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Pan C, Reinert K. Leaf: an ultrafast filter for population-scale long-read SV detection. Genome Biol 2024; 25:155. [PMID: 38872200 PMCID: PMC11170821 DOI: 10.1186/s13059-024-03297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
Advances in sequencing technology have facilitated population-scale long-read structural variant (SV) detection. Arguably, one of the main challenges in population-scale analysis is developing effective computational pipelines. Here, we present a new filter-based pipeline for population-scale long-read SV detection. It better captures SV signals at an early stage than conventional assembly-based or alignment-based pipelines. Assessments in this work suggest that the filter-based pipeline helps better resolve intra-read rearrangements. Moreover, it is also more computationally efficient than conventional pipelines and thus may facilitate population-scale long-read applications.
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Affiliation(s)
- Chenxu Pan
- Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195, Berlin, Germany.
| | - Knut Reinert
- Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
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2
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Madrigal G, Minhas BF, Catchen J. Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs. Mol Ecol Resour 2024:e13982. [PMID: 38800997 DOI: 10.1111/1755-0998.13982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.
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Affiliation(s)
- Giovanni Madrigal
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bushra Fazal Minhas
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Julian Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Kwak H, Lee D, Kim Y, Park J, Yeum H, Kim D, Dong YW, Nakano T, Jeong C, Park JK. Genome assembly and population genomic data of a pulmonate snail Ellobium chinense. Sci Data 2024; 11:31. [PMID: 38177233 PMCID: PMC10766999 DOI: 10.1038/s41597-023-02851-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024] Open
Abstract
Ellobium chinense is an airbreathing, pulmonate gastropod species that inhabits saltmarshes in estuaries of the northwestern Pacific. Due to a rapid population decline and their unique ecological niche in estuarine ecosystems, this species has attracted special attention regarding their conservation and the genomic basis of adaptation to frequently changing environments. Here we report a draft genome assembly of E. chinense with a total size of 949.470 Mb and a scaffold N50 of 1.465 Mb. Comparative genomic analysis revealed that the GO terms enriched among four gastropod species are related to signal transduction involved in maintaining electrochemical gradients across the cell membrane. Population genomic analysis using the MSMC model for 14 re-sequenced individuals revealed a drastic decline in Korean and Japanese populations during the last glacial period, while the southern Chinese population retained a much larger effective population size (Ne). These contrasting demographic changes might be attributed to multiple environmental factors during the glacial-interglacial cycles. This study provides valuable genomic resources for understanding adaptation and historical demographic responses to climate change.
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Affiliation(s)
- Haena Kwak
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Damin Lee
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Yukyung Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Joohee Park
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Heeseung Yeum
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Donghee Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Yun-Wei Dong
- Fisheries College, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Tomoyuki Nakano
- Seto Marine Biological Laboratory, Kyoto University, 459 Shirahama, Nishimuro, Wakayama, 649-2211, Japan
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea.
- Natural History Museum, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea.
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Chakraborty A, Mahajan S, Bisht MS, Sharma VK. Genome sequencing of Syzygium cumini (jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1260414. [PMID: 38046611 PMCID: PMC10693344 DOI: 10.3389/fpls.2023.1260414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/22/2023] [Indexed: 12/05/2023]
Abstract
Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome for the first time from the world's largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. We also sequenced and assembled the transcriptome of S. cumini in this study. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families resulting from gene duplication events compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.
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Affiliation(s)
| | | | | | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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5
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Fuller T, Bickhart DM, Koch LM, Kucek LK, Ali S, Mangelson H, Monteros MJ, Hernandez T, Smith TPL, Riday H, Sullivan ML. A reference assembly for the legume cover crop hairy vetch ( Vicia villosa). GIGABYTE 2023; 2023:gigabyte98. [PMID: 38023065 PMCID: PMC10659084 DOI: 10.46471/gigabyte.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
Vicia villosa is an incompletely domesticated annual legume of the Fabaceae family native to Europe and Western Asia. V. villosa is widely used as a cover crop and forage due to its ability to withstand harsh winters. Here, we generated a reference-quality genome assembly (Vvill1.0) from low error-rate long-sequence reads to improve the genetic-based trait selection of this species. Our Vvill1.0 assembly includes seven scaffolds corresponding to the seven estimated linkage groups and comprising approximately 68% of the total genome size of 2.03 Gbp. This assembly is expected to be a useful resource for genetically improving this emerging cover crop species and provide useful insights into legume genomics and plant genome evolution.
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Affiliation(s)
- Tyson Fuller
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Derek M. Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Lisa M. Koch
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Lisa Kissing Kucek
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Shahjahan Ali
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | | | - Maria J. Monteros
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Timothy Hernandez
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Timothy P. L. Smith
- US Meat Animal Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), PO Box 166 (State Spur 18D), Clay Center, NE 68933, USA
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Michael L. Sullivan
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
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6
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Chakraborty A, Bisht MS, Saxena R, Mahajan S, Pulikkan J, Sharma VK. Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds. Genes Genomics 2023; 45:1399-1408. [PMID: 37231295 DOI: 10.1007/s13258-023-01401-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Indian cattle breeds (Bos indicus) are known for their remarkable adaptability to hot and humid climates, higher nutritious quality of milk, better disease tolerance, and greater ability to perform in poor feed compared to taurine cattle (Bos taurus). Distinct phenotypic differences are observed among the B. indicus breeds; however, the whole genome sequences were unavailable for these indigenous breeds. OBJECTIVE We aimed to perform whole genome sequencing to construct the draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur (the smallest cattle of the world). METHODS We sequenced the whole genomes using Illumina short-read technology, and constructed de novo and reference-based genome assemblies of these native B. indicus breeds for the first time. RESULTS The draft de novo genome assemblies of B. indicus breeds ranged from 1.98 to 3.42 Gbp. We also constructed the mitochondrial genome assemblies (~ 16.3 Kbp), and yet unavailable 18S rRNA marker gene sequences of these B. indicus breeds. The genome assemblies helped to identify the bovine genes related to distinct phenotypic characteristics and other biological processes for this species compared to B. taurus, which are plausibly responsible for providing better adaptive traits. We also identified the genes that showed sequence variation in dwarf and non-dwarf breeds of B. indicus compared to B. taurus. CONCLUSIONS The genome assemblies of these Indian cattle breeds, the 18S rRNA marker genes, and identification of the distinct genes in B. indicus breeds compared to B. taurus will help in future studies on these cattle species.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Joby Pulikkan
- Department of Genomic Science, Central University of Kerala, Kasaragod, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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7
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Le N, Heras J, Herrera MJ, German DP, Crummett LT. The genome of Anoplarchus purpurescens (Stichaeidae) reflects its carnivorous diet. Mol Genet Genomics 2023; 298:1419-1434. [PMID: 37690047 PMCID: PMC10657299 DOI: 10.1007/s00438-023-02067-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Digestion is driven by digestive enzymes and digestive enzyme gene copy number can provide insights on the genomic underpinnings of dietary specialization. The "Adaptive Modulation Hypothesis" (AMH) proposes that digestive enzyme activity, which increases with increased gene copy number, should correlate with substrate quantity in the diet. To test the AMH and reveal some of the genetics of herbivory vs carnivory, we sequenced, assembled, and annotated the genome of Anoplarchus purpurescens, a carnivorous prickleback fish in the family Stichaeidae, and compared the gene copy number for key digestive enzymes to that of Cebidichthys violaceus, a herbivorous fish from the same family. A highly contiguous genome assembly of high quality (N50 = 10.6 Mb) was produced for A. purpurescens, using combined long-read and short-read technology, with an estimated 33,842 protein-coding genes. The digestive enzymes that we examined include pancreatic α-amylase, carboxyl ester lipase, alanyl aminopeptidase, trypsin, and chymotrypsin. Anoplarchus purpurescens had fewer copies of pancreatic α-amylase (carbohydrate digestion) than C. violaceus (1 vs. 3 copies). Moreover, A. purpurescens had one fewer copy of carboxyl ester lipase (plant lipid digestion) than C. violaceus (4 vs. 5). We observed an expansion in copy number for several protein digestion genes in A. purpurescens compared to C. violaceus, including trypsin (5 vs. 3) and total aminopeptidases (6 vs. 5). Collectively, these genomic differences coincide with measured digestive enzyme activities (phenotypes) in the two species and they support the AMH. Moreover, this genomic resource is now available to better understand fish biology and dietary specialization.
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Affiliation(s)
- Ninh Le
- Life Sciences Concentration, Soka University of America, Aliso Viejo, CA, 92656, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Joseph Heras
- Department of Biology, California State University, San Bernardino, CA, 92407, USA
| | - Michelle J Herrera
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Lisa T Crummett
- Life Sciences Concentration, Soka University of America, Aliso Viejo, CA, 92656, USA.
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8
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Otero-Ruiz A, Rodriguez-Anaya LZ, Lares-Villa F, Lozano Aguirre Beltrán LF, Lares-Jiménez LF, Gonzalez-Galaviz JR, Cruz-Mendívil A. Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes. Sci Rep 2023; 13:14318. [PMID: 37653073 PMCID: PMC10471605 DOI: 10.1038/s41598-023-41657-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Balamuthia mandrillaris is a pathogenic protozoan that causes a rare but almost always fatal infection of the central nervous system and, in some cases, cutaneous lesions. Currently, the genomic data for this free-living amoeba include the description of several complete mitochondrial genomes. In contrast, two complete genomes with draft quality are available in GenBank, but none of these have a functional annotation. In the present study, the complete genome of B. mandrillaris isolated from a freshwater artificial lagoon was sequenced and assembled, obtaining an assembled genome with better assembly quality parameter values than the currently available genomes. Afterward, the genome mentioned earlier, along with strains V039 and 2046, were subjected to functional annotation. Finally, comparative genomics analysis was performed, and it was found that homologous genes in the core genome potentially involved in the virulence of Acanthamoeba spp. and Trypanosoma cruzi. Moreover, eleven of fifteen genes were identified in the three strains described as potential target genes to develop new treatment approaches for B. mandrillaris infections. These results describe proteins in this protozoan's complete genome and help prioritize which target genes could be used to develop new treatments.
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Affiliation(s)
- Alejandro Otero-Ruiz
- Programa de Doctorado en Ciencias Especialidad en Biotecnología, Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | - Luis Fernando Lozano Aguirre Beltrán
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas de la Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Abraham Cruz-Mendívil
- CONAHCYT-Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, 81101, Guasave, Sinaloa, Mexico
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Raiyemo DA, Bobadilla LK, Tranel PJ. Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes. BMC Biol 2023; 21:37. [PMID: 36804015 PMCID: PMC9940365 DOI: 10.1186/s12915-023-01539-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/08/2023] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Amaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions. RESULTS We provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination. CONCLUSIONS The results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.
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Affiliation(s)
- Damilola A Raiyemo
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
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Bastide H, López-Villavicencio M, Ogereau D, Lledo J, Dutrillaux AM, Debat V, Llaurens V. Genome assembly of 3 Amazonian Morpho butterfly species reveals Z-chromosome rearrangements between closely related species living in sympatry. Gigascience 2022; 12:giad033. [PMID: 37216769 PMCID: PMC10202424 DOI: 10.1093/gigascience/giad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/13/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
The genomic processes enabling speciation and species coexistence in sympatry are still largely unknown. Here we describe the whole-genome sequencing and assembly of 3 closely related species from the butterfly genus Morpho: Morpho achilles (Linnaeus, 1758), Morpho helenor (Cramer, 1776), and Morpho deidamia (Höbner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing color pattern, suggesting local mimicry. By sequencing, assembling, and annotating their genomes, we aim at uncovering prezygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the 3 species and a chromosomal number ranging from 2n = 54 for M. deidamia to 2n = 56 for M. achilles and M. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in prezygotic isolation like genes controlling color discrimination (L-opsin). Altogether, the assembly and the annotation of these 3 new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishing Morpho butterflies as a new eco-evolutionary model.
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Affiliation(s)
| | - Manuela López-Villavicencio
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
| | | | - Joanna Lledo
- GeT-PlaGe, Bât G2, INRAe, 31326 Castanet-Tolosan Cedex, France
| | - Anne-Marie Dutrillaux
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
| | - Vincent Debat
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE/UA), Muséum National d’Histoire Naturelle–CP50, 75005 Paris, France
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11
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Filipović I, Rašić G, Hereward J, Gharuka M, Devine GJ, Furlong MJ, Etebari K. A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros). BMC Genomics 2022; 23:426. [PMID: 35672676 PMCID: PMC9172067 DOI: 10.1186/s12864-022-08628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background An optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle’s mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation. Results High-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.1%). These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle (Tribolium castaneum). The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes, with only 2.8% missing BUSCOs, and the expected number of non-coding RNAs. The number and structure of paralogous genes in a gene family like Sigma GST is lower than in another scarab beetle (Onthophagus taurus), but higher than in the red flour beetle (Tribolium castaneum), which suggests expansion of this GST class in Scarabaeidae. The quality of our gene models was also confirmed with the correct placement of O. rhinoceros among other members of the rhinoceros beetles (subfamily Dynastinae) in a phylogeny based on the sequences of 95 protein-coding genes in 373 beetle species from all major lineages of Coleoptera. Finally, we provide a list of 30 candidate dsRNA targets whose orthologs have been experimentally validated as highly effective targets for RNAi-based control of several beetles. Conclusions The genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08628-z.
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Affiliation(s)
- Igor Filipović
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia. .,Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - James Hereward
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Maria Gharuka
- Research Division, Ministry of Agriculture and Livestock, Honiara, Solomon Islands
| | - Gregor J Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, St. Lucia, Australia
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12
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Alexandre NM, Haji D, Bakhtiari M, Chatla K, Aguilar JM, Arzumanova K, Whiteman NK. A Reference Genome Assembly of Hybrid-Derived California Wild Radish (Raphanus sativus × raphanistrum). J Hered 2022; 113:197-204. [PMID: 35575080 PMCID: PMC9113464 DOI: 10.1093/jhered/esab076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 01/30/2023] Open
Abstract
For agriculturally important plants, pollination and herbivory are 2 ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus × raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and antiherbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by 2 opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.
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Affiliation(s)
- Nicolas M Alexandre
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Diler Haji
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Moe Bakhtiari
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ksenia Arzumanova
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Noah K Whiteman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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13
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Maloney JG, Molokin A, Solano-Aguilar G, Dubey JP, Santin M. A hybrid sequencing and assembly strategy for generating culture free Giardia genomes. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100114. [PMID: 35909595 PMCID: PMC9325754 DOI: 10.1016/j.crmicr.2022.100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022] Open
Abstract
Giardia duodenalis is a pathogenic intestinal protozoan parasite of humans and many other animals. Giardia duodenalis is found throughout the world, and infection is known to have adverse health consequences for human and other mammalian hosts. Yet, many aspects of the biology of this ubiquitous parasite remain unresolved. Whole genome sequencing and comparative genomics can provide insight into the biology of G. duodenalis by helping to reveal traits that are shared by all G. duodenalis assemblages or unique to an individual assemblage or strain. However, these types of analyses are currently hindered by the lack of available G. duodenalis genomes, due, in part, to the difficulty in obtaining the genetic material needed to perform whole genome sequencing. In this study, a novel approach using a multistep cleaning procedure coupled with a hybrid sequencing and assembly strategy was assessed for use in producing high quality G. duodenalis genomes directly from cysts obtained from feces of two naturally infected hosts, a cat and dog infected with assemblage A and D, respectively. Cysts were cleaned and concentrated using cesium chloride gradient centrifugation followed by immunomagnetic separation. Whole genome sequencing was performed using both Illumina MiSeq and Oxford Nanopore MinION platforms. A hybrid assembly strategy was found to produce higher quality genomes than assemblies from either platform alone. The hybrid G. duodenalis genomes obtained from fecal isolates (cysts) in this study compare favorably for quality and completeness against reference genomes of G. duodenalis from cultured isolates. The whole genome assembly for assemblage D is the most contiguous genome available for this assemblage and is an important reference genome for future comparative studies. The data presented here support a hybrid sequencing and assembly strategy as a suitable method to produce whole genome sequences from DNA obtained from G. duodenalis cysts which can be used to produce novel reference genomes necessary to perform comparative genomics studies of this parasite. Assemblage A and D genomes were generated directly from cysts isolated from feces. Genomes were sequenced using Illumina and Oxford Nanopore sequencing platforms. A hybrid sequencing/assembly strategy was used to generate G. duodenalis genomes. A hybrid strategy yields reference quality genomes from fecal isolates. These methods have generated the most contiguous Assemblage D genome to date.
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14
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Pfenninger M, Schönnenbeck P, Schell T. ModEst: Accurate estimation of genome size from next generation sequencing data. Mol Ecol Resour 2021; 22:1454-1464. [PMID: 34882987 DOI: 10.1111/1755-0998.13570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/11/2023]
Abstract
Accurate estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. Here we present a fast, easy-to-implement and accurate method to estimate genome size from the number of bases sequenced and the mean sequencing depth. To estimate the latter, we take advantage of the fact that an accurate estimation of the Poisson distribution parameter lambda is possible from truncated data, restricted to the part of the sequencing depth distribution representing the true underlying distribution. With simulations we show that reasonable genome size estimates can be gained even from low-coverage (10×), highly discontinuous genome drafts. Comparison of estimates from a wide range of taxa and sequencing strategies with flow cytometry estimates of the same individuals showed a very good fit and suggested that both methods yield comparable, interchangeable results.
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Affiliation(s)
- Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Philipp Schönnenbeck
- Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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15
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Abstract
Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale.
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Affiliation(s)
- Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
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16
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Lloret-Villas A, Bhati M, Kadri NK, Fries R, Pausch H. Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. BMC Genomics 2021; 22:363. [PMID: 34011274 PMCID: PMC8132449 DOI: 10.1186/s12864-021-07554-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between the bovine reference genome (ARS-UCD1.2) and a highly continuous Angus-based assembly (UOA_Angus_1). RESULTS Read mapping accuracy did not differ notably between the ARS-UCD1.2 and UOA_Angus_1 assemblies. We discovered 22,744,517 and 22,559,675 high-quality variants from ARS-UCD1.2 and UOA_Angus_1, respectively. The concordance between sequence- and array-called genotypes was high and the number of variants deviating from Hardy-Weinberg proportions was low at segregating sites for both assemblies. More artefactual INDELs were genotyped from UOA_Angus_1 than ARS-UCD1.2 alignments. Using the composite likelihood ratio test, we detected 40 and 33 signatures of selection from ARS-UCD1.2 and UOA_Angus_1, respectively, but the overlap between both assemblies was low. Using the 161 sequenced Brown Swiss cattle as a reference panel, we imputed sequence variant genotypes into a mapping cohort of 30,499 cattle that had microarray-derived genotypes using a two-step imputation approach. The accuracy of imputation (Beagle R2) was very high (0.87) for both assemblies. Genome-wide association studies between imputed sequence variant genotypes and six dairy traits as well as stature produced almost identical results from both assemblies. CONCLUSIONS The ARS-UCD1.2 and UOA_Angus_1 assemblies are suitable for reference-guided genome analyses in Brown Swiss cattle. Although differences in read mapping and genotyping accuracy between both assemblies are negligible, the choice of the reference genome has a large impact on detecting signatures of selection that already reached fixation using the composite likelihood ratio test. We developed a workflow that can be adapted and reused to compare the impact of reference genomes on genome analyses in various breeds, populations and species.
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Affiliation(s)
| | - Meenu Bhati
- Animal Genomics, ETH Zürich, Lindau, 8315 Switzerland
| | | | - Ruedi Fries
- Chair of Animal Breeding, TU München, Freising-Weihenstephan, 85354 Germany
| | - Hubert Pausch
- Animal Genomics, ETH Zürich, Lindau, 8315 Switzerland
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17
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Fischer C, Koblmüller S, Börger C, Michelitsch G, Trajanoski S, Schlötterer C, Guelly C, Thallinger GG, Sturmbauer C. Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. Sci Rep 2021; 11:4309. [PMID: 33619328 PMCID: PMC7900123 DOI: 10.1038/s41598-021-81030-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/28/2020] [Indexed: 01/01/2023] Open
Abstract
With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3-9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.
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Affiliation(s)
- C Fischer
- Institute of Biology, University of Graz, Graz, Austria
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - S Koblmüller
- Institute of Biology, University of Graz, Graz, Austria
| | - C Börger
- Institute of Biology, University of Graz, Graz, Austria
| | - G Michelitsch
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - S Trajanoski
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - C Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - C Guelly
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - G G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - C Sturmbauer
- Institute of Biology, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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18
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Jaiswal SK, Mahajan S, Chakraborty A, Kumar S, Sharma VK. The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms. iScience 2021; 24:102079. [PMID: 33644713 PMCID: PMC7889978 DOI: 10.1016/j.isci.2021.102079] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/18/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Aloe vera is a species from Asphodelaceae family having characteristics like drought resistance and numerous medicinal properties. However, the genetic basis of these phenotypes is yet unknown primarily due to unavailability of its genome sequence. Thus, we report the first Aloe vera genome sequence comprising of 12.93 Gbp and harboring 86,177 protein-coding genes. It is the first genome from Asphodelaceae family and the largest angiosperm genome sequenced and assembled till date. We also report the first genome-wide phylogeny of monocots including Aloe vera to resolve its phylogenetic position. The comprehensive comparative analysis of Aloe vera with other available high-quality monocot genomes revealed adaptive evolution in several genes of drought stress response, CAM pathway, and circadian rhythm and positive selection in DNA damage response genes in Aloe vera. This study provides clues on the genetic basis of evolution of drought stress tolerance capabilities of Aloe vera.
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Affiliation(s)
- Shubham K. Jaiswal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Sudhir Kumar
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
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19
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Cechova M. Probably Correct: Rescuing Repeats with Short and Long Reads. Genes (Basel) 2020; 12:48. [PMID: 33396198 PMCID: PMC7823596 DOI: 10.3390/genes12010048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome-estimated 50-69%-is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chromosomes from "telomere to telomere". Moreover, identical reads or repeat arrays can be differentiated based on their epigenetic marks, such as methylation patterns, aiding in the assembly process. This is despite the fact that long reads still contain a modest percentage of sequencing errors, disorienting the aligners and assemblers both in accuracy and speed. Here, I review the proposed and implemented solutions to the repeat resolution and the multi-mapping read problem, as well as the downstream consequences of reference choice, repeat masking, and proper representation of sex chromosomes. I also consider the forthcoming challenges and solutions with regards to long reads, where we expect the shift from the problem of repeat localization within a single individual to the problem of repeat positioning within pangenomes.
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Affiliation(s)
- Monika Cechova
- Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Central European Institute of Technology (CEITEC), 621 00 Brno, Czech Republic
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20
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Tsuchiya MTN, Dikow RB, Koepfli KP, Frandsen PB, Rockwood LL, Maldonado JE. Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor). Genome Biol Evol 2020; 13:6040737. [PMID: 33331895 PMCID: PMC7851585 DOI: 10.1093/gbe/evaa255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 01/20/2023] Open
Abstract
Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes. We discovered significant variation in contig and scaffold N50 and L50 statistics and genome completeness depending on the de novo assembler used. We compared the performance of these three assembly algorithms in hopes that this study will aid others looking to improve the quality of existing draft genome assemblies even without additional sequence data. We also estimate the demographic histories of raccoons and kinkajous using the Pairwise Sequentially Markovian Coalescent and discuss the variation in population sizes with respect to climatic change during the Pleistocene, as well as aspects of their ecology and taxonomy. Our goal is to achieve a better understanding of the evolutionary history of procyonids and to create robust genomic resources for future studies regarding adaptive divergence and selection.
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Affiliation(s)
- Mirian T N Tsuchiya
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason Univeristy, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Paul B Frandsen
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA.,Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Larry L Rockwood
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.,Department of Biology, George Mason University, Fairfax, VA, USA
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