Journal of Genetics and Genomics

A pangenomic study of Bacillus thuringiensis

Yongjun Fang, Zhaolong Li, Jiucheng Liu, Changlong Shu, Xumin Wang, Xiaowei Zhang, Xiaoguang Yu, Duojun Zhao, Guiming Liu, Songnian Hu, Jie Zhang, Ibrahim Al-Mssallem, Jun Yu

2011, 38(12): 567-576. doi: 10.1016/j.jgg.2011.11.001

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Abstract:
Bacillus thuringiensis (B. thuringiensis) is a soil-dwelling Gram-positive bacterium and its plasmid-encoded toxins (Cry) are commonly used as biological alternatives to pesticides. In a pangenomic study, we sequenced seven B. thuringiensis isolates in both high coverage and base-quality using the next-generation sequencing platform. The B. thuringiensis pangenome was extrapolated to have 4196 core genes and an asymptotic value of 558 unique genes when a new genome is added. Compared to the pangenomes of its closely related species of the same genus, B. thuringiensis pangenome shows an open characteristic, similar to B. cereus but not to B. anthracis; the latter has a closed pangenome. We also found extensive divergence among the seven B. thuringiensis genome assemblies, which harbor ample repeats and single nucleotide polymorphisms (SNPs). The identities among orthologous genes are greater than 84.5% and the hotspots for the genome variations were discovered in genomic regions of 2.3–2.8Mb and 5.0–5.6Mb. We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed, are very useful for pangenomic studies.

Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes

Yuan Chen, Yun Ding, Zuming Zhang, Wen Wang, Jun-Yuan Chen, Naoto Ueno, Bingyu Mao

2011, 38(12): 577-584. doi: 10.1016/j.jgg.2011.10.004

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Abstract:
The evolution of the central nervous system (CNS) is one of the most striking changes during the transition from invertebrates to vertebrates. As a major source of genetic novelties, gene duplication might play an important role in the functional innovation of vertebrate CNS. In this study, we focused on a group of CNS-biased genes that duplicated during early vertebrate evolution. We investigated the tempo-spatial expression patterns of 33 duplicate gene families and their orthologs during the embryonic development of the vertebrate Xenopus laevis and the cephalochordate Brachiostoma belcheri. Almost all the identified duplicate genes are differentially expressed in the CNS in Xenopus embryos, and more than 50% and 30% duplicate genes are expressed in the telencephalon and mid-hindbrain boundary, respectively, which are mostly considered as two innovations in the vertebrate CNS. Interestingly, more than 50% of the amphioxus orthologs do not show apparent expression in the CNS in amphioxus embryos as detected by in situ hybridization, indicating that some of the vertebrate CNS-biased duplicate genes might arise from non-CNS genes in invertebrates. Our data accentuate the functional contribution of gene duplication in the CNS evolution of vertebrate and uncover an invertebrate non-CNS history for some vertebrate CNS-biased duplicate genes.

A novel mutation in the MITF may be digenic with GJB2 mutations in a large Chinese family of Waardenburg syndrome type II

Xukun Yan, Tianyu Zhang, Zhengmin Wang, Yi Jiang, Yan Chen, Hongyan Wang, Duan Ma, Lei Wang, Huawei Li

2011, 38(12): 585-591. doi: 10.1016/j.jgg.2011.11.003

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Abstract:
Waardenburg syndrome type II (WS2) is associated with syndromic deafness. A subset of WS2, WS2A, accounting for approximately 15% of patients, is attributed to mutations in the microphthalmia-associated transcription factor (MITF) gene. We examined the genetic basis of WS2 in a large Chinese family. All 9 exons of the MITF gene, the single coding exon (exon 2) of the most common hereditary deafness gene GJB2 and the mitochondrial DNA (mtDNA) 12S rRNA were sequenced. A novel heterozygous mutation c.[742_743delAAinsT;746_747delCA] in exon 8 of theMITF gene co-segregates with WS2 in the family. The MITF mutation results in a premature termination codon and a truncated MITF protein with only 247 of the 419 wild type amino acids. The deaf proband had this MITF gene heterozygous mutation as well as a c.[109G>A]+[235delC] compound heterozygous pathogenic mutation in theGJB2 gene. No pathogenic mutation was found in mtDNA 12S rRNA in this family. Thus, a novel compound heterozygous mutation, c.[742_743delAAinsT;746_747delCA] inMITF exon 8 was the key genetic reason for WS2 in this family, and a digenic effect of MITF and GJB2 genes may contribute to deafness of the proband.

Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon

Lei Tian, Lubin Tan, Fengxia Liu, Hongwei Cai, Chuanqing Sun

2011, 38(12): 593-601. doi: 10.1016/j.jgg.2011.11.005

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Abstract:
Soil salinity is one of the major abiotic stresses affecting plant growth and crop production. In the present study, salt tolerance at rice seedling stage was evaluated using 87 introgression lines (ILs), which were derived from a cross between an elite indica cultivar Teqing and an accession of common wild rice (Oryza rufipogon Griff.). Substantial variation was observed for four traits including salt tolerance score (STS), relative root dry weight (RRW), relative shoot dry weight (RSW) and relative total dry weight (RTW). STS was significantly positively correlated with all other three traits. A total of 15 putative quantitative trait loci (QTLs) associated with these four traits were detected using single-point analysis, which were located on chromosomes 1, 2, 3, 6, 7, 9 and 10 with 8%–26% explaining the phenotypic variance. TheO. rufipogon-derived alleles at 13 QTLs (86.7%) could improve the salt tolerance in the Teqing background. Four QTL clusters affecting RRW, RSW and RTW were found on chromosomes 6, 7, 9 and 10, respectively. Among these four QTL clusters, a major cluster including three QTLs (qRRW10, qRSW10 and qRTW10) was found near the maker RM271 on the long arm of chromosome 10, and the O. rufipogon-derived alleles at these three loci increased RRW, RSW and RTW with additive effects of 22.7%, 17.3% and 18.5%, respectively, while the phenotypic variance explained by these three individual QTLs for the three traits varied from 19% to 26%. In addition, several salt tolerant ILs were selected and could be used for identifying and utilizing favorable salt tolerant genes from common wild rice and used in the salt tolerant rice breeding program.

Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare

Hua Zhang, Qiang Zhao, Zhi-Zhong Sun, Chang-Quan Zhang, Qi Feng, Shu-Zhu Tang, Guo-Hua Liang, Ming-Hong Gu, Bin Han, Qiao-Quan Liu

2011, 38(12): 603-611. doi: 10.1016/j.jgg.2011.11.004

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Abstract:
Chromosome segment substitution lines (CSSLs) are useful for the precise mapping of quantitative trait loci (QTLs) and dissection of the genetic basis of complex traits. In this study, two whole-genome sequenced rice cultivars, the japonica Nipponbare and indica 9311 were used as recipient and donor, respectively. A population with 57 CSSLs was developed after crossing and back-crossing assisted by molecular markers, and genotypes were identified using a high-throughput resequencing strategy. Detailed graphical genotypes of 38 lines were constructed based on resequencing data. These CSSLs had a total of 95 substituted segments derived fromindica 9311, with an average of about 2.5 segments per CSSL and eight segments per chromosome, and covered about 87.4% of the rice whole genome. A multiple linear regression QTL analysis mapped four QTLs for 1000-grain weight. The largest-effect QTL was located in a region on chromosome 5 that contained a cloned major QTL GW5/qSW5 for grain size in rice. These CSSLs with a background of Nipponbare may provide powerful tools for future whole-genome discovery and functional study of essential genes/QTLs in rice, and offer ideal materials and foundations for japonica breeding.

2011 Vol. 38, No. 12