Introduction
The Trichomycteridae genera Listrura de Pinna 1988 and Microcambeva Costa and Bockmann 1994 currently include 13 and eight species respectively, of diminutive and elusive catfishes. Listrura species have a distinctive morphology, characterized by a slender and elongate body, nearly eel-like in some species, with a unique caudal-fin morphology with a prominent membrane on the caudal peduncle supported by numerous procurrent rays, and entirely lacking pelvic fins and girdle (Fig. 1a and 1b) (de Pinna 1988; Villa-Verde et al. 2013, 2022). Microcambeva species are characterized by a translucent, miniaturized morphology (standard length not exceeding 50mm) (Fig. 1c to 1g). They are distinguished by relatively subtle morphological characters (Costa and Bockmann 1994; Sarmento-Soares et al. 2019).
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Both Listrura and Microcambeva are endemic to coastal drainages of the Atlantic Forest biome in Brazil (Fig. 2). Those catfish species are found in habitats that are relatively unusual for most freshwater fish. Listrura species are typically found in shallow marginal water bodies with dense leaf litter and/or sandy substrates where they hide, often separated from the main river channel (Nico and de Pinna 1996; Villa-Verde et al. 2022). Those habitats are found in coastal drainages draining the Serra do Mar and Serra Geral Mountain ranges, with the exception of Listrura depinnai Villa-Verde, Ferrer & Malabarba which occurs in the Pampa Biome (Villa-Verde, Ferrer, and Malabarba 2014; Medeiros et al. 2024). Microcambeva species are found in shallow sandy riverbanks in narrow streams in coastal drainages of the eastern margin of the Brazilian Shield, where they are often buried, with only their nasal barbels exposed (Costa and Bockmann 1994; Sarmento-Soares et al. 2019; Medeiros, Sarmento-Soares, and Lima 2021).
For a considerable time, records of specimens of these two genera were scarce, with the majority of them comprising a few specimens from the type series. The scarcity of Listrura and Microcambeva specimens in museum collections can be attributed to a number of factors, including their diminutive size, small population size, secretive and cryptic habits, and the lack of collecting efforts focused on the environment favored by those species (Sarmento-Soares et al. 2019; Villa-Verde et al. 2022). Knowledge on the biodiversity of those genera has undergone considerable progress over the past two decades. During that period, the majority of the currently known species of both genera have been described, 11 of Listrura and seven of Microcambeva (Medeiros et al. 2020; Medeiros, Sarmento-Soares, and Lima 2021; Medeiros et al. 2024). Additionally, the first proposals of phylogenetic relationships among their species have been published in the past four years (Costa, Henschel, and Katz 2020; Costa and Katz 2021; Medeiros et al. 2024). Due to the particular fragility of their habitats and the paucity of available records, species of both genera are frequently included in Brazilian lists of threatened species. In the latest published list (2024), two species of Listrura, L. camposae and L. nematopteryx, were classified as ‘Critically Endangered’ (CR), while L. picinguabae was listed as ‘Near Threatened’ (NT). Listrura depinnai and L. boticario were classified as ‘Least Concern’ (LC), whereas L. costai and L. tetraradiata were categorized as ‘Data Deficient’ (DD). Remaining species were not evaluated (ICMBio 2024). Regarding Microcambeva species, Medeiros et al. (2020) suggested that M. bendego should be classified as CR. Officially, M. draco was classified as ‘Endangered’ (EN), and M. watu as NT, and both M. ribeirae and M. filamentosa as LC. Remaining species were classified as DD.
Here, we present the draft version of the whole-genome sequencing efforts for two species of Listrura – L. nematopteryx, and L. boticario – and five of Microcambeva – M. barbata, M. watu, M. jucuensis, M. bendego, and M. ribeirae –, including the type-species of each genus, filling a key knowledge gap about the genetic diversity within those elusive and endangered genera. Such data will serve as a foundation for more in depth studies of evolutionary and systematics in those of related taxa and unique catfish species.
Methods
Tissues samples from one specimen per species were used, obtained from Museu Nacional, Rio de Janeiro (MNRJ), Museu de Zoologia da Universidade de São Paulo, São Paulo (MZUSP), Coleção Ictiológica da Universidade Federal do Rio Grande do Norte, Natal (CIUFRN) and Coleção Ictiológica da Universidade Federal do Rio Grande do Sul, Porto Alegre (UFRGS). Listrura nematopteryx (Fig. 1a) was collected from a small stream near the Imbariê region, municipality of Duque de Caxias, Rio de Janeiro (22°39’09.5"S 43°13’04.0"W) (Fig. 2), close to its type locality, which has since been destroyed by urban growth. Listrura boticario (Fig. 1b) was collected from the Figueira River, in the municipality of Guaraqueçaba, Paraná (25°10’43.0"S 48°18’42.0"W) (Fig. 2). Microcambeva barbata (Fig. 1c) was collected in the Aldeia Velha river, municipality of Cassimiro de Abreu, Rio de Janeiro (22°29’53.0"S 42°16’03.0"W) (Fig. 2). Microcambeva ribeirae (Fig. 1d) was collected in the Rio Preto, Sete Barra municipality, São Paulo (24°11’33.0"S 47°53’25.0"W) (Fig. 2). Microcambeva jucuensis (Fig. 1e), was collected in the Jucu river, in the musicality of Viana, in Espírito Santo (20°22’52.98"S 40°30’14.98"W) (Fig. 2). Microcambeva bendego (Fig. 1f) was collected in the type locality, in the Guapiaçu river, in the Guapimirim municipality, in the Rio de Janeiro (22°35’33"S, 42°53’20"W) (Fig. 2). Microcambeva watu (Fig. 1g) was collected in the type locality in a small stream near the road between São João de Petropolis and Vila Vinte e Cinco de Julho, in Santa Teresa municipality, Espírito Santo (19°47’2.00"S 40°38’52.00"W) (Fig. 2).
DNA was extracted using the Qiagen DNeasy Genomic Extraction Kit following standard protocol. A paired-end sequencing library was then prepared with the Illumina TruSeq kit, adhering to the manufacturer’s instructions. Sequencing was carried out on an Illumina Hi-Seq platform, using a paired-end 2 × 150 bp format. The resulting FASTQ files were processed to remove adapter/primer sequences, as well as low-quality regions, using Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The cleaned sequences were assembled with SPAdes v2.5 (Bankevich et al. 2012), followed by a final assembly step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Genome assembly statistics
Genome assembly completeness was analyzed with BUSCO v5 (Simão et al. 2015) and CEGMA 2.4 (Parra, Bradnam, and Korf 2007) using the gVolante server (Nishimura, Hara, and Kuraku 2017, https://gvolante.riken.jp).
Results and Data Availability
All raw read data and assembled genomes are available in the GenBank database (Table 1). The quality assessments conducted using BUSCO and CEGMA indicated that the genome assemblies range from average to good. However, a significant proportion of the genomes appear to be fragmented (Table 1). Further assembly steps are needed to improve the continuity of the assemblies presented here.
Funding
Funding for sequencing analysis was provided by the Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa. LSM is grateful to CAPES for a PhD scholarship (#88887.483610/2020–00). SMQL and MP are grateful to Conselho Nacional de Desenvolvimento Científico e Tecnológico, Ministério de Ciência e Tecnologia (CNPq) (SMQL: #312066/2021–0 and MP: #310688/2019–1).