A draft genome assembly of the solar-powered sea slug Elysia chlorotica

Cai, Huimin; Li, Qiye; Fang, Xiaodong; Ji, Li; Curtis, Nicholas E.; Altenburger, Andreas; Shibata, Tomoko; Feng, Mingji; Maeda, Taro; Schwartz, Julie; Shigenobu, Shuji; Lundholm, Nina; Nishiyama, Tomoaki; Yang, Huanming; Hasebe, Mitsuyasu; Li, Shuai Cheng; Pierce, Sidney K.; Wang, Jian

doi:10.1038/sdata.2019.22

Cited by 49 publications

(44 citation statements)

References 75 publications

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“…Adding to this evolutionary genetic complexity, there are also technical and bioinformatic caveats, making complete and perfect genome assemblies unlikely. Presently, the published genome assemblies are often estimated to be around 90% complete [17,18], being in thousands of scaffolds instead of a few tens of chromosomes. Moreover, numerous kinds of assembly errors [19,20] can further complicate the annotation process.…”

Section: Introductionmentioning

confidence: 99%

Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

2020

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Background: Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). Results: The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. Conclusions: Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.

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Section: Introductionmentioning

confidence: 99%

Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

2020

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“…The genome size of L. d. dumerilii was estimated to be around 2.54 Gb (Table 2), which was calculated as the number of effective k -mers (i.e. total k -mers – erroneous k -mers) divided by the homozygous peak depth following Cai et al [29]. It is noteworthy that, the presence of a distinct heterozygous peak, which displayed half of the depth of the homozygous peak in the k -mer frequency distribution, suggests that the diploid genome of this wild-caught individual has a high level of heterozygosity (Fig.…”

Section: Methodsmentioning

confidence: 99%

A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)

Guo

Zhou

et al. 2020

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34Amphibian genomes are usually challenging to assemble due to large genome size and high 35 repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and 36 New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it 37 represents an important lineage in the amphibian tree of life but lacks reference genomes. Here 38 we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii 39 dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold 40 N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and 41 annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that 42 more than 94% of the expected vertebrate genes were present in the genome assembly and the 43 gene set. We anticipate that this annotated genome assembly will advance the future study of 44 anuran phylogeny and amphibian genome evolution. 45

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“…Sacoglossan transcriptome reads were acquired in previous work by other groups 11,23 from 19 specimens of Elysia chlorotica, Elysia timida , and Elysia cornigera (Extended Data Table 3). We downloaded the reads from the NCBI Sequence Read Archive (SRA) and assembled them using IDBA-UD 44 .…”

Section: Methodsmentioning

confidence: 99%

“…ocellatus and E. diomedea genomic assembly. Contig hits were then submitted to AUGUSTUS to predict genes based on parameters built using the reported E. chlorotica genome assembly and protein sequences 50 . The resulting predicted gene fragments were queried against EcPKS1, EcPKS2 and EcFAS using blastp search (E-value = 1.0 × e -10 ) and were ranked according to bitscore and E-value to determine the best hit.…”

Section: Methodsmentioning

confidence: 99%