MODB: a comprehensive mitochondrial genome database for Mollusca

Abstract

Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to explore the mitochondrial genome of Mollusca. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. We also integrated a series of analysis and visualization tools, such as BLAST, MUSCLE, GENEWISE and LASTZ. In particular, a phylogenetic tree was implemented in this database to visualize the evolutionary relationships between species. The original version contains 616 species whose mitochondrial genomes have been sequenced. The database provides comprehensive information and analysis platform for researchers interested in understanding the biological characteristics of mollusks. Database URL: http://modb.ytu.edu.cn/

Mining NCBI Sequence Read Archive Database: An Untapped Source of Organelle Genomes for Taxonomic and Comparative Genomics Research

“…In Tables 1 and 2, we find that the average length of the mtDNA genomes was approximately 16 kb. The average length of the mtDNA genomes obtained through de novo read assembly in the WGS and RNA-Seq datasets was consistent with the literature and mitochondrial genome database for Mollusca [37].…”

“…We selected the phylum "mollusca" to test the practical application of the developed workflow. The phylum Mollusca was also chosen for the following reasons: (i) Mollusca, one of the most diverse animal phyla, accounts for approximately 23% of all known marine species [37]; (ii) these ecologically and economically significant invertebrates inhabit a wide array of marine, freshwater, and terrestrial ecosystems, displaying adaptability to various challenging oceanic environments [38]; (iii) there is a significant amount of NGS data available for the Mollusca phylum in the NCBI SRA database due to the reasons mentioned above. The OrgaMiner pipeline workflow, which consists of two phases, is depicted in Figure 1.…”