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Genetic Evolution of Marine Shellfish
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Genetic Evolution of Marine Shellfish

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 7515

Special Issue Editor

Dr. Haiyan Wang

E-Mail Website
Guest Editor
Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
Interests: Mollusca; phylogeny; evolution; genetic diversity; taxonomy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Mollusca is the second largest phylum in the animal kingdom following Arthropoda. Around 85,000 extant species are recognized, and this group could contain up to 200,000, comprising almost a quarter of all named marine organisms. Most of the species that have ever lived vanished in ancient history since mollusks first appeared in the earliest Cambrian, leaving only 35,000 known fossil species. Global environmental changes and geological events continue to drive biological evolution, altering the biodiversity of Mollusca and genetic information of taxa. To better explain the relationships within Mollusca, massive phylogenetic hypotheses have been raised, with data continuously enriched by morphological, ultrastructural, molecular, developmental, and fossil records.

This Special Issue aims to present new original articles in taxonomy and phylogeny, biodiversity, genetic diversity, and the evolutionary characteristics and mechanisms of marine shellfish with respect to genes, genetics and genomics. Additionally, review articles that cover the latest studies on the genetic evolution of marine shellfish are welcome.

Dr. Haiyan Wang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • phylogeny
  • taxonomy
  • biodiversity
  • genetic diversity
  • genomics
  • evolution
  • Mollusca

Published Papers (4 papers)

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Research

12 pages, 3623 KiB  
Article
The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei
by Tianzhe Zhang, Yunan Wang and Hao Song
Genes 2023, 14(1), 210; https://doi.org/10.3390/genes14010210 - 13 Jan 2023
Viewed by 1797
Abstract
The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial [...] Read more.
The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs. Full article
(This article belongs to the Special Issue Genetic Evolution of Marine Shellfish)
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11 pages, 1837 KiB  
Article
The Complete Mitochondrial Genome of Entemnotrochus rumphii, a Living Fossil for Vetigastropoda (Mollusca: Gastropoda)
by Yunan Wang, Peizhen Ma, Zhen Zhang, Cui Li, Yumeng Liu, Ya Chen, Jiahui Wang, Haiyan Wang and Hao Song
Genes 2022, 13(11), 2061; https://doi.org/10.3390/genes13112061 - 07 Nov 2022
Cited by 2 | Viewed by 1542
Abstract
Pleurotomarioidea represents a truly isolated and basally diverging lineage in Vetigastropoda (Mollusca: Gastropoda) whose fossil record can date back to the late Cambrian, thus providing rare insights into the evolutionary history of molluscs. Here, we sequenced and assembled the complete mitochondrial genome of [...] Read more.
Pleurotomarioidea represents a truly isolated and basally diverging lineage in Vetigastropoda (Mollusca: Gastropoda) whose fossil record can date back to the late Cambrian, thus providing rare insights into the evolutionary history of molluscs. Here, we sequenced and assembled the complete mitochondrial genome of one representative species from Pleurotomarioidea—Entemnotrochus rumphii (Schepman, 1879)—of which the mitogenome is 15,795 bp in length, including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The nucleotide composition was biased toward AT, and A + T content reached 65.2%. E. rumphii was recovered as sister to all other living vetigastropods according to mitogenome-based phylogenetic analysis. The mitochondrial gene order was consistent with major vetigastropods and the hypothetical ancestral gastropoda, suggesting the deep conservation of mitogenome arrangement in Vetigastropoda. Full article
(This article belongs to the Special Issue Genetic Evolution of Marine Shellfish)
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18 pages, 5814 KiB  
Article
Bioinformatic Characterization and Molecular Evolution of the Lucina pectinata Hemoglobins
by Ingrid M. Montes-Rodríguez, Carmen L. Cadilla, Juan López-Garriga and Ricardo González-Méndez
Genes 2022, 13(11), 2041; https://doi.org/10.3390/genes13112041 - 05 Nov 2022
Cited by 2 | Viewed by 1467
Abstract
(1) Introduction: Lucina pectinata is a clam found in sulfide-rich mud environments that has three hemoglobins believed to be responsible for the transport of hydrogen sulfide (HbILp) and oxygen (HbIILp and HbIIILp) to chemoautotrophic endosymbionts. The physiological roles [...] Read more.
(1) Introduction: Lucina pectinata is a clam found in sulfide-rich mud environments that has three hemoglobins believed to be responsible for the transport of hydrogen sulfide (HbILp) and oxygen (HbIILp and HbIIILp) to chemoautotrophic endosymbionts. The physiological roles and evolution of these globins in sulfide-rich environments are not well understood. (2) Methods: We performed bioinformatic and phylogenetic analyses with 32 homologous mollusk globin sequences. Phylogenetics suggests a first gene duplication resulting in sulfide binding and oxygen binding genes. A more recent gene duplication gave rise to the two oxygen-binding hemoglobins. Multidimensional scaling analysis of the sequence space shows evolutionary drift of HbIILp and HbIIILp, while HbILp was closer to the Calyptogena hemoglobins. Further corroboration is seen by conservation in the coding region of hemoglobins from L. pectinata compared to those from Calyptogena. (3) Conclusions: Presence of glutamine in position E7 in organisms living in sulfide-rich environments can be considered an adaptation to prevent loss of protein function. In HbILp a substitution of phenylalanine in position B10 is accountable for its unique reactivity towards H2S. It appears that HbILp has been changing over time, apparently not subject to functional constraints of binding oxygen, and acquired a unique function for a specialized environment. Full article
(This article belongs to the Special Issue Genetic Evolution of Marine Shellfish)
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14 pages, 7432 KiB  
Article
Testing Efficacy of Assembly-Free and Alignment-Free Methods for Species Identification Using Genome Skims, with Patellogastropoda as a Test Case
by Tao Xu, Lingfeng Kong and Qi Li
Genes 2022, 13(7), 1192; https://doi.org/10.3390/genes13071192 - 02 Jul 2022
Cited by 1 | Viewed by 2169
Abstract
Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based “genome skimming” alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample identification, using unassembled [...] Read more.
Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based “genome skimming” alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample identification, using unassembled genome skims, which can effectively improve phylogenetic signal and identification resolution. Studies have shown that the software Skmer and APPLES work well at estimating genomic distance and performing phylogenetic placement in birds and insects using low-coverage genome skims. In this study, we use Skmer and APPLES based on genome skims of 11 patellogastropods to perform assembly-free and alignment-free species identification and phylogenetic placement. Whether or not data corresponding to query species are present in the reference database, Skmer selects the best matching or closest species with COI barcodes under different sizes of genome skims except lacking species belonging to the same family as a query. APPLES cannot place patellogastropods in the correct phylogenetic position when the reference database is sparse. Our study represents the first attempt at assembly-free and alignment-free species identification of marine mollusks using genome skims, demonstrating its feasibility for patellogastropod species identification and flanking the necessity of establishing a database to share genome skims. Full article
(This article belongs to the Special Issue Genetic Evolution of Marine Shellfish)
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