Corresponding author: Lingfeng Kong (
Academic editor: M. Haase
In this study,
Qi L, Kong L, Li Q (2020) Redescription of
The
Samples were collected from a mud flat in the Yellow River estuary (
Library construction and sequencing were performed by Beijing Novogene Technology Co., Ltd (China) from total genomic DNA on the HiSeq X platform (Illumina Inc.) with 150-bp paired-end reads. Raw data were initially quality-trimmed using Trimmomatic v0.36 (
No mitochondrial genomes of stenothyrids were available from GenBank, so we reconstructed the phylogenetic trees of the genus
GenBank accession numbers for specimens included in the molecular analyses. For COI and 16S, see GenBank accession number of the mitochondrial genome (
Family | Species | COI | 16S | 28S |
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The best partition schemes and best-fit models of substitution for the data sets for phylogenetic analyses were identified using Partition Finder 2 (
Phylogenetic analyses were carried out using maximum likelihood (
The best partition schemes and best-fit models of substitution for the data sets.
Data set | Set Partition | Best Model |
---|---|---|
Best Partition to rRNA genes | 16s | GTR+I+G |
28s | GTR+I+G | |
Best Partition to COI |
cox1 1th | GTR+I |
cox1 2th | F81 | |
cox1 3th | HKY+G |
China • 4, specimens; Shandong province, Dongying, Yellow River estuary mud flat;
“S. testa oblonga, laevi, polita, semipellucida, aurantiaca; anfractibus 4½, convexis, supremis transversim obsolete striates; suturis marginatis; peritremate continuo; anfraetu ultimo ad aperturam concentrice striato” (A.
Shell ovate, dorso-ventrally compressed, with well-inflated body whorl and narrowly constricted aperture, without dotted spiral lines. Dome-shaped, smooth protoconch (1¾ whorls) with some pits. Posterior foot pointed, with metapodial tentacle.
Estuary of the Pei-ho River (also known as the Hai River in the current name), North China.
From Fujian to Hebei on coast of China (A.
Inhabiting on the surface of mud flat or attaching to the under-surface of floating leaves in the freshwater estuary.
The type locality of
The radular morphology is one of the diagnostic morphological characters, but the Rachidian tooth and general radular shape of
The pairwise distance between species or non-conspecific subspecies ranged from 9.1% (
Pairwise
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0.109 | ||||||||||
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0.135 | 0.129 | |||||||||
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0.135 | 0.138 | 0.152 | ||||||||
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0.126 | 0.132 | 0.141 | 0.149 | |||||||
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0.105 | 0.109 | 0.126 | 0.146 | 0.057 | ||||||
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0.121 | 0.120 | 0.141 | 0.155 | 0.049 | 0.052 | |||||
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0.118 | 0.091 | 0.132 | 0.146 | 0.111 | 0.097 | 0.109 | ||||
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0.126 | 0.121 | 0.123 | 0.151 | 0.161 | 0.136 | 0.148 | 0.123 | |||
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0.132 | 0.106 | 0.108 | 0.141 | 0.133 | 0.120 | 0.138 | 0.109 | 0.124 | ||
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0.135 | 0.114 | 0.103 | 0.139 | 0.135 | 0.126 | 0.141 | 0.109 | 0.133 | 0.030 | |
0.117 | 0.118 | 0.118 | 0.129 | 0.136 | 0.115 | 0.126 | 0.115 | 0.112 | 0.120 | 0.114 |
The circular mitogenome of
Map of the complete mitochondrial genome of
The total length of the concatenated 13
Codon usage, relative synonymous codon usage (
Annotated mitochondrial genome of
Gene | Direction | Position | Size | Intergenic | Condon | Anti-codon | ||
---|---|---|---|---|---|---|---|---|
From | To | Nucleotides | Start | Stop | ||||
trnL2 | F | 1 | 68 | 68 | – | – | – | TAA |
trnL1 | F | 70 | 138 | 69 | 1 | – | – | TAG |
nad1 | F | 139 | 1080 | 942 | 0 | ATG | TAA | – |
trnP | F | 1088 | 1156 | 69 | 7 | – | – | TGG |
nad6 | F | 1158 | 1659 | 502 | 1 | ATG | T | – |
cytb | F | 1660 | 2799 | 1140 | 0 | ATG | TAA | – |
trnS2 | F | 2800 | 2865 | 66 | 0 | – | – | TGA |
trnT | R | 2866 | 2932 | 67 | 0 | – | – | TGT |
nad4L | F | 2937 | 3234 | 297 | 4 | ATG | TAG | – |
nad4 | F | 3228 | 4601 | 1374 | -5 | ATG | TAA | – |
trnH | F | 4603 | 4667 | 65 | 1 | – | – | GTG |
nad5 | F | 4668 | 6392 | 1725 | 0 | ATG | TAA | – |
trnF | F | 6376 | 6443 | 68 | -15 | – | – | GAA |
cox3 | F | 7077 | 7856 | 780 | 633 | ATG | TAA | – |
trnK | F | 7868 | 7934 | 67 | 11 | – | – | TTT |
trnA | F | 7935 | 8002 | 68 | 0 | – | – | TGC |
trnR | F | 8004 | 8072 | 69 | 1 | – | – | TCG |
trnN | F | 8073 | 8141 | 69 | 0 | – | – | GTT |
trnI | F | 8143 | 8210 | 68 | 1 | – | – | GAT |
nad3 | F | 8224 | 8597 | 374 | 13 | TTG | TAA | |
trnS1 | F | 8566 | 8633 | 68 | -30 | – | – | GCT |
nad2 | F | 8634 | 9692 | 1059 | 0 | ATG | TAA | – |
cox1 | F | 9694 | 11229 | 1536 | 1 | ATG | TAA | – |
cox2 | F | 11256 | 11942 | 687 | 26 | ATG | TAA | – |
trnD | F | 11944 | 12012 | 69 | 1 | – | – | GTC |
atp8 | F | 12013 | 12171 | 159 | 0 | ATG | TAA | – |
atp6 | F | 12177 | 12872 | 696 | 5 | ATG | TAA | – |
trnM | R | 12930 | 12996 | 67 | 57 | – | – | CAT |
trnY | R | 13002 | 13066 | 65 | 5 | – | – | GTA |
trnC | R | 13071 | 13134 | 64 | 4 | – | – | GCA |
trnW | R | 13136 | 13201 | 66 | 1 | – | – | TCA |
trnQ | R | 13203 | 13264 | 62 | 1 | – | – | TTG |
trnG | R | 13265 | 13331 | 67 | 0 | – | – | TCC |
trnE | R | 13335 | 13403 | 69 | 3 | – | – | TTC |
rrnS | F | 13404 | 14349 | 873 | 0 | – | – | – |
trnV | F | 14349 | 14415 | 37 | -1 | – | – | TAC |
rrnL | F | 14416 | 15830 | 1415 | 0 |
The sizes of 22
The genes rrnL and rrnS are 1415 bp and 946 bp in size, with 72.6% and 70.3% A+T content, respectively (Table
The nucleotide composition of
Genes or regions | Size | Nucleotides composition (%) | A+T | AT Skew | GC Skew | |||
---|---|---|---|---|---|---|---|---|
T | C | A | G | (%) | ||||
Complete mitogenome | 15830 | 41 | 12.5 | 28.7 | 17.8 | 69.7 | -0.236 | 0.175 |
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11271 | 43 | 13 | 25.9 | 18.2 | 68.9 | -0.248 | 0.167 |
1447 | 33.7 | 13.5 | 34.7 | 18.1 | 68.4 | 0.014 | 0.144 | |
rRNA genes | 2361 | 35.6 | 10.9 | 36.1 | 17.4 | 71.7 | 0.0065 | 0.229 |
lrRNA | 1415 | 36.7 | 10.7 | 35.9 | 16.7 | 72.6 | 0.0107 | 0.216 |
SrRNA | 946 | 33.9 | 11.3 | 36.4 | 18.4 | 70.3 | 0.035 | 0.238 |
A+T-rich region | 633 | 37.4 | 10 | 36.2 | 16.4 | 73.6 | -0.017 | 0.246 |
Phylogenetic reconstruction by
Summary tree from Maximum Likelihood analysis of concatenated COI, 16S and 28S sequences. Support indices are
The phylogenetic analysis of stenothyrids, including most
The redescription of
This research was supported by the National Natural Science Foundation of China (31772414), the Fundamental Research Funds for the Central Universities (201964001) and the National Infrastructure of Fishery Germplasm Resources (2019DKA30470). We thank Dr. Takenori Sasaki from the University of Tokyo, for his advices on the morphological research.
Relative synonymous codon usage (
image
Secondary structure of
doxc