1
|
Yao K, Cui J, Jian J, Peng D, Huang W, Kong L, Wang Q, Peng H. Chromosome-level genome assembly of the cereal cyst nematode Heterodera flipjevi. Sci Data 2024; 11:637. [PMID: 38886380 PMCID: PMC11183081 DOI: 10.1038/s41597-024-03487-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
As an economically important plant parasitic nematode (PPN), Heterodera filipjevi causes great damage on wheat, and now it was widely recorded in many countries. While multiple genomes of PPNs have been published, high-quality genome assembly and annotation on H. filipjevi have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for H. filipjevi, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The genome consists of 9 pseudo-chromosomes that contain 134.19 Mb of sequence, with a scaffold N50 length of 11.88 Mb. In total, 10,036 genes were annotated, representing 75.20% of the total predicted protein-coding genes. Our study provides the first chromosome-scale genome for H. filipjevi, which is also the inaugural high-quality genome of cereal cyst nematodes (CCNs). It provides a valuable genomic resource for further biological research and pest management of cereal cyst nematodes disease.
Collapse
Affiliation(s)
- Ke Yao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiangkuan Cui
- National Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jinzhuo Jian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Qianghui Wang
- Novogene, Bioinformatics Institute, Beijing, 100193, China.
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
2
|
Zhuge J, Zhou X, Zhou L, Hu J, Guo K. The Plant Parasitic Nematodes Database: A Comprehensive Genomic Data Platform for Plant Parasitic Nematode Research. Int J Mol Sci 2023; 24:16841. [PMID: 38069165 PMCID: PMC10706385 DOI: 10.3390/ijms242316841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/24/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Plant parasitic nematodes are important phytopathogens that greatly affect the growth of agricultural and forestry plants. Scientists have conducted several studies to prevent and treat the diseases they cause. With the advent of the genomics era, the genome sequencing of plant parasitic nematodes has been considerably accelerated, and a large amount of data has been generated. This study developed the Plant Parasitic Nematodes Database (PPND), a platform to combine these data. The PPND contains genomic, transcriptomic, protein, and functional annotation data, allowing users to conduct BLAST searches and genome browser analyses and download bioinformatics data for in-depth research. PPND will be continuously updated, and new data will be integrated. PPND is anticipated to become a comprehensive genomics data platform for plant parasitic nematode research.
Collapse
Affiliation(s)
| | | | | | | | - Kai Guo
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China; (J.Z.); (X.Z.); (L.Z.); (J.H.)
| |
Collapse
|
3
|
Lai CK, Lee YC, Ke HM, Lu MR, Liu WA, Lee HH, Liu YC, Yoshiga T, Kikuchi T, Chen PJ, Tsai IJ. The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes. Mol Ecol Resour 2023; 23:905-919. [PMID: 36597348 DOI: 10.1111/1755-0998.13752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023]
Abstract
Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.
Collapse
Affiliation(s)
- Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Yi-Chien Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Min R Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-An Liu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Peichen J Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| |
Collapse
|
4
|
Abstract
The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.
Collapse
Affiliation(s)
- Peter M Carlton
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO 80045, USA.,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
5
|
Wang S, Gao S, Nie J, Tan X, Xie J, Bi X, Sun Y, Luo S, Zhu Q, Geng J, Liu W, Lin Q, Cui P, Hu S, Wu S. Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics. FRONTIERS IN PLANT SCIENCE 2022; 12:769700. [PMID: 35126409 PMCID: PMC8813773 DOI: 10.3389/fpls.2021.769700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/20/2021] [Indexed: 05/28/2023]
Abstract
In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the indica cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the indica cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of waxy make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of Oryza groups in molecular breeding programs.
Collapse
Affiliation(s)
- Sen Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jingyi Nie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junhua Xie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaochun Bi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sainan Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qianhui Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianing Geng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wanfei Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiang Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peng Cui
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| |
Collapse
|
6
|
Zhang ZY, Guan JY, Cao YR, Dai XY, Storey KB, Yu DN, Zhang JY. Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus. INSECTS 2021; 12:453. [PMID: 34069253 PMCID: PMC8157225 DOI: 10.3390/insects12050453] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 01/23/2023]
Abstract
We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4-5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.
Collapse
Affiliation(s)
- Zi-Yi Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (Z.-Y.Z.); (J.-Y.G.); (Y.-R.C.); (X.-Y.D.)
| | - Jia-Yin Guan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (Z.-Y.Z.); (J.-Y.G.); (Y.-R.C.); (X.-Y.D.)
| | - Yu-Rou Cao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (Z.-Y.Z.); (J.-Y.G.); (Y.-R.C.); (X.-Y.D.)
| | - Xin-Yi Dai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (Z.-Y.Z.); (J.-Y.G.); (Y.-R.C.); (X.-Y.D.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (Z.-Y.Z.); (J.-Y.G.); (Y.-R.C.); (X.-Y.D.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (Z.-Y.Z.); (J.-Y.G.); (Y.-R.C.); (X.-Y.D.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| |
Collapse
|
7
|
Banerjee S, Bhandary P, Woodhouse M, Sen TZ, Wise RP, Andorf CM. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. BMC Bioinformatics 2021; 22:205. [PMID: 33879057 PMCID: PMC8056616 DOI: 10.1186/s12859-021-04120-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative. RESULTS We present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species. CONCLUSIONS FINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision-ideal for bench researchers with limited experience in handling computational tools.
Collapse
Affiliation(s)
- Sagnik Banerjee
- Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | - Priyanka Bhandary
- Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Margaret Woodhouse
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, 50011, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, USDA-Agricultural Research Service, Albany, CA, 94710, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, 50011, USA
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Carson M Andorf
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, 50011, USA.
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA.
| |
Collapse
|