Table2_Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus).XLS

Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.</p

Table3_Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus).XLS

Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.</p

Table4_Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus).XLS

Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.</p

Table1_Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus).DOCX

Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.</p

Table5_Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus).XLS

Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.</p

DataSheet_1_An Updated Genome Assembly Improves Understanding of the Transcriptional Regulation of Coloration in Midas Cichlid.docx

Midas cichlid (Amphilophus citrinellus), a popular aquarium fish, attracts extensive attention from worldwide biologists mainly due to its morphological polymorphism (dark versus gold). Continuous efforts have therefore been paid to address mechanisms of its coloration variants, while it is far away from the detailed illustration of a clear regulatory network. Some limits may come from the absence of a high-quality genome assembly and a relatively accurate gene set. In this study, we sequenced about 149 Gb of nucleotide sequences of Midas cichlid, generating a genome assembly with a total size of 933.5 Mb, which exhibits a good genome continuity with a contig N50 of 10.5 Mb. A total of 25,911 protein-coding genes were annotated and about 90% completeness was achieved, which helps to build a good gene pool for understanding expressional differences of color variation. With the assistance of the final gene set, we identified a total of 277 differential expressional genes (DEGs), of which 97 up- and 180 downregulated were determined in dark-vs-gold comparisons. Two protein-protein interaction (PPI) networks were constructed from these DEGs, and three key functional modules were classified. Hub genes within each module were evaluated, and we found that the third key module contains tyrp1b, oca2, pmela, tyr, and slc24a5, which were previously proven to be associated with melanin formation. Two downregulated DEGs (myl1 and pgam2) in the first key module may be involved in muscle movement and spermatogenesis, implying that certain side effects could result from the morphological polymorphism. The first key module, consisting of proteins encoded by upregulated DEGs that were associated with MAPK signaling, Toll-like receptor signaling, and gonadotropin-releasing hormone pathways, may contribute to a negative upstream regulation or downstream influence on melanin biosynthesis. Taken together, our new genome assembly and gene annotation of Midas cichlid provide a high-quality genetic resource for biological studies on this species, and the newly identified key networks and hub genes in dark-vs-gold comparisons enhance our understanding of the transcriptional regulatory mechanisms underlying coloration changes not only in Midas cichlid but also in other fishes from freshwater to marine ecosystems.</p

A review of freshwater fish introductions to the Guangdong province, China

In the last few decades, non-native freshwater fishes have been introduced all over the world for economic purposes, including aquaculture and aquarium trade, as well as improvement for wild stocks resulting in adverse environmental and socio-economic effects. The Guangdong province of China is at a high risk of fish invasions owing to its warm and humid climate, abundance of water courses, flourishing aquaculture and ornamental fish trade, and extensive sea ports. A total of 160 non-native freshwater species were introduced in the Guangdong province and 71.9% of them were imported for aquarium purposes. Fourteen species have established self-sustaining populations and 21 species were found in the main river basin of the Guangdong province. Propagule pressure, rapid evolution and abundant resources in the environment were the factors likely to contribute to successful invasion by non-native fishes. The invasion of non-native fishes in the Guangdong province has already resulted in economic losses, decline of native species, as well as negative impacts on the functional diversity of native fish assemblages. To mitigate these effects and prevent future non-native fish invasions, scientists, policy makers and stakeholders should collaborate on the management of non-native fish introductions by developing risk assessments, statutory regulations, public education and scientific research.</p

Additional file 1: Table S1. of The complete mitochondrial genomes of two freshwater snails provide new protein-coding gene rearrangement models and phylogenetic implications

Summary of Radix swinhoei and Planorbarius corneus using Illumina sequencing. Table S2. General characteristics of the mitochondrial genomes of various members of pulmonate gastropods. Table S3. Nucleotide composition and AT- and GC-skews of the mitochondrial protein-coding and ribosomal RNA genes in the complete Radix swinhoei mt genome. Table S4. Nucleotide composition and AT- and GC-skews of the mitochondrial protein-coding and ribosomal RNA genes in the complete Planorbarius corneus mt genome. Table S5. Codon usage of Radix swinhoei mitochondrial protein-coding genes. Table S6. Codon usage of Planorbarius corneus mitochondrial protein-coding genes. Figure S1. Comparison of AT and GC skews among the 30 pulmonate species in Table S2. Circles and triangles separately represent AT and GC skews of the complete mitochondrial genomes. Figure S2. Gene specific strand composition of mitochondrial genome in Radix swinhoei and Planorbarius corneus. Figure S3. Graphical summary of nucleotide composition across complete mitochondrial genomes. Figure S4. Percentage of synonymous codon usage for each amino acid in Radix swinhoei and Planorbarius corneus mitochondrial protein-coding genes. Figure S5. Linear comparison of the gene distribution pattern of mitochondrial genomes between Radix swinhoei and Planorbarius corneus. (DOC 1430 kb

Functional response curves of the invasive and high impact alien, the non-invasive and low impact alien, and the benign native snail species, when feeding on four plant species.

<p>The invasive alien species <i>Pomacea canaliculata</i> fed on (A) <i>Ipomoea aquatica</i>, (B) <i>Cabomba caroliniana</i>, (C) <i>Hygrophila difformis</i> and (D) <i>Rotala indica</i>, and the non-invasive alien <i>Planorbarius corneus</i> fed on these same plant species (E, F, G, H) and similarly for the native <i>Bellamya aeruginosa</i> (I, J, K, L); modelled by the Rogers’ random predator equation for a Type II response; <i>n</i> = 3 per initial plant biomass. Error bars represent standard errors.</p

Comparison of functional response parameters associated with the three snail species feeding on four plant species.

<p>The mean (A) attack rate <i>a</i>, (B) handling time <i>h</i> and (C) maximum feeding rate <i>1/hT</i> were respectively derived from bootstrapping (n = 10 each) the parameter values of each of three snail species (<i>Pomacea canaliculata</i>, <i>Planorbarius corneus</i> and <i>Bellamya aeruginosa</i>) feeding on each of four plant species (<i>Ipomoea aquatica</i>, <i>Cabomba caroliniana</i>, <i>Hygrophila difformis</i> and <i>Rotala indica</i>). Error bars represent standard errors.</p