Biodiversity Data Journal 9: e62395 CO) doi: 10.3897/BDJ.9.e62395 open access Research Article Complete mitochondrial DNA sequence of the Psammocora profundacella (Scleractinia, Psammocoridae): mitogenome characterisation and phylogenetic implications Peng Tian?, Jiaguang Xiaot, Zhiyu Jia*, Feng Guot, Xiaolei Wang?, Wei Wang, Jianjia Wang}, Dingyong Huangt, Wentao Niu* $ Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Corresponding author: Peng Tian (tianpeng1230@163.com), Jiaguang Xiao (xiaojiaguang@tio.org.cn), Wentao Niu (wentaoniu@tio.org.cn) Academic editor: Danwei Huang Received: 23 Dec 2020 | Accepted: 13 Apr 2021 | Published: 19 Apr 2021 Citation: Tian P, Xiao J, Jia Z, Guo F, Wang X, Wang W, Wang J, Huang D, Niu W (2021) Complete mitochondrial DNA sequence of the Psammocora profundacella (Scleractinia, Psammocoridae): mitogenome characterisation and phylogenetic implications. Biodiversity Data Journal 9: e62395. https://doi.org/10.3897/BDJ.9.e62395 Abstract Complete mitochondrial DNA sequence data have played a significant role in phylogenetic and evolutionary studies of scleractinian corals. In this study, the complete mitogenome of Psammocora profundacella Gardiner, 1898, collected from Guangdong Province, China, was sequenced by next-generation sequencing for the first time. Psammocora profundacella is the first species for which a mitogenome has been sequenced in the family Psammocoridae. The length of its assembled mitogenome sequence was 16,274 bp, including 13 protein-coding genes, two tRNAs and two rRNAs. Its gene content and gene order were consistent with the other Scleractinia species. All genes were encoded on the H strand and the GC content of the mitochondrial genome was 30.49%. Gene content and order were consistent with the other Scleractinia species. Based on 13 protein-coding genes, Maximum Likelihood phylogenetic analysis showed that P profundacella belongs to the “Robust” clade. Mitochondrial genome data provide important molecular information for © Tian P et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 2 Tian P etal understanding the phylogeny of stony corals. More variable markers and additional species should be sequenced to confirm the evolutionary relationships of Scleractinia in the future. Keywords evolutionary relationships, mitochondrial genome, next-generation sequence (NGS), phylogenetics Introduction Scleractinia (Cnidaria, Anthozoa), including numerous hermatypic corals, have always been highlighted by ecologists and taxonomists for their important role in maintaining the balance of ecosystems in shallow tropical and subtropical seas (Fukami et al. 2000). Traditionally, reef-building corals were described, using morphological characteristics of their skeletons, whereas the skeletal structures, especially of colonial corals, can be extremely variable due to environment-induced phenotypic plasticity. In addition, it was difficult to discriminate cryptic species and species that have arisen via introgression or hybridisation without genetic and ecological data (Niu et al. 2018,Combosch and Vollmer 2015, Richards and Hobbs 2015). Molecular technologies have changed the taxonomic landscape and the integration of morphological and molecular analyses have promoted a more rigorous classification and precise phylogeny of stony corals (Kitahara et al. 2016). Though mitochondrial genes have been known for producing erroneous phylogenetic inferences amongst anthozoans, mitochondrial phylogenies of scleractinians may still provide insight into mitochondrial and gene evolution and may provide preliminary insights into evolutionary relationships (Lin et al. 2014). Cnidarian mitogenome data contain important phylogenetic information for understanding its evolutionary history (Kayal et al. 2013). Single or multiple gene analysis of mitochondrial genes have been used to infer phylogenetic relationships amongst scleractinians (Arrigoni et al. 2020, Kitahara et al. 2016). Data of complete mitochondrial genomes have also become important sources for assessing scleractinian phylogenies due to the declining cost of next-generation sequencing (NGS) technologies (Jex et al. 2010, Niu et al. 2018, Schuster 2008). Nevertheless, there are more than 1600 species, whereas only approximately 100 complete mitogenomes of Scleractinia species have been collected in NCBI (https:/www.ncbi.nim. nih.gov/) to date (Hoeksema and Cairns 2020). Psammocora profundacella Gardiner, 1898 is a species of small-polyp stony coral with grey, brown, tan or cream colours, belonging to the family Psammocoridae (Chevalier and Beauvais 1987). Its colonies are sub-massive or encrusting, corallites are in short valleys and walls are rounded, although they may have a central ridge. Petaloid septa and enclosed petaloid septa are always present and rice-grain shaped (Benzoni et al. 2010, Benzoni et al. 2007). There is only one genus, Psammocora Dana 1846, in the Complete mitochondrial DNA sequence of the Psammocora profundacella (Scleractinia, ... 3 Psammocoridae and is widely distributed in the Indo-Pacific. It had been placed in the family Siderastreidae until Benzoni et al. (2007) published strong evidence to distinguish Psammocora from other siderastreids and resurrected Psammocoridae to accommodate this genus. Benzoni et al. (2010) revised all 24 species in Psammocora, reducing the number to seven species using a combination of morphological and molecular analyses; subsequently, Randall (2015) identified a new species, Psammocora eldredgei. In the present research, the complete mitochondrial genome of P. profundacella was sequenced using NGS and its genome structure was analysed for the first time. Simultaneously, it was also the first species within the family PSammocoridae for which the mitogenome had been sequenced. The phylogenetic analyses of P. profundacella, based on protein coding genes (PCGs) of the mitogenome, combined with 81 other scleractinians, will help determine its taxonomic status and facilitate further study on stony coral evolutionary and phylogenetic relationships. Material and methods Sample collection and genomic DNA extraction A specimen of P. profundacella (Fig. 1) was collected from Yangmeikeng of Daya Bay in Guangdong Province and it was kept in our Coral Sample Repository with a special code, 20190718-D17. Identification was conducted according to the description of Benzoni et al. (2010): calices are between 1.4 and 1.7 mm in diameter, the columella is made of one central process surrounded by 4-6 granules positioned at the inner end of the septa and up to 6 septa reaching the fossa are petaloid. Complete genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Shanghai, China). Electrophoresis with 1% agarose gel was used to measure the integrity of the genomic DNA and the spectrophotometer NanoDrop 2000 (Thermo Scientific, USA) was used to measure the genomic DNA concentration. Genome sequence assembly and analyses After DNA extraction and quality detection, the sequencing library was produced using the Illumina Truseq™ DNA Sample Preparation Kit (Illumina, San Diego, USA) according to the manufacturer's recommendations. Five ug of double-stranded DNA was sheared to ~ 300 bp using a M200 Focused-ultrasonicator (Covaris, Woburn, MA, USA). The prepared library was loaded on the Illumina HiSeq X Ten platform for PE 2 x 150 bp sequencing. The quality and quantity of data were assessed by FastQC (Andrews 2010). Filtered clean reads were obtained by removing reads containing poly-N regions, adapters and by eliminating low-quality reads using fastp (Chen et al. 2018). The median of insert sizes and average read length were used to reconstruct the mitochondrial genome via NOVOPIlasty 3.8.3 (Nicolas et al. 2016). A total of 60,910 of 128,526,740 raw reads (approximately 0.05%) were de novo assembled to produce the mitogenome with the guidance of seed sequence and the average coverage was 565x. 4 Tian P etal ’ Figure 1. EES Photos of P profundacella in this study. (A) In-situ photograph of P. profundacella; (B) Skeleton photograph of P. profundacella; (C) Microskeletal photograph of P. profundacella. Mitogenome analyses The circularised contig was submitted to MITOS (Bernt et al. 2013) WebServer (http://mitos.bioinf.uni-leipzig.de/index.py) for preliminary mitochondrial genome annotation. We then identified and annotated all 13 PCGs and two rRNA genes by alignments of homologous mitogenomes with other scleractinians that had been reported through BLAST searches in NCBI. All the PCG codon usage and nucleotide frequencies were obtained through Molecular Evolutionary Genetics Analysis software MEGA7 (Kumar et al. 2016). tRNA genes were identified by comparing the results predicted by tRNAscan- SE 2.0, based on its unique cloverleaf secondary structure information and we also validated the result using ARWEN (Laslett and Canback 2008, Lowe and Chan 2016). Phylogenetic analyses The phylogenetic position of P profundacella was inferred using 13 tandem mitogenome PCG sequences (ND5 + ND1 + Cytb + ND2 + ND6 + ATP6 + ND4 + COIll + COIll + ND4L + ND3 + ATP8 + COl) together with 81 other Scleractinia species that we obtained from GenBank (see Suppl. material 1). We used MEGA7 to choose the best-fitting model, based on the Akaike Information Criterion (AIC) and then constructed a Maximum Likelihood (ML) tree with 500 bootstrap replicates. Complete mitochondrial DNA sequence of the Psammocora profundacella (Scleractinia, ... Results and Discussion Characteristics and composition of mitogenome The mitochondrial genome size of P. profundacella (GenBank accession number: MT576637) was 16,274 bp, including 13 PCGs, 2 tRNA (tRNA™* tRNAT?) and 2 rRNA genes (see Table 1,Fig. 2). The mitogenome of P profundacella offered no distinct structure and its gene order, gene identity and gene number were the same as those of published stony coral mitogenomes (Wang et al. 2013). The base composition of complete mitogenome was 26.34% A, 11.32% C, 19.17 G and 43.17% T, which showed a higher AT content (69.51%) than GC content (30.49%) (see Fig. 3, Table 2). In addition, all genes remained encoded on the H-strand. Table 1. Organisation of the mitochondrial genome of P. profundacella. Gene tRNAMet 16S rRNA ND5 5' ND1 Cyt b ND2 ND6 ATP6 ND4 12S rRNA COIll COll ND4L ND3 ND5 3' tRNATP ATP8 Col Position From 1 233 1970 2813 3768 5110 6214 6774 7451 9000 9906 10842 11564 11833 12230 13329 13421 13669 To 72 1936 2680 3760 4901 6213 6774 7451 8890 9905 10685 11549 11830 12174 13330 13398 13615 15210 Length (bp) Anticodon Codon 72 CAU 1704 711 948 1134 1104 561 678 1440 906 780 708 267 342 1101 70 UCA 195 1542 Start ATG ATG TTA ATT ATG ATG ATG ATG ATG TTG ATG ATG ATG Stop TAA TAA TAA TAA TAA TAG TAA TAG TAA TAA TAG TAA TAA Intergenic nucleotides* 53 Strand Tyry roy ry Tye] oC] rT] Ty CT Cy Ty Ty CT] rT] ty ct] Notes: * Data are numbers of nucleotides between the given gene and its previous gene, negative numbers indicate overlapping nucleotides; H indicated that the genes are transcribed on the heavy strand. 6 Tian P etal Table 2. Nucleotide composition in different regions of mitochondrial genome of P. profundacella. Gene/Region T(%) C(%) A(%) G(%) At+T(%) Size (bp) ND5 47.46 10.65 23.84 18.05 71.30 1812 ND1 45.89 11.18 23.21 19.73 69.10 948 Cyt b 48.94 10.67 23.99 16.40 72.93 1134 ND2 50.36 10.24 23.19 16.21 73.55 1104 ND6 49.73 10.70 23.89 15.69 73.62 561 ATP6 48.82 11.36 25.07 14.75 73.89 678 ND4 48.19 11.11 22.36 18.33 70.55 1440 COIIl 44.74 13.21 22.31 19.74 67.05 780 COll 40.96 11.44 25.00 22.60 65.96 708 ND4L 43.82 10.49 25.09 20.60 68.91 267 ND3 50.00 9.36 19.01 21.64 69.01 342 ATP8 48.72 8.72 29.74 12.82 78.46 195 Col 42.41 13.16 23.80 20.62 66.21 1542 PCGs 46.80 11.20 23.60 18.40 70.40 11511 Ae 37.00 12.60 23.20 27.00 60.20 3837 2 48.19 17.96 18.37 15.48 66.56 3837 ort 55.07 3.15 29.11 12.67 84.18 3837 tRNA 26.06 19.01 30.28 24.65 56.34 142 rRNA 33.98 10.15 37.32 18.54 71.30 2610 Overall 43.17 11.32 26.34 19.17 69.51 16274 q NDI NDS 3". | simp | —~ } | ile \ \\q | Psammocora nierstraszi *\ | Bi 16,274 bp mene a ye 5 \ ue Jt /// f é sont. Figure 2. EES] The mitochondrial genome of P. profundacella. Gene order and positions are shown. COl, COIIl and COlll refer to the cytochrome oxidase subunits, Cyt b refers to cytochrome b and ND1-ND6 refers to NADH dehydrogenase components. All the genes are encoded on the H- strand. Complete mitochondrial DNA sequence of the Psammocora profundacella (Scleractinia, ... 7 60.00 @1(%) BC(%) BA(%) BH G(%) 50.00 40.00 30.00 20.00 NL WL MT Le A all al 0.00 @ p PCGs 1st 2st 3st tRNA rRNA Overall Figure 3. EES Codon usage bias in different regions of mitochondrial genome of P. profundacella. Protein-coding genes and its codon usages The length of all 13 protein-coding genes sequence was 11,511 bp, with base composition of 23.6%, 11.2%, 18.4% and 46.8% for A, C, G and T, respectively. ND5 gene had an intron insertion of 9,549 bp. The start codon of all PCGs used ATG, except for Cyt b using TTA and ND2 using ATT. Three PCGs (COII, ND4 and ND5) terminated with TAG, the other ten PCGs (ATP6, Cyt 6, ND1, ND2, ND3, ND4L, ND6, ATP8, COIl and COIII) stopping with TAA. The shortest gene was ATP8 (195 bp) and the longest gene was ND5 (1,812 bp). The intergenic region between cytb and ND2 was 208 bp (see Table 1). According to the results of Al-skew and GC-skew analysis (Fig. 4), all PCGs showed a stronger nucleotide asymmetry, with AT-skew higher than GC-skew. Amongst L, F, V, G and S, codon use frequency was higher, accounting for 52.5% of a total of 3837 codons. Amongst the 20 amino acids, the majority were were non-polar amino acids which accounted for 68.0%; the minority were polarity-charged amino acids accounting for 11.1% and the remainder were polar amino acids which accounted for 20.5% (Fig. 5). —@— AT skew 0.5 —®— GC skew 0.4 0.3 0.2 0.1 0.0 01 ND5 ND1i CYTB ND2 NDO6 ATP6 ND4 COoOlll COll ND4t ND3 ATPS8 col 0.2 -0.3 -0.4 -0.5 Figure 4. EES] The PCGs’ AT-skew and GC-skew of mitochondrial genome of P. profundacella. 8 Tian P etal 16.0% 15.14% 14.0% 13.19% 8.0% 6.0% 3.49% 3.60% 4.0% 2.74% 2.95% 1.93% 1.829 4% i I L I 1 1 [ 1 0.0% li "T ~ Qh Phe(F) Leu(L) tle(l) Met(M) Val(V) Ser(S) Thr(T) Ala(A) Tyr(Y) His(H) Gln(Q) Asr ys(K) Asp(D) Glu(E) ) (W) Arg(R) Gly(G Figure 5. | doi | The PCGs’ codons use frequency of mitochondrial genome of P. profundacella. rRNA and tRNA genes The encoding genes 12S and 16S rRNA in P profundacella were 906 bp and 1,704 bp in size, respectively. Both the two rRNAs’ base composition was 37.32% A, 10.15% C, 18.54% G and 33.98% T. There were also two tRNA encoding genes- tRNA™®t (72 bp) and tRNA? (70 bp). They were folded into the classic cloverleaf structure which included an amino acid accept arm, DHU loop, anticodon loop and TwC loop (Fig. 6). Amino acid accept arm tRNA-Trp ot UYU bees TYC loop Anticodon loop Figure 6. EESl Putative secondary structures of two tRNA of P. profundacella. Phylogenetic analyses The ML tree topology of the 82 stony corals species showed that P profundacella belongs to the “Robust” clade and is closely related to Polycyathus chaishanensis (Caryophylliidae) with high bootstrap support (Fig. 7). These findings are consistent with the results of Lin et al. (2012), which clearly showed that Polycyathus chaishanensis is closely related to a clade comprising Psammocora, Coscinaraea, Leptastrea and Fungiidae. The mitochondrial genome data have provided important molecular information for understanding evolutionary relationships amongst stony corals, but more variable markers and additional Complete mitochondrial DNA sequence of the Psammocora profundacella (Scleractinia, ... 9 species should be sequenced to confirm the evolutionary relationships of Scleractinia in the future. Acropora humilis Acropora muricata Acropora hyacinthus Acropora horrida Acropora aculeus Acropora divaricata Acropora robusta Acroporidae Isopora togianensis 10 -— Euphyliia ancora a Fimbriaphyilia ancora. | Euphyillidae Galaxea fascicularis =| co somes eo | milis 100 Pavona ciavus age 100 Pavona decussate 100 Pseudosiderastrea formosa 100 Pseudosiderastrea tayami Siderastreidae Siderastrea radians -————_ Fungiacyathus stephanus Funglacyathidae —— 9 Tubastraea coccinea Tubastraea tagusensis Dendrophyilia arbuscula Dendrophyiiia cribrose «| D®4rophyiliidae Turbinaria bifrons Turbinaria pettata Gontopora columna Goniopora djiboutiensis Porites fontanesti Porites panamensis Gardineria hawaliensis Gardineriidae Se Letepsammia formosissima =) Letepsammia superstes Micrabaciidae 100 Rhombopsammia niphada Paraconotrochus antarcticus Caryophylilidae 100 Desmophylium pertusum a Lophelia pertusa a Desmophylium dianthus nee res Solenosmilia variabilis 1 or Seriatopora hystrix i \— Seriatopora caliendrum 100} Stylophora pistiliata -— Pociliopora eydoux! ocilloporidze Be in \— Pocillopora damicomis ; —| |__________ Madracis mirabitis u—__—_—__—_ Madrepora oculata Oculinidae ‘| 100 -— @ Psammocora profundacelia Psammocoridae L Polycyathus chaishanensis Caryophylliidae I at nar Astrangia poculata =. Rhtzangiidae _| spe Piesiastrea versipora Plesiastreidae ead | 100 Mussa angulosa | Colpophyitia natens _|Faviktae _)| —_______—- Echinophyilia aspera _ Lobophyliliidae | 1 — Orbicella faveolata Orbicella franksi Orbicella annularis Merulinidae Figure 7. EES Inferred phylogenetic relationships, based on the concatenated nucleotide sequences of 13 mitochondrial PCGs, using Maximum Likelihood (ML) analysis. Numbers on branches are bootstrap percentages. Conclusions The complete mitochondrial genome of P. profundacella was sequenced for the first time and it was also the first species in the family Psammocoridae whose mitogenome had been sequenced. The mitogenome of FP. profundacella is 16,274 bp in size and shows 10 Tian P etal similar gene order and gene composition with other scleractinian mitogenomes. The phylogenetic analysis of P profundacella, on the basis of its mitochondrial protein-coding genes along with 81 other scleractinians, while preliminary, will help facilitate further studies on stony coral evolutionary and phylogenetic relationships. Acknowledgements The authors would like to thank Prof. Changfeng Dai and Prof. Francesca Benzoni for their help in morphological identification. We also thank Yordanka Banalieva for her help in linguistic modification. The corresponding authors also thank reviewers for their comments, which were very helpful in revising the manuscript. This study was funded by the National Natural Science Foundation of China (grant number 42006128; 42006085; 42006098) and the Scientific Research Foundation of Third Institute of Oceanography, Ministry of Natural Resources (grant number 2020006; 2020005). Author contributions Peng Tian, Jiaguang Xiao and Wentao Niu conceived, designed and performed the study. 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Mitochondrial DNA 24 (3): 194-195. https://doi.org/10.3109/ 19401736.2012.744981 Supplementary material Suppl. material 1: Representative Scleractinia species included in this study for comparison EE} Authors: Peng Tian Data type: genomic Download file (130.67 kb)