Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly

被引:70
作者
Li, Yiyuan [1 ]
Park, Hyunjin [1 ]
Smith, Thomas E. [1 ]
Moran, Nancy A. [1 ]
机构
[1] Univ Texas Austin, Dept Integrat Biol, Austin, TX 78712 USA
基金
美国国家科学基金会;
关键词
proximity ligation; structural variation; duplication; paralogs; insect genome; HOLOCENTRIC CHROMOSOMES; STRUCTURAL VARIATION; ADAPTIVE EVOLUTION; READ ALIGNMENT; ANNOTATION; PLANT; VERTEBRATE; EXPANSIONS; EXPRESSION; BACTERIAL;
D O I
10.1093/molbev/msz138
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Genome structural variations, including duplications, deletions, insertions, and inversions, are central in the evolution of eukaryotic genomes. However, structural variations present challenges for high-quality genome assembly, hampering efforts to understand the evolution of gene families and genome architecture. An example is the genome of the pea aphid (Acyrthosiphon pisum) for which the current assembly is composed of thousands of short scaffolds, many of which are known to be misassembled. Here, we present an improved version of the A. pisum genome based on the use of two long-range proximity ligation methods. The new assembly contains four long scaffolds (40-170 Mb), corresponding to the three autosomes and the X chromosome of A. pisum, and encompassing 86% of the new assembly. Assembly accuracy is supported by several quality assessments. Using this assembly, we identify the chromosomal locations and relative ages of duplication events, and the locations of horizontally acquired genes. The improved assembly illuminates the mode of gene family evolution by providing proximity information between paralogs. By estimating nucleotide polymorphism and coverage depth from resequencing data, we determined that many short scaffolds not assembling to chromosomes represent hemizygous regions, which are especially frequent on the highly repetitive X chromosome. Aligning the X-linked aphicarus region, responsible for male wing dimorphism, to the new assembly revealed a 50-kb deletion that cosegregates with the winged male phenotype in some clones. These results show that long-range scaffolding methods can substantially improve assemblies of repetitive genomes and facilitate study of gene family evolution and structural variation.
引用
收藏
页码:2143 / 2156
页数:14
相关论文
共 82 条
[1]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[2]   Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition [J].
Bellott, Daniel W. ;
Skaletsky, Helen ;
Pyntikova, Tatyana ;
Mardis, Elaine R. ;
Graves, Tina ;
Kremitzki, Colin ;
Brown, Laura G. ;
Rozen, Steve ;
Warren, Wesley C. ;
Wilson, Richard K. ;
Page, David C. .
NATURE, 2010, 466 (7306) :612-U3
[3]   Comparisons with Caenorhabditis (∼100 Mb) and Drosophila (∼175 Mb) using flow cytometry show genome size in Arabidopsis to be ∼157 Mb and thus ∼25 % larger than the Arabidopsis genome initiative estimate of ∼125 Mb [J].
Bennett, MD ;
Leitch, IJ ;
Price, HJ ;
Johnston, JS .
ANNALS OF BOTANY, 2003, 91 (05) :547-557
[4]   CHROMOSOME-NUMBERS IN THE APHIDIDAE AND THEIR TAXONOMIC SIGNIFICANCE [J].
BLACKMAN, RL .
SYSTEMATIC ENTOMOLOGY, 1980, 5 (01) :7-25
[5]   Genetic mapping of aphicarus -: a sex-linked locus controlling a wing polymorphism in the pea aphid (Acyrthosiphon pisum) [J].
Braendle, C ;
Caillaud, MC ;
Stern, DL .
HEREDITY, 2005, 94 (04) :435-442
[6]   The pea aphid, Acyrthosiphon pisum:: an emerging genomic model system for ecological, developmental and evolutionary studies [J].
Brisson, Jennifer A. ;
Stern, David L. .
BIOESSAYS, 2006, 28 (07) :747-755
[7]   Aphid wing dimorphisms: linking environmental and genetic control of trait variation [J].
Brisson, Jennifer A. .
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2010, 365 (1540) :605-616
[8]   Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum [J].
Brisson, Jennifer A. ;
Nuzhdin, Sergey V. ;
Stern, David L. .
BMC GENETICS, 2009, 10
[9]   MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes [J].
Cantarel, Brandi L. ;
Korf, Ian ;
Robb, Sofia M. C. ;
Parra, Genis ;
Ross, Eric ;
Moore, Barry ;
Holt, Carson ;
Alvarado, Alejandro Sanchez ;
Yandell, Mark .
GENOME RESEARCH, 2008, 18 (01) :188-196
[10]   Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis [J].
Castresana, J .
MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (04) :540-552