Xiao-Ping Wu

The Complete Maternally and Paternally Inherited Mitochondrial Genomes of the Endangered Freshwater Mussel Solenaia carinatus (Bivalvia: Unionidae) and Implications for Unionidae Taxonomy

Doubly uniparental inheritance (DUI) is an exception to the typical maternal inheritance of mitochondrial (mt) DNA in Metazoa, and found only in some bivalves. In species with DUI, there are two highly divergent gender-associated mt genomes: maternal (F) and paternal (M), which transmit independently and show different tissue localization. Solenaia carinatus is an endangered freshwater mussel species exclusive to Poyang Lake basin, China. Anthropogenic events in the watershed greatly threaten the survival of this species. Nevertheless, the taxonomy of S. carinatus based on shell morphology is confusing, and the subfamilial placement of the genus Solenaia remains unclear. In order to clarify the taxonomic status and discuss the phylogenetic implications of family Unionidae, the entire F and M mt genomes of S. carinatus were sequenced and compared with the mt genomes of diverse freshwater mussel species. The complete F and M mt genomes of S. carinatus are 16716 bp and 17102 bp in size, respectively. The F and M mt genomes of S. carinatus diverge by about 40% in nucleotide sequence and 48% in amino acid sequence. Compared to F counterparts, the M genome shows a more compact structure. Different gene arrangements are found in these two gender-associated mt genomes. Among these, the F genome cox2-rrnS gene order is considered to be a genome-level synapomorphy for female lineage of the subfamily Gonideinae. From maternal and paternal mtDNA perspectives, the phylogenetic analyses of Unionoida indicate that S. carinatus belongs to Gonideinae. The F and M clades in freshwater mussels are reciprocal monophyly. The phylogenetic trees advocate the classification of sampled Unionidae species into four subfamilies: Gonideinae, Ambleminae, Anodontinae, and Unioninae, which is supported by the morphological characteristics of glochidia.

The complete mitochondrial genome of Chinese land snail Mastigeulota kiangsinensis (Gastropoda: Pulmonata: Bradybaenidae)

Abstract Mastigeulota kiangsinensis is an endemic and widespread land snail in China. The complete mitochondrial genome of M. kiangsinensis was first determined using long PCR reactions and primer walking method (accession number KM083123). The genome has a length of 14,029 bp, containing 37 typical mitochondrial genes (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes). The base composition of the whole heavy strand is A 29.48%, T 37.92%, C 14.38% and G 18.22%. Gene order of M. kiangsinensis is identical to Euhadra herklotsi, but gene rearrangements are found compared with other mitochondrial genomes described in Stylommatophora. tRNAThr is located in COIII, which has not been found in other helicoids so far. This new complete mitochondrial genome can be the basic data for further studies on mitogenome comparison, molecular taxonomy and phylogenetic analysis in land snails and Molluscs at large.

Complete maternal mitochondrial genome of freshwater mussel Anodonta lucida (Bivalvia: Unionidae: Anodontinae)

Abstract The taxonomy of genus Anodonta is rather ambiguous, as it has great variation on the shell shape. Anodonta lucida is an endemic species of freshwater mussel in China, characterized by shining epidermis. The complete maternal mitochondrial genome of freshwater mussel A. lucida was first determined (GenBank accession no. KF667529). The genome is 16,285 bp long with an AT content of 64.02%. All the 37 typical animal mitochondrial genes are found, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The genome also contains 24 unassigned regions, ranking from 1 to 830 bp in length, the largest of which is the putative control region (CR). The base composition of the genome is A (36.32%), G (13.01%), T (27.70%) and C (22.98%). Gene order is identical to other species of Unionidae except Gonideinae.

Complete maternal mitochondrial genome of freshwater mussel Aculamprotula tientsinensis (Bivalvia: Unionidae: Unioninae)

Abstract Aculamprotula tientsinensis is a rare and endemic species of freshwater mussel in China. This study firstly determined the complete F-type mitochondrial genome of A. tientsinensis. The circle genome (15 695 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 FORF gene. Except for cob, nad5 and nad6, the remaining protein-coding genes initiate with the orthodox start codon (ATG, ATA, ATT). There are 26 non-coding regions in the mitogenome of A. tientsinensis, ranging in size from 1 to 229 bp. The base composition of the genome is A (37.83%), G (12.69%), T (25.43%) and C (24.06%). Gene order is identical to other female species of Unionidae but for Gonideinae. The phylogenetic analyses of Unionidae indicate that A. tientsinensis is closely related to A. tortuosa and A. coreana, which belong to Unioninae. The complete mitogenome can deepen comparative and evolutionary genomics of Unionidae and be more comprehensive to parse the genetic relationship between the species and the ownership beyond species.

The complete F-type mitochondrial genome of threatened Chinese freshwater mussel Solenaia oleivora (Bivalvia: Unionidae: Gonideinae).

Abstract The freshwater mussel Solenaia oleivora is considered threatened due to anthropogenic habitat modification and pollution. The complete F-type mitochondrial genome (mitogenome) of S. oleivora was first determined (GenBank accession no. KF296320). The length of this mitogenome is 16,392 bp with an AT content of 59.9%. There are 37 typical animal mitochondrial genes and a putative control region. Within the control region, 5 tandem repeats of a 106 bp element were identified. The gene order rearrangement of cox2-rrnS in F-type mitogenome compared to that of other freshwater mussels, is not unique for S. oleivora, but is shared with all other available freshwater mussels in the subfamily Gonideinae. The complete mitogenome can provide a basic data for the further studies on molecular taxonomy, phylogenetic analyses and conservation genetics.

The complete maternal mitochondrial genome of rare Chinese freshwater mussel Lepidodesma languilati (Bivalvia: Unionidae: Unioninae).

Abstract Lepidodesma languilati is considered threatened because of the influence of human activities in China. The complete F-type mitochondrial genome of L. languilati was determined in this study (GenBank accession no. KT381195). It is a 15 754-bp-long circular molecule that consists of 37 genes that are typically found in other invertebrates. The overall base composition of the entire sequence is as follows: A (39.1%), T (25.7%), C (23.4%), and G (11.8%). Except for cox1 (TTG), cob (ATT), nad1 (ATT), nad6 (ATA), nad4 (TTG), and atp8 (GTG), 7 of the 13 protein-coding genes initiate with orthodox ATG start codon. All the 13 protein-coding genes have complete termination codon TAA or TAG. Phylogenetic tree indicates that L. languilati belongs to Unioninae. The newly sequenced complete mitogenome can provide basic data for comparative studies on mitochondrial genomes of Unionidae. It could also lay the important theoretical foundation for phylogenetics, population genetics, germplasm resources protection, sustainable, and reasonable utilization.

The complete F-type mitochondrial genome of Chinese Anodonta arcaeformis (Bivalvia: Unionidae: Anodontinae)

Abstract Anodonta arcaeformis is a Chinese common species. The complete F-type mitochondrial genome was first determined. The complete genome is 15,672 bp in length, with AT content 64.59%. All the 37 typical animal mitochondrial genes were identified, including 13 protein coding genes, 22 tRNA genes and 2 rRNA genes. And a novel FORF (277 bp, 92aa) was found between tRNAGlu and ND2, which was considered to be involved in sex determination. The putative control region (270 bp) is located between ND5 and tRNAGln, with an A + T content of 70.07%. The gene order is identical to other species of Unionidae female mitochondrial except Gonideinae.

The complete mitochondrial genome of Chinese land snail Aegista aubryana (Gastropoda: Pulmonata: Bradybaenidae).

Abstract Aegista aubryana is an endemic land snail in China. The complete mitochondrial genome of A. aubryana was first determined using long PCR reactions and primer walking method (accession number KT192071). The genome has a length of 14 238 bp, containing 37 typical mitochondrial genes (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes). The base composition of the whole heavy strand is A 31.32%, T 37.86%, C 14.46% and G 16.36%. The results of phylogenetic analyses showed that the A. aubryana is most closely related to Mastigeulota kiangsinensis. This new complete mitochondrial genome can be the basic data for further studies on mitogenome comparison, molecular taxonomy and phylogenetic analyses in bradybaenid snails and Molluscs at large.

Genetic diversity analysis of mitochondrial DNA control region in artificially propagated Chinese sucker Myxocyprinus asiaticus.

Abstract The genetic diversity of the three major artificially propagated populations of Chinese sucker, an endangered freshwater fish species, was investigated using the sequences of mitochondrial DNA (mtDNA) control regions. Among the 89 individuals tested, 66 variable sites (7.26%) and 10 haplotypes were detected (Haplotype diversity Hd = 0.805, Nucleotide diversity π = 0.0287). In general, genetic diversity was lower in artificially propagated populations than in wild populations. This reduction in genetic diversity may be due to population bottlenecks, genetic drift and human selection. A stepping-stone pattern of gene flow was detected in the populations studied, showing much higher gene flow between neighbouring populations. To increase the genetic diversity, wild lineages should be introduced, and more lineages should be shared among artificially propagated populations.

Community characteristics of aquatic organisms and management implications after construction of Shihutang Dam in the Gangjiang River, China

ABSTRACT Liu X, Hu X, Ao X, Wu X, Ouyang S. 2017. Community characteristics of aquatic organisms and management implications after construction of Shihutang Dam in the Gangjiang River, China. Lake Reserv Manage. 34:42–57. The Ganjiang River is the largest river in Jiangxi Province, China, and plays a significant role in maintaining and replenishing the aquatic biodiversity for Poyang Lake and the Yangtze River. Understanding the effects of dam construction on aquatic biodiversity is critical because of the increasing number of dams and their adverse environmental impacts on the Ganjiang River. In this study, community structure of aquatic organisms and physicochemical parameters in the Shihutang Dam were investigated during March, July, and December 2015. We found that species number, density, and biomass of phytoplankton upstream of the dam were greater than downstream of the dam. Moreover, analysis of aquatic biodiversity showed that phytoplankton, zooplankton, and macrozoobenthos upstream of the dam were more abundant and richer than downstream of the dam, and fish downstream of the dam were more abundant and the fish community richer than upstream of dam. Fish life habits revealed that resident fish were the dominant species, but the proportion of migratory fish was low. Additionally, species composition of aquatic organisms was related to dissolved oxygen, turbidity, water depth, some nutrients, and velocity, based on redundancy analysis. The study showed that aquatic organism community structure was influenced by the Ganjiang River dam. We therefore proposed a series of dam management strategies, such as establishing artificial fish spawning substrate and implementing eco-hydraulic regulations. These dam management strategies can play an important role in protecting aquatic biodiversity and sustaining the resources in the Ganjiang River.