Chromosome Genome Assembly and Annotation of the Capitulum mitella With PacBio and Hi-C Sequencing Data.

Abstract

A pedunculate barnacle Capitulum mitella (Linnaeus, 1758) is a dominant intertidal cirripede (Lee et al., 2000). C. mitella distribute in the mid- and high-intertidal zone of tropical and subtropical coasts and is common in the East Sea and South Sea of China. C. mitella has a great commercial value in China, the petiole muscle of which has been a source of traditional delicious seafood (Yuan et al., 2016). The local market demand led to high-intensity catching activity, and this behavior caused significant decrease in quantity and habitat destruction in recent years. Artificial aquaculture of fishery resources will help to reduce overexploitation of natural stocks and meet market needs for fishery products. In general, the barnacle life cycle consists of six nauplius instars and a nonfeeding cyprid instar. In the barnacle life history, the cyprid is a transitory phase between the pelagic and sessile lifestyle. The cyprid role is responsible for locating, exploring, and attaching to a suitable substratum; subsequently, a complex metamorphosis and permanent settlement happen (Lagersson and Hoeg, 2002). Cypris attachment and metamorphosis are also known as “cypris settlement” (Clare and Matsumura, 2000; Franco et al., 2016). The cypris settlement is a crucial event for the survival and development of both adults and subsequent generations. Within the last three decades, the basic biology of C. mitella such as reproductive characteristics, sperm ultrastructure, and larval culture conditions was investigated in our lab. C. mitella cyprids have been cultured on a relatively large scale. However, they cannot attach and metamorphose into juveniles in an artificial environment, so they would die eventually and interrupt their life history. In recent years, the cypris morphology of C. mitella has been depicted minutely using SEM (Rao and Lin, 2014). After we had successfully induced metamorphosis of the C. mitella cyprids into juveniles, we described a time line and specific morphological changes during the metamorphosis under microscopy and SEM (Lin and Rao, 2017). The impacts of external (i.e., water temperature and salinity) and internal (i.e., cyprid age) factors on the metamorphosis of C. mitella were researched (Rao and Lin, 2020). These efforts are possible for completing the life history in an artificial environment and aquaculture of C. mitella. Not only is the artificial aquaculture for C. mitella a production activity but also it helps to reduce the stress on overexploited populations. Barnacles are frequently dominant marine foulings and widely distributed around the world that play crucial roles in marine ecology (Marechal and Hellio, 2011). Recently, there are a few transcriptome researches on barnacles, such as a model animal Amphibalanus amphitrite (Chen et al., 2011; Yan et al., 2012; Chandramouli et al., 2015; Sarah et al., 2016), a giant barnacle Megabalanus volcano (Yan et al., 2017) and a stalked barnacle Neolepas marisindica (Ryu et al., 2019). These efforts showed that the transcriptome databases could greatly promote the research on molecular mechanisms of barnacle settlement. Genome sequencing has been performed for an acorn barnacle Amphibalanus amphitrite, but there is still no genome sequencing information for a stalked barnacle. Numerous reports on C. mitella were mainly related to mitochondrial DNA sequencing and quantitative proteomics analyses (Song and Yoon, 2013; Yoon et al., 2013; Yuan et al., 2016; Tian et al., 2020). So far, no genome literature on the C. mitella is available. Whereas a lack of genome information on the barnacles has obstructed further inquiry on the molecular mechanisms with development, attachment, metamorphosis, genetic evolution, and so on, so does on C. mitella. Accordingly, in this study, we aimed to sequence and assemble the genome of C. mitella. The baseline data obtained from this study will be very useful in taxonomical identification, phylogenetic analysis, larval settlement mechanisms, artificial breeding and aquaculture, and species protection for C. mitella.