Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage

Abstract

Cryptosporidium spp. are important enteric pathogens in a wide range of vertebrates including humans. Previous comparative analysis revealed conservation in genome composition, gene content, and gene organization among Cryptosporidium spp., with a progressive reductive evolution in metabolic pathways and invasion-related proteins. In this study, we sequenced the genome of zoonotic pathogen Cryptosporidium felis and conducted a comparative genomic analysis. While most intestinal Cryptosporidium species have similar genomic characteristics and almost complete genome synteny, fewer protein-coding genes and some sequence inversions and translocations were found in the C. felis genome. The C. felis genome exhibits much higher GC content (39.6 %) than other Cryptosporidium species (24.3–32.9 %), especially at the third codon position (GC3) of protein-coding genes. Thus, C. felis has a different codon usage, which increases the use of less energy costly amino acids (Gly and Ala) encoded by GC-rich codons. While the tRNA usage is conserved among Cryptosporidium species, consistent with its higher GC content, C. felis uses a unique tRNA for GTG for valine instead of GTA in other Cryptosporidium species. Both mutational pressures and natural selection are associated with the evolution of the codon usage in Cryptosporidium spp., while natural selection seems to drive the codon usage in C. felis. Other unique features of the C. felis genome include the loss of the entire traditional and alternative electron transport systems and several invasion-related proteins. Thus, the preference for the use of some less energy costly amino acids in C. felis may lead to a more harmonious parasite–host interaction, and the strengthened host-adaptation is reflected by the further reductive evolution of metabolism and host invasion-related proteins.

High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species

“…muris RN66, and C. andersoni 30 847 were obtained from the release 59 of the CryptoDB database (https://cryptodb.org/cryptodb/) [30], while the WGS data of C . felis 44 884 were downloaded from the NCBI database (https://www.ncbi.nlm.nih.gov/genome/) [19]. For comparison, WGS data of Plasmodium spp.…”

“…For additional verifications of sequence rearrangements in the genomes, SPAdes 3.13.0 (https://github.com/ablab/spades/releases) [47] was used in a secondary assembly of the genomes. PCR analysis of the genomic DNA of mink- and fox-derived C. canis was used to confirm the inversions and translocations using primers spanning the joint of the putative rearrangements (Table S1, available in the online version of this article) as described recently [19].…”

“…Whole genome sequence (WGS) data of C. hominis UdeA01 [29] [30], while the WGS data of C. felis 44 884 were downloaded from the NCBI database (https://www.ncbi.nlm.nih.gov/genome/) [19]. For comparison, WGS data of Plasmodium spp.…”

“…These invasion-associated proteins include mucin-like glycoproteins (MUC), insulinase-like proteases (INS), and MEDLE secretory proteins, which have lower copy numbers in species with narrow host range (such as C. hominis, C. felis, C. bovis, and C. ryanae) than in the broadly infective C. parvum. Similarly, a reductive evolution of pathways and enzymes associated with mitochondrial metabolism has accompanied the divergence of some Cryptosporidium species [15,18,19]. In addition to the interspecific differences, differences in copy numbers of genes encoding MEDLE proteins and INS have been observed among host-adapted C. parvum subtypes [20].…”

“…Further evidence suggests that the VSA genes together with other subtelomeric genes are highly expressed in different developmental stages of P. falciparum and prefer to use amino acid residues (Gly and Ala) encoded by GC-rich codons [27,28]. Although most Cryptosporidium species sequenced thus far have low genomic GC content of 24.3-32.9 %, the recently reported C. felis genome has much higher GC content (39.6 %) [19].…”