First reference genome assembly of the Indochinese silvered langur (Trachypithecus germaini).
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ABSTRACT:
SUBMITTER: Wu JW
PROVIDER: S-EPMC9336458 | biostudies-literature | 2022 Jul
REPOSITORIES: biostudies-literature
Publications
First reference genome assembly of the Indochinese silvered langur (Trachypithecus germaini).
Wu Jin-Wei JW Zhang Ru R Qin Ya-Lin YL Wang Li L Han Ming-Bo MB Zhao Zi-Fan ZF Jing Pei P Sun Hai-Lu HL Wang Song S Huang Ning N Li Bao-Guo BG Wu Dong-Dong DD Zhang Chi C Qi Xiao-Guang XG
Zoological research 20220701 4
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Project description:BackgroundSillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family.FindingsUsing the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated ∼27.3 Gb genomic DNA sequences for the Chinese sillago. We reconstructed a genome assembly of 534 Mb using a strategy that takes advantage of complementary strengths of two genome assembly programs, Canu and FALCON. The genome size was consistent with the estimated genome size based on k-mer analysis. The assembled genome consisted of 802 contigs with a contig N50 length of 2.6 Mb. We annotated 22,122 protein-coding genes in the Chinese sillago genomes using a de novo method as well as RNA sequencing data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, the Chinese sillago is closely related to Larimichthys crocea and Dicentrarchus labrax and diverged from their ancestor around 69.5-82.6 million years ago.ConclusionsUsing long reads generated with PacBio sequencing technology, we have built a draft genome assembly for the Chinese sillago, which is the first reference genome for Sillaginidae species. This genome assembly sets a stage for comparative analysis of the diversification and adaptation of fishes in Sillaginidae.
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