23 and trnI; ndhH and ndhF; and trnI and trnH, respectively, and the location of the SSC/IRb junction within the coding region of the ndhA gene made pseudogenes of the ndhA gene of 484 bp in length (Fig. 2). The distance from ndhH to the IRA/SSC boundary and the length of the ndhA gene located in the IRB is the same.

Repetitive sequence analysis

In total, we used 40 Ipomoea species for comparison (Table S1). The number of repetitive sequences in these chloroplast genomes ranged from 57 (I. pedicellaris) to 89 pairs (Table S6). Half of the chloroplast genomes had 88 or 89 pairs of repeats. The forward and palindromic repeats occupied 50.37% and 49.63% of the total repeats, respectively (Figs. 3A and 3C). The number of forward repeats ranged from 19 (I. pes-caprae) to 50 (I. biflora) and the number of palindromic repeats ranged from 28 (I. pedicellaris) to 61 (I. pes-caprae) (Table S6). The most common repetitive sequence lengths were 30–59 bp (58.55%), while those with >140 bp were least abundant (3.40%) (Figs. 3A and 3C). Most of the repeats were located in the ycf1 gene region (most abundant region), ycf2 gene region, and the intergenic regions between trnN-GUU and ycf1 or trnI-CAU and ycf2; all of which were in IR regions. Those repeats distributed in the LSC region were mostly in the accD gene, ycf3 gene, and the intergenic regions between rpl23 and trnI-CAU. We also identified few repeats located in ndhH-ndhF within the SSC regions (Table S6). The separate analysis of the two large clades (Batatas clade and Quamoclit clade) showed similar results with genus Ipomoea (Fig. 3C). Interestingly, the I. nil belonging to the Quamoclit clade was different from the other species. It had 43.2% (38 in 88) repeats distributed in the intergenic regions between ycf2 and trnI-CAU (Table S6).

Simple sequence repeats are tandemly-repeated nucleotides in DNA sequences. We found the Ipomoea chloroplast genomes we analyzed contained 39–64 SSRs. The most common SSRs were mononucleotides which accounted for 70.77%, followed by tetranucleotides which accounted for 16.95% (Figs. 3B and 3D). Almost all of the mononucleotide repeat sequences were comprised of A/T repeats, while the tetranucleotides varied among different species. All the dinucleotide repeats were AT/TA repeats comprising 1.51% of the total SSRs. The proportion of pentanucleotides and hexanucleotides were 3.56% and 1.78%, respectively, while not all the species had them. Trinucleotides accounted for 0.40% in all the SSRs and were the least abundant, with only 10 trinucleotides detected across all the 40 Ipomoea species (Figs. 3B and 3D). Except for the mononucleotides and dinucleotides, five tetranucleotide repeats (AATA, CAAT, GAAA, TATC, and TTTC) were shared in the Quamoclit clade (Table S7). In the Batatas clade, more tetranucleotides were shared including AAAT, AATA, AGAT, ATAG, CAAT, GAAA, TATC, and TTTC. The tetranucleotide GAAA was only absent in I. splendor-sylvae (Table S7). In addition, the pentanucleotides (TTCTA) were present in 93.7% (15/16) and the hexanucleotides were present in 81.2% (13/16) of the Batatas clade. SSRs are different from the repetitive sequences identified by REPuter; they are almost all located in LSC regions (Table S7).

Divergence hotspot regions

We conducted divergence analysis of the Ipomoea genus, including 40 species. Additionally, separate analysis in the Batatas group (16 species) and Quamoclit group (10 species) were conducted. Across the Ipomoea genus, the percentage of identical sites was 78.5%. The mean value of the variation was 5.12% and six regions which had a variation rate >13% were thought to be highly variable regions. Five of them were intergenic regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ) and one was in a gene coding region (ndhF) (Fig. 4A). Except rps16-trnQ which was located in the LSC region, all other highly variable regions were located in the SSC region.

In the Batatas group, the percentage of identical sites was 94.8% and the mean value of the variation was 1.26%. The regions with a variation rate >3.2% were considered to be highly variable regions. They were trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3 (Fig. 4B). One of these was located in the IRA/SSC boundary (ndhH-ndhF), three of eight were located in the LSC region, and four of them were located in the SSC region (rpl32-trnL, ndhA intron, ndhF-rpl32, and ccsA-ndhD).

In the Quamoclit group, 10 species showed highly consistent sequences, with 92.0% identical sites. The mean value of variation was 2.66%. Eight relatively high variable regions with a variation rate >7.5% were detected, including ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG (Fig. 4C). Two of them were in the SSC region (rpl32-trnL, ndhA intron), the others were located in the LSC region, and all of them were from non-coding regions.

Phylogenetic analysis

The phylogenetic tree was constructed based on 40 Ipomoea whole chloroplast genomes, using M. quinquefolia (KF242501) and O. macrocarpa (KF242502) as outgroups (Fig. 5). These 40 Ipomoea species were divided into two major clades and were further divided into seven small clades with strong support values, including Batatas, Murucoides, Pes-caprae, Quamoclit, Cairica, Obscura, and Pes-tigridis (Eserman et al., 2014). The Cairica, Pes-tigridis, and Obscura groups formed one major clade and the other four groups formed another clade. The support value for the Cairica clade was lower than those of other small clades. Among these seven groups, two larger groups, Quamoclit and Batatas, included the most species. Ipomoea setosa and I. sepacuitensis were located as the sister group of I. ser. Batatas and constituted the Batatas group. In I. ser. Batatas, I. splendor-sylvae was located at the most basal position. In the Quamoclit group, I. dumetorum was clustered as the sister group with others.

Variations among the Ipomoea species

In the present study, eight chloroplast genomes in I. ser. Batatas were assembled. They were highly conserved in terms of genome structure and size. They displayed a typical quadripartite structure and length of the chloroplast genome sequence in the eight-wild species, ranging from 161,225 to 161,721 bp. The expansion or contraction of IR regions was thought to be the main reason for the divergences in chloroplast genome size (Ravi et al., 2008). Two models were proposed to explain the expansion of the IR region. Gene conversion is used to explain the small IR expansion and movements, and double-strand DNA breaks and recombination were considered to be the reason for major IR expansion (Goulding et al., 1996). Among the eight species, the LSC/IRa/SSC/IRb boundary genes were highly conserved, with slight structural variations and there was no significant expansion/contraction of IRs among these species. According to the studies conducted by Eserman et al. (2014), the SC/IR boundary was highly conserved even across the whole tribe Ipomoeeae with some exceptions only occurring in a few species. Our eight chloroplast genomes contained 121 genes and the infA gene, which encodes a translation initiation factor and is almost lost in all rosid species, has also been lost in our species (Millen et al., 2001; Gitzendanner et al., 2018).

Repeat motifs are thought to have a significant impact on genome phylogeny and rearrangement (Yue et al., 2008). Larger and more complex repeat sequences may play an important role in the rearrangement of chloroplast genomes and sequence divergence (Timme et al., 2007; Weng et al., 2014). Here, we conducted repeat analysis in 40 Ipomoea species and separate analyses in the Batatas and Quamoclit groups. In Ipomoea, only forward and palindromic repeats were found, and they were almost equal in measure in each species. The repeats distributed mainly in the ycf1 and ycf2 genes. Interestingly, I. pes-caprae had 19 forward repeats and 61 palindromic repeats; in I. nil, 43.2% of repeats were located in the ycf2 -trnI-CAU region rather than in the ycf1 and ycf2 genes. Additionally, in contrast with the Quamoclit group, the Batatas group had a slightly higher proportion of 30–59 bp repeats and a lower proportion of 60–79 bp and >140 bp repeats.

We also investigated and compared the numbers and distributions of SSRs across the 40 Ipomoea species. Compared with the long repeats, the SSRs were distributed more widely throughout the chloroplast genomes and were usually located in LSC regions. Most of the SSRs were found in non-coding regions; only a few were located in the coding regions (e.g., rpoC2, rpoB, atpB, ycf1, ycf2, and ndhF). The predominant type of SSRs were mononucleotides and almost all of them were A or T repeats. This is consistent with the previous findings that suggested that chloroplast SSRs are generally comprised of short polyA or polyT repeats and rarely contain tandem G or C repeats (Kuang et al., 2011). By comparing the Quamoclit and Batatas groups, extremely rare trinucleotides were detected in the Batatas group (0.1%) and rare hexanucleotides were detected in the Quamoclit group (0.89%). Because of the high polymorphism of SSRs in the chloroplast genome, SSRs are potentially important molecular markers in the analysis of plant population genetics as well as evolutionary and ecological studies (Kuang et al., 2011). In sweet potato, chloroplast SSRs ((A)_n and (T)_n) combined with nuclear SSRs have been used to investigate the genetic diversity of sweet potato and further provided strong support for the prehistoric transfer of sweet potato (Roullier et al., 2011, 2013a).

In addition, nucleotide substitution (SNVs, indels, and proportions of variability) may play a critical role in plant evolutionary processes. We conducted three independent analyses which included one in the Ipomoea genus and two in small clades (Batatas and Quamoclit groups) and they showed different divergence regions. Only two regions presented in all the three analyses—rpl32-trnL and ndhA intron. One of them (rpl32 -trnL) has been used in previous studies to disentangle the origins of sweet potato (Roullier et al., 2013b). Like other angiosperms (Liu et al., 2017), the IR regions were more conserved than the SC regions in Ipomoea chloroplast genomes. This phenomenon possibly occurred because of copy correction between IR sequences by gene conversion (Khakhlova & Bock, 2006).

Phylogenetic relationships

The phylogenetic relationships in tribe Ipomoeeae have been constructed based on whole chloroplast genomes of 30 species including Ipomoea and nine other genera (Eserman et al., 2014). Here, we constructed a phylogenetic tree of the Ipomoea with 21 chloroplast genomes downloaded from GenBank, eleven from Muñoz-Rodríguez’s group’s research (Muñoz-Rodríguez et al., 2018), and our eight chloroplast genomes. Our results also divided the 40 Ipomoea species into seven groups that confirmed previous studies (Eserman et al., 2014). Determination of taxonomy and species in I. ser. Batatas is particularly difficult because individuals often exhibit intermediate morphologies between descriptions of named species (McDonald & Austin, 1990; Austin, 1978), and several species may be of hybrid origin (Diaz, Schmiediche & Austin, 1996). Phylogenetic analysis in I. ser. Batatas has been performed using DNA markers, such as RFLP, RAPD, ISSR, chloroplast restriction site variation, gene sequences, and morphological analyses (Rajapakse et al., 2004; Huang & Sun, 2000; Jarret & Austin, 1994; Jarret, Gawel & Whittemore, 1992). These studies have indicated the phylogenetic relationships between sweet potato and its wild relatives; however, the support values were low. The latest study conducted by Muñoz-Rodríguez et al. (2018) presented strong support for the relationships in this series based on the amounts of chloroplast genomes and nuclear data. Our studies showed a similar result as that shown in a study by Muñoz-Rodríguez et al. (2018), which suggested that the chloroplast genome is a very useful tool for resolving the phylogenetic relationships of I. ser. Batatas. Ipomoea setosa and I. sepacuitensis were clustered, and together with I. ser. Batatas formed the Batatas group. The taxonomy of the Quamoclit clade was mostly consistent with the ITS phylogeny (Miller, McDonald & Manos, 2004); for example, I. indica was more closely related to I. nil than I. purpurea. Conversely, I. alba grouped with I. tricolor rather than with I. nil or I. purpurea.