Ortega, J. M. | Search bioRxiv

bioRxiv2020

Assessing the sex-related genomic composition difference using a K-mer-based approach: a case of study in Arapaima gigas (Pirarucu).

Arapaima gigas is one of the largest freshwater bony fish in the world, in which adults could weigh 200 kilograms and measure 3 meters in length. Due to its large size and its low-fat meat, Arapaima gigas has quickly become a species of special interest in fish-farming. One challenge faced during their production is the lack of an efficient sexing methodology, since their sexual maturation occurs late (around the third to the fifth year) and the genetic mechanisms linked to their sex determination system are not known yet. For a more sustainable management, it is of paramount importance to seek an effective and non-invasive method to differentiate sexually juvenile individuals of Arapaima gigas. For this, the establishment of genetic markers associated with sexual differentiation would be an advantageous tool. In this study, we proposed a k-mer based approach to identify genome features with sex-determining properties. For this purpose, we used genomic data from four adult representatives of Arapaima gigas, two males and two females, and counted the k-mers comprising them. As result, we found k-mers from repetitive regions with high difference and disproportion in the count among individuals of the opposite sex. These differences in the k-mer-based genomic composition indicate the existence of genetic factors involved in the sexing of individuals in Arapaima gigas.

genomics↗

bioRxiv2019

A potential genomic recombination site upstream of the rfb locus in Leptospira interrogans is associated with serogroup Serjoe and serovar Hardjo classification

Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of the genus Leptospira. It has a global distribution and affects domestic animals, including cattle. In livestock production, Leptospira interrogans serogroup Sejroe serovar Hardjo is the major reproductive disease leading to economic losses. The whole-genome sequence of the first Brazilian clinical isolate classified as L. interrogans serogroup Sejroe serovar Hardjo strain Norma enabled the evaluation of its genomic features. Here, we investigated particularities of this isolate, obtained from a leptospirosis outbreak. Bioinformatic analysis using the L. interrogans serovar Hardjo str. Norma was applied as a reference for genomic evaluation and comparative analysis among L. interrogans and L. borgpetersenii serovars. Our data suggest the occurrence of genomic recombination in L. interrogans serovar Hardjo str. Norma encompassing 45 Kb located upstream of the rfb locus. A hallmark of genetic evolution was predicted through an orthologue analysis that identified that sugar enzymes associated with carbohydrate and lipid biosynthesis and metabolism composed this genetic module. Comparative genomics revealed a wide range of relatedness among the bacterial strains of serogroup Sejroe that are classified as L. interrogans and L. borgpetersenii species. Furthermore, identification of an IS3 family suggests a genetic recombination site in L. interrogans serovar Hardjo str. Norma that is distinct among L. interrogans serovars and may contribute to clarify the taxonomic classification of Leptospira spp.\n\nImpact StatementLeptospirosis remains an important neglected disease with worldwide distribution. This zoonotic disease impacts in the livestock production and the bovine infection is currently associated to species L. borgpetersenii and L. interrogans serovar Hardjo. L.interrogans serovar Hardjo infection is recognized as reproductive disease associated with abortion and economic lost. In this context, we studied a unique whole genome sequence of L. interrogans serovar Hardjo subtype Hardjo-prajitno isolated from bovine leptospirosis outbreaks in Brazilian dairy farm, one of the greatest country of milk production in world. We compared L. interrogans and L. borgpetersenii genomes with L. interrogans serogroup Sejroe serovar Hardjo subtype Hardjo-prajitno focusing on rfb locus and sugars biosynthesis. Leptospira spp. taxonomy and serology information are strictly associated with rfb locus and we found high correlation among bacterial strains classified in serogroup Sejroe. Although L. interrogans and L. borgpetersenii classified in serogroup Sejroe possess a greater genetic correlation, we uniquely identified that serovar Hardjo strains often possess identical loci carrying predicted sugar biossinthesis genes and mobile elements. The Sru (Sejroe specific Rfb Upstream locus) locus associated to rfb locus probably contribute to Leptospira spp. genetic information concerning serogroup and serovar degrees of taxonomic and serology in this microbiology field.\n\nData SummaryAll Leptospira spp. genome sequences used in this study were retrieved from National Center for Biotechnology Information (NCBI) (Table 1) with NCBI ID: NZ_CP006723.1, NZ_CP012603.1, NC_004342.2, NZ_CP011934.1, NZ_AKXA02000040.1, NZ_CP013147.1, NZ_CP012029.1, NZ_CP015048.1, NC_008508.1, GCA_000216175.3,GCA_000244115.3, NC005823.1, GCA_000244395.3, GCA_000346975.1.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@843b1eorg.highwire.dtl.DTLVardef@1453917org.highwire.dtl.DTLVardef@1a75127org.highwire.dtl.DTLVardef@1c0e185org.highwire.dtl.DTLVardef@160aa4_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1:C_FLOATNO O_TABLECAPTIONLeptospira spp. strains used in this study.\n\nC_TABLECAPTION C_TBL HighlightsO_LIThe study identified potential molecular features associated with serovar Hardjo subtype Hardjo-prajitno, present in both L. interrogans and L. borgpetersenii, by comparative genomics.\nC_LIO_LIA new potential recombinant site found upstream of the rfb locus contains proteins that correlate with serogroup taxonomy in the Leptospira genus.\nC_LIO_LIThe proteins encoded in the recombinant locus are associated with the synthesis of serological surface determinants such as carbohydrates and lipopolysaccharides.\nC_LI

genomics↗